From e34a84a06df134fdfe09702ecdf104642d09fe0d Mon Sep 17 00:00:00 2001 From: Will Graham <32364977+willGraham01@users.noreply.github.com> Date: Fri, 23 Feb 2024 11:38:00 +0000 Subject: [PATCH] Merge with atlasgen (#199) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Initial commit * Update README.md * First commit * gitignore * Almost at complete atlas autogeneration * Finalized script for automatic atlas generation * Added template script for atlas generation * Template description * First working version of script for auto deployment * Fixed metadata link * Trying to fix windows permission error when deleting folders * add 50um to allen mouse * v1.2 for allen mouse * blacked * Update requirements * vtkplotter -> vedo * Format with black * Update kim mouse atlas generation * Improve downsampling * revert roations * add kim to main script * rotate annotation volume for meshes * add osten mouse atlas * Added function for creating intermediate hierarchy structures masks * Fix extract_largest_region and compare_mesh_volume * reformat with black * save additional metadata * consistent syntax for empty dict * Update docstring * Add atlas packager metadata * python 3.8 compatibility * Add mouse spinal cord atlas * add WHS SD Rat atlas * add xmltodict to requirements.txt * remove structures that are missing from annotation volume * remove structures that are missing from annotation volume * Fixed vedo Slicer import issue * Update mesh_utils.py * Create azba_zfish.py * Standardise temporary output directory * add [allenmouse] extra dependency (#17) * Allow multiple downloads at once, updated citation * Mesh cleaning improvements (#15) * gitignore: added vscode * gitignore: added vscode * added rich fancy traceback for easier debugging * replaced mesh cleaning with decimation * pre-commit cleanup * added TEST mode to atlas creation * added smoothing options to all atlas gen scripts * removed ratlas.py since outdated and theres a better atlas * atlas gen update * added smoothing and decimation to adult zebrafish atlas Co-authored-by: Luigi Petrucco * Update azba_zfish.py Changing the reference file to be af and the additional references to be topro * some fixes for mpin atlas * Fix tiny typo (#22) * Update README.md * Add lsfm atlas script (#18) * Update lsfm mouse atlas script * 2nd update LSFM mouse atlas script Co-authored-by: Johanna Co-authored-by: Johanna Perens * Update requirements.txt * Add ADMBA 3D developing mouse atlases (#25) * Add ADMBA 3D developing mouse atlases Extend the `mouse_e15_5` script by @pr4deepr to build all the atlases in the 3D reconstructed version of the Allen Developing Mouse Brain Atlas series. This build script is essentially the same except for the addition of a data class to configure the atlas parameters, which is implemented for each atlas. * Fix atlas orientation to LSA Change the input orientation to LSA to fit the NumPy convention used in BrainGlobe. Add docstrings describing the orientation and resolution assumptions in the configuration data class. * Update package authors * Add script for the Princeton mouse brain atlas. (#27) * Added atlas generation script for the Princeton mouse brain atlas. Modified mesh_utils.py for fix. * Modified atlas minor version, changed atlas orientation, and removed unnecessary html fetch of region hierarchy. * Finalised atlas minor version. Co-authored-by: Sam * KimLabDevCCFv001 (neuroinformatics team form) (#31) * Create KimLabDevCCFv001.py * Update KimLabDevCCFv001.py * Update and rename KimLabDevCCFv001.py to KimLabDevCCF.py * Update KimLabDevCCF.py * first commit * updated up to mesh creation, working through VTK type error * kimlabdevccf working version 1 reference only * rename atlasgen file * start adding additional references * add filenames for additional references * fix unfinished handling of multi-templates * update pre-commit black version to fix error with _unicode fun import from click * tidy and install pre-commit * fix change of plotter I erronoeusly made when using older python version * testing kim atlsa with additional references * Update requirements.txt * add loguru requirement (at least windows 10) * fix VTK type error * remove path * remove test code * update to new download dir * used to run atlas * update atlas code for general use * remove standard tempalte from additional references * further clean up * edit to run in single script * fix False flag used to not run meshes * get working on UNIX * use PARALLEL and update atlas name * update template key STP to stp Co-authored-by: NovaFae <33562343+faekronman@users.noreply.github.com> Co-authored-by: Adam Tyson * Add testing config (#35) * Add testing config * Specify branchs for workflow trigger * Bump pre-commit versions * Fix cov flag * Run black on code base * Clean up requirements * Move requirements to setup.py * Fix setup.py black * Replace brainglobe with NI actions (#37) * Use pyproject.toml * Update supported Python metadata * Clean manifest check * Remove cibuildwheel config * Catch warnings during tests (#39) * Add standard pre-commit config (#40) * Add standard pre-commit config * Add automated pre-commit fixes * Ignore line too long * Fix branches that CI is run on (#42) * Update link (#48) * [pre-commit.ci] pre-commit autoupdate (#49) updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.240 → v0.0.272](https://github.com/charliermarsh/ruff-pre-commit/compare/v0.0.240...v0.0.272) - [github.com/psf/black: 23.1.0 → 23.3.0](https://github.com/psf/black/compare/23.1.0...23.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#50) updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.272 → v0.0.275](https://github.com/charliermarsh/ruff-pre-commit/compare/v0.0.272...v0.0.275) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#52) updates: - https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit - [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.276](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.275...v0.0.276) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#53) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.276 → v0.0.277](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.276...v0.0.277) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#54) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.277 → v0.0.278](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.277...v0.0.278) - [github.com/psf/black: 23.3.0 → 23.7.0](https://github.com/psf/black/compare/23.3.0...23.7.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#55) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.278 → v0.0.280](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.278...v0.0.280) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#57) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.280 → v0.0.281](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.280...v0.0.281) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#59) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.281 → v0.0.282](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.281...v0.0.282) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update to newer vedo API (#58) * [pre-commit.ci] pre-commit autoupdate (#64) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.282...v0.0.284) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * scale mesh points before mapping to new anatomical space (#62) Co-authored-by: Will Graham <32364977+willGraham01@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#66) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.284 → v0.0.285](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.284...v0.0.285) * update type assertion --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson * [pre-commit.ci] pre-commit autoupdate (#67) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.286](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.285...v0.0.286) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Set pre-commit autoupdate frequency to monthly (#68) * [pre-commit.ci] pre-commit autoupdate (#70) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.286 → v0.0.287](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.286...v0.0.287) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#83) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.287 → v0.0.292](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.287...v0.0.292) - [github.com/psf/black: 23.7.0 → 23.9.1](https://github.com/psf/black/compare/23.7.0...23.9.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#95) updates: - [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0) - [github.com/astral-sh/ruff-pre-commit: v0.0.292 → v0.1.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.292...v0.1.4) - [github.com/psf/black: 23.9.1 → 23.10.1](https://github.com/psf/black/compare/23.9.1...23.10.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#107) updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.4 → v0.1.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.4...v0.1.6) - [github.com/psf/black: 23.10.1 → 23.11.0](https://github.com/psf/black/compare/23.10.1...23.11.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#109) updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.6 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.6...v0.1.9) - [github.com/psf/black: 23.11.0 → 23.12.1](https://github.com/psf/black/compare/23.11.0...23.12.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * draft validation functions (#90) * draft validation functions * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * run on all atlases, don't crash on assertion error * fixing atlas path * Clearer output printing * tidy up validation script, remove weird test_git * add dev install, make test structure, initial tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add tests and return for _assert_close() * add test for validate mesh matches annotation * fix linting * update version for actions * drop py3.8 in tox, run pytest in tox * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix copy-paste error in pytest command * drop py3.8 from gh action workflow file too * Adding docstrings to validation script * Making path tests stricter, breaking up long strings, adding diff_tolerance argument to _assert_close function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * restructuring validate_mesh_matches_image_extents function, adding comments * testing expected files and meshes directory separately * looping through validation functions and parameters to catch individual errors * removing hard coded path, generalising to all atlases * adding successful_validations list * tidying up duplications * fix recursive bug * addressing Niko's final comments, cleaning code --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder Co-authored-by: alessandrofelder * Structure validation (#110) * draft validation functions * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * run on all atlases, don't crash on assertion error * fixing atlas path * Clearer output printing * tidy up validation script, remove weird test_git * add dev install, make test structure, initial tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add tests and return for _assert_close() * add test for validate mesh matches annotation * fix linting * update version for actions * drop py3.8 in tox, run pytest in tox * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix copy-paste error in pytest command * drop py3.8 from gh action workflow file too * Adding docstrings to validation script * wip: draft structure validation function * Making path tests stricter, breaking up long strings, adding diff_tolerance argument to _assert_close function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * restructuring validate_mesh_matches_image_extents function, adding comments * testing expected files and meshes directory separately * looping through validation functions and parameters to catch individual errors * removing hard coded path, generalising to all atlases * adding successful_validations list * tidying up duplications * fix recursive bug * checkout finished validate_atlases.py from validation branch * adding validate_mesh_structure_pairs function * Update bg_atlasgen/validate_atlases.py Co-authored-by: Alessandro Felder * adding assertion to validate_mesh_structure_pairs function * checking IDs via bg_atlasapi, checking if IDs have mesh files and accesible through the atlas * Update bg_atlasgen/validate_atlases.py Co-authored-by: Alessandro Felder * passing atlas_name to validate_mesh_structure_pairs function * addressing Niko's final comments, cleaning code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder Co-authored-by: alessandrofelder * simplify validation function (#113) * simplify validation function - all validation functions just take an atlas object - means we don't need a parameters list - also simplify output list to be dicts of lists mapping the atlas name to values - another advantage of this is that it simplifies mocking of atlas functions in the tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix bug found in code review --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#117) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.2.0) - [github.com/psf/black: 23.12.1 → 24.1.1](https://github.com/psf/black/compare/23.12.1...24.1.1) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add manifest to ci (#118) * Add manifest to CI * Standardise tox.ini into pyproject * printing data frames with validation function information (#115) * first test functions for validate_mesh_structure_pairs * storing atlases and successful/failed validation functions in a data frame * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * restoring test_validation.py to the original merged version. Chages are implemented on another branch * validate_atlases.py: going back to the version on main, appending only the name of the successful and failed functions (not the function object) to lists in validate_atlases function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * populating dictionaries in for loop, writing JSON files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * saving JSON files to ~/.brainglobe/atlases/validation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * printing where to find the result files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update bg_atlasgen/validate_atlases.py Co-authored-by: Alessandro Felder * Update bg_atlasgen/validate_atlases.py removing unused variables Co-authored-by: Alessandro Felder * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * saving only one JSON file with all the information * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * uncommenting test functions --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder * bg-atlasapi -> brainglobe-atlasapi * bg_atlasapi -> brainglobe_atlasapi, package restructure * Move tests for API into separate subfolder * Revert "bg_atlasapi -> brainglobe_atlasapi, package restructure" This reverts commit 120c3b2c183060d698105a2820d33447a5eced04. * bg_atlasapi -> brainglobe_atlasapi, package restructure * Update manifest * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Pre-commit pass * fixing small bug: validation_functions function argument as variable instead of all_validation_functions (#119) * Bump NIU action versions * Move conftest back to top-level directory * Refactor atlasgen into a submodule * pre-commit pass * test functions for validate_mesh_structure_pairs (#114) * first test functions for validate_mesh_structure_pairs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * adding docstring * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * writing docstrings to explain the behaviour of the test functions * validate_atlases.py: updated validate_mesh_structure_pairs function, test_validation.py: updated tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * spliting validate_mesh_structure_pairs function, checking mesh files and structures separately * writing tests for catch_missing_mesh_files and catch_missing_structures validation functions * creating an atlas with a missing structure to test catch_missing_structures function * Update tests/test_unit/test_validation.py Co-authored-by: Alessandro Felder --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder * Revert "Prepare for merge and rename (#198)" This reverts commit 9d5317db83020cb0df06aee0ca2e236aa84aa2df. * Update pyproject.toml Co-authored-by: Alessandro Felder --------- Co-authored-by: Luigi Petrucco Co-authored-by: Adam Tyson Co-authored-by: Mathieu Co-authored-by: Adam Tyson Co-authored-by: Ben Kantor Co-authored-by: Kailyn Fields <84587654+kailynkfields@users.noreply.github.com> Co-authored-by: Federico Claudi Co-authored-by: Gubra-ApS <61732801+Gubra-ApS@users.noreply.github.com> Co-authored-by: Johanna Co-authored-by: Johanna Perens Co-authored-by: David Young Co-authored-by: Sam Clothier Co-authored-by: Sam Co-authored-by: Joe Ziminski <55797454+JoeZiminski@users.noreply.github.com> Co-authored-by: NovaFae <33562343+faekronman@users.noreply.github.com> Co-authored-by: David Stansby Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder Co-authored-by: viktorpm <50667179+viktorpm@users.noreply.github.com> Co-authored-by: alessandrofelder --- .github/workflows/test_and_deploy.yml | 13 +- .gitignore | 5 +- .pre-commit-config.yaml | 7 - CITATION.cff | 4 +- LICENSE | 10 +- MANIFEST.in | 5 + README.md | 126 +- bg_atlasapi/__init__.py | 22 - brainglobe_atlasapi/__init__.py | 13 + .../atlas_generation/__init__.py | 5 + .../atlas_scripts/__init__.py | 0 .../atlas_scripts/admba_3d_dev_mouse.py | 401 ++ .../atlas_scripts/allen_cord.py | 298 ++ .../atlas_scripts/allen_mouse.py | 115 + .../atlas_scripts/azba_zfish.py | 247 ++ .../atlas_scripts/example_mouse.py | 114 + .../atlas_scripts/humanatlas.py | 302 ++ .../kim_developmental_ccf_mouse.py | 355 ++ .../atlas_scripts/kim_mouse.py | 245 ++ .../atlas_scripts/mpin_zfish.py | 266 ++ .../atlas_scripts/osten_mouse.py | 242 ++ .../atlas_scripts/perens_lsfm_mouse.py | 357 ++ .../atlas_scripts/princeton_mouse.py | 246 ++ .../atlas_scripts/template_script.py | 75 + .../atlas_scripts/whs_sd_rat.py | 318 ++ .../atlas_generation/main_script.py | 138 + .../atlas_generation/mesh_utils.py | 311 ++ .../atlas_generation/metadata_utils.py | 146 + .../atlas_generation/stacks.py | 63 + .../atlas_generation/structure_json_to_csv.py | 84 + .../atlas_generation/structures.py | 116 + .../atlas_generation/validate_atlases.py | 246 ++ .../atlas_generation/volume_utils.py | 108 + .../atlas_generation/wrapup.py | 229 ++ .../bg_atlas.py | 8 +- {bg_atlasapi => brainglobe_atlasapi}/cli.py | 6 +- .../config.py | 0 {bg_atlasapi => brainglobe_atlasapi}/core.py | 6 +- .../descriptors.py | 2 +- .../list_atlases.py | 2 +- .../structure_class.py | 2 +- .../structure_tree_util.py | 0 .../update_atlases.py | 21 +- {bg_atlasapi => brainglobe_atlasapi}/utils.py | 0 pyproject.toml | 63 +- tests/atlasapi/__init__.py | 0 tests/{ => atlasapi}/test_bg_atlas.py | 2 +- tests/{ => atlasapi}/test_cli.py | 2 +- tests/{ => atlasapi}/test_config_file.py | 4 +- tests/{ => atlasapi}/test_core_atlas.py | 2 +- tests/{ => atlasapi}/test_list_atlases.py | 2 +- tests/{ => atlasapi}/test_structure_dict.py | 6 +- tests/{ => atlasapi}/test_update_atlas.py | 2 +- tests/{ => atlasapi}/test_utils.py | 2 +- tests/atlasgen/test_validation.py | 123 + tests/conftest.py | 2 +- tutorials/Atlas API usage.ipynb | 3426 ++++++++--------- 57 files changed, 7052 insertions(+), 1863 deletions(-) delete mode 100644 bg_atlasapi/__init__.py create mode 100644 brainglobe_atlasapi/__init__.py create mode 100644 brainglobe_atlasapi/atlas_generation/__init__.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/__init__.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_cord.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_mouse.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/azba_zfish.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/example_mouse.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_developmental_ccf_mouse.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_mouse.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/mpin_zfish.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/osten_mouse.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_lsfm_mouse.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/princeton_mouse.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/template_script.py create mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/whs_sd_rat.py create mode 100644 brainglobe_atlasapi/atlas_generation/main_script.py create mode 100644 brainglobe_atlasapi/atlas_generation/mesh_utils.py create mode 100644 brainglobe_atlasapi/atlas_generation/metadata_utils.py create mode 100644 brainglobe_atlasapi/atlas_generation/stacks.py create mode 100644 brainglobe_atlasapi/atlas_generation/structure_json_to_csv.py create mode 100644 brainglobe_atlasapi/atlas_generation/structures.py create mode 100644 brainglobe_atlasapi/atlas_generation/validate_atlases.py create mode 100644 brainglobe_atlasapi/atlas_generation/volume_utils.py create mode 100644 brainglobe_atlasapi/atlas_generation/wrapup.py rename {bg_atlasapi => brainglobe_atlasapi}/bg_atlas.py (96%) rename {bg_atlasapi => brainglobe_atlasapi}/cli.py (91%) rename {bg_atlasapi => brainglobe_atlasapi}/config.py (100%) rename {bg_atlasapi => brainglobe_atlasapi}/core.py (98%) rename {bg_atlasapi => brainglobe_atlasapi}/descriptors.py (95%) rename {bg_atlasapi => brainglobe_atlasapi}/list_atlases.py (98%) rename {bg_atlasapi => brainglobe_atlasapi}/structure_class.py (96%) rename {bg_atlasapi => brainglobe_atlasapi}/structure_tree_util.py (100%) rename {bg_atlasapi => brainglobe_atlasapi}/update_atlases.py (72%) rename {bg_atlasapi => brainglobe_atlasapi}/utils.py (100%) create mode 100644 tests/atlasapi/__init__.py rename tests/{ => atlasapi}/test_bg_atlas.py (93%) rename tests/{ => atlasapi}/test_cli.py (96%) rename tests/{ => atlasapi}/test_config_file.py (92%) rename tests/{ => atlasapi}/test_core_atlas.py (98%) rename tests/{ => atlasapi}/test_list_atlases.py (95%) rename tests/{ => atlasapi}/test_structure_dict.py (91%) rename tests/{ => atlasapi}/test_update_atlas.py (88%) rename tests/{ => atlasapi}/test_utils.py (98%) create mode 100644 tests/atlasgen/test_validation.py diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 47bb8da4..3eab1b34 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -13,7 +13,7 @@ jobs: linting: runs-on: ubuntu-latest steps: - - uses: neuroinformatics-unit/actions/lint@v1 + - uses: neuroinformatics-unit/actions/lint@v2 manifest: runs-on: ubuntu-latest @@ -36,22 +36,17 @@ jobs: python-version: "3.9" steps: - - uses: neuroinformatics-unit/actions/test@v1 + - uses: neuroinformatics-unit/actions/test@v2 with: python-version: ${{ matrix.python-version }} build_sdist_wheels: name: Build source distribution and wheel needs: [test] - if: ( - github.event_name == 'push' && github.ref_type == 'tag' - ) || ( - github.event_name == 'pull_request' && - contains(github.event.pull_request.labels.*.name, 'Test packaging') - ) + if: github.event_name == 'push' && github.ref_type == 'tag' runs-on: ubuntu-latest steps: - - uses: neuroinformatics-unit/actions/build_sdist_wheels@v1 + - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2 upload_all: name: Publish build distributions diff --git a/.gitignore b/.gitignore index 0ca94130..b6daa6de 100644 --- a/.gitignore +++ b/.gitignore @@ -1,9 +1,11 @@ -bg_atlasapi/bg_config.conf +brainglobe_atlasapi/bg_config.conf workspace.py .vscode/ # Byte-compiled / optimized / DLL files +__pycache__ +*.__pycache__ __pycache__/ *.py[cod] *$py.class @@ -138,6 +140,5 @@ dmypy.json .vs/ *.~lock.* - # macOS *.DS_Store diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 74f2506c..3117de90 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,10 +23,3 @@ repos: rev: 24.1.1 hooks: - id: black - - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.8.0 - hooks: - - id: mypy - additional_dependencies: - - types-setuptools - - types-requests diff --git a/CITATION.cff b/CITATION.cff index 52ec8511..2b47b3c0 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -19,9 +19,9 @@ authors: affiliation: 'Sainsbury Wellcome Centre, University College London' orcid: 'https://orcid.org/0000-0003-3225-1130' email: code@adamltyson.com -repository-code: 'https://github.com/brainglobe/bg-atlasapi' +repository-code: 'https://github.com/brainglobe/brainglobe-atlasapi' url: >- - https://brainglobe.info/documentation/bg-atlasapi/index.html + https://brainglobe.info/documentation/brainglobe-atlasapi/index.html abstract: >- A common interface for programmers to download and process brain atlas data from multiple sources. diff --git a/LICENSE b/LICENSE index da1fff8b..9d39e902 100644 --- a/LICENSE +++ b/LICENSE @@ -1,19 +1,17 @@ BSD 3-Clause License -Copyright (c) 2020, brainglobe +Copyright (c) 2020, BrainGlobe All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -* Redistributions of source code must retain the above copyright notice, this +- Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. - -* Redistributions in binary form must reproduce the above copyright notice, +- Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. - -* Neither the name of the copyright holder nor the names of its +- Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. diff --git a/MANIFEST.in b/MANIFEST.in index 0b37b229..4e46edeb 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -4,4 +4,9 @@ include README.md include requirements.txt exclude .codecov.yml +exclude .pre-commit-config.yaml + +graft brainglobe_atlasapi *.py + +prune tests prune tutorials diff --git a/README.md b/README.md index 3a0c127d..00a18a4a 100644 --- a/README.md +++ b/README.md @@ -1,60 +1,61 @@ -# This package has moved! +# brainglobe-atlasapi -This package has been renamed to `brainglobe-atlasapi`. -To continue receiving updates, please switch over to using [the new package](https://github.com/brainglobe/brainglobe-atlasapi). - -# BG-atlasAPI - -[![Python Version](https://img.shields.io/pypi/pyversions/bg-atlasapi.svg)](https://pypi.org/project/bg-atlasapi) -[![PyPI](https://img.shields.io/pypi/v/bg-atlasapi.svg)](https://pypi.org/project/bg-atlasapi/) -[![Wheel](https://img.shields.io/pypi/wheel/bg-atlasapi.svg)](https://pypi.org/project/bg-atlasapi) +[![Python Version](https://img.shields.io/pypi/pyversions/brainglobe-atlasapi.svg)](https://pypi.org/project/brainglobe-atlasapi) +[![PyPI](https://img.shields.io/pypi/v/brainglobe-atlasapi.svg)](https://pypi.org/project/brainglobe-atlasapi/) +[![Wheel](https://img.shields.io/pypi/wheel/brainglobe-atlasapi.svg)](https://pypi.org/project/brainglobe-atlasapi) [![Development Status](https://img.shields.io/pypi/status/brainatlas-api.svg)](https://github.com/SainsburyWellcomeCentre/brainatlas-api) -[![Downloads](https://pepy.tech/badge/bg-atlasapi)](https://pepy.tech/project/bg-atlasapi) -[![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/bg-atlasapi/test_and_deploy.yml?branch=main)]( - https://github.com/brainglobe/bg-atlasapi/actions) -[![codecov](https://codecov.io/gh/brainglobe/bg-atlasapi/branch/master/graph/badge.svg?token=WTFPFW0TE4)](https://codecov.io/gh/brainglobe/bg-atlasapi) +[![Downloads](https://pepy.tech/badge/brainglobe-atlasapi)](https://pepy.tech/project/brainglobe-atlasapi) +[![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/brainglobe-atlasapi/test_and_deploy.yml?branch=main)]( + https://github.com/brainglobe/brainglobe-atlasapi/actions) +[![codecov](https://codecov.io/gh/brainglobe/brainglobe-atlasapi/branch/master/graph/badge.svg?token=WTFPFW0TE4)](https://codecov.io/gh/brainglobe/brainglobe-atlasapi) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black) [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/) [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit) [![DOI](https://joss.theoj.org/papers/10.21105/joss.02668/status.svg)](https://doi.org/10.21105/joss.02668) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) [![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://docs.brainglobe.info/cellfinder/contributing) -[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info/documentation/bg-atlasapi/index.html) +[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info/documentation/brainglobe-atlasapi/index.html) [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe) - -The brainglobe atlas API (BG-AtlasAPI) provides a common interface for programmers to download and process brain atlas data from multiple sources. +The brainglobe atlas API (brainglobe-atlasapi) provides a common interface for programmers to download and process brain atlas data from multiple sources. ## Atlases available A number of atlases are in development, but those available currently are: -* [Allen Mouse Brain Atlas](https://www.brain-map.org) at 10, 25, 50 and 100 micron resolutions -* [Allen Human Brain Atlas](https://www.brain-map.org) at 100 micron resolution -* [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de) at 1 micron resolution -* [Enhanced and Unified Mouse Brain Atlas](https://kimlab.io/brain-map/atlas/) at 10, 25, 50 and 100 micron resolutions -* [Smoothed version of the Kim et al. mouse reference atlas](https://doi.org/10.1016/j.celrep.2014.12.014) at 10, 25, 50 and 100 micron resolutions -* [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8) at 20 micron resolution -* [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008) at 20 x 10 x 10 micron resolution -* [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625) at 4 micron resolution -* [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1016/j.neuroimage.2014.04.001) at 39 micron resolution -* [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) (E13, E15, E18, P4, P14, P28 & P56) -* [Princeton Mouse Brain Atlas](https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links) at 20 micron resolution -* [Kim Lab Developmental CCF (P56)](https://data.mendeley.com/datasets/2svx788ddf/1) at 10 micron resolution with 8 reference images - STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2) + +- [Allen Mouse Brain Atlas](https://www.brain-map.org) at 10, 25, 50 and 100 micron resolutions +- [Allen Human Brain Atlas](https://www.brain-map.org) at 100 micron resolution +- [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de) at 1 micron resolution +- [Enhanced and Unified Mouse Brain Atlas](https://kimlab.io/brain-map/atlas/) at 10, 25, 50 and 100 micron resolutions +- [Smoothed version of the Kim et al. mouse reference atlas](https://doi.org/10.1016/j.celrep.2014.12.014) at 10, 25, 50 and 100 micron resolutions +- [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8) at 20 micron resolution +- [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008) at 20 x 10 x 10 micron resolution +- [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625) at 4 micron resolution +- [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1016/j.neuroimage.2014.04.001) at 39 micron resolution +- [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) (E13, E15, E18, P4, P14, P28 & P56) +- [Princeton Mouse Brain Atlas](https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links) at 20 micron resolution +- [Kim Lab Developmental CCF (P56)](https://data.mendeley.com/datasets/2svx788ddf/1) at 10 micron resolution with 8 reference images - STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2) ## Installation -BG-AtlasAPI works with Python >3.6, and can be installed from PyPI with: + +brainglobe-atlasapi works with Python >3.6, and can be installed from PyPI with: + ```bash -pip install bg-atlasapi +pip install brainglobe-atlasapi ``` ## Usage -Full information can be found in the [documentation](https://brainglobe.info/documentation/bg-atlasapi/index.html) + +Full information can be found in the [documentation](https://brainglobe.info/documentation/brainglobe-atlasapi/index.html) + ### Python API -**List of atlases** -To see a list of atlases use `bg_atlasapi.show_atlases` +#### List of atlases + +To see a list of atlases use `brainglobe_atlasapi.show_atlases` + ```python -from bg_atlasapi import show_atlases +from brainglobe_atlasapi import show_atlases show_atlases() # Brainglobe Atlases # ╭──────────────────────────────────┬────────────┬───────────────┬──────────────╮ @@ -71,19 +72,19 @@ show_atlases() # ╰──────────────────────────────────┴────────────┴───────────────┴──────────────╯ ``` -**Using the atlases** +#### Using the atlases All the features of each atlas can be accessed via the `BrainGlobeAtlas` class. - e.g. for the 25um Allen Mouse Brain Atlas: ```python -from bg_atlasapi.bg_atlas import BrainGlobeAtlas +from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas atlas = BrainGlobeAtlas("allen_mouse_25um") ``` The various files associated with the atlas can then be accessed as attributes of the class: + ```python # reference image reference_image = atlas.reference @@ -101,9 +102,10 @@ print(hemispheres_image.shape) # (528, 320, 456) ``` -**Brain regions** +#### Brain regions There are multiple ways to work with individual brain regions. To see a dataframe of each brain region, with it's unique ID, acronym and full name, use `atlas.lookup_df`: + ```python atlas.lookup_df.head(8) # acronym id name @@ -118,6 +120,7 @@ atlas.lookup_df.head(8) ``` Each brain region can also be access by the acronym, e.g. for primary visual cortex (VISp): + ```python from pprint import pprint VISp = atlas.structures["VISp"] @@ -131,20 +134,55 @@ pprint(VISp) # 'structure_id_path': [997, 8, 567, 688, 695, 315, 669, 385]} ``` -### Note on coordinates in `bg-atlasapi` -Working with both image coordinates and cartesian coordinates in the same space can be confusing! In `bg-atlasapi`, the origin is always assumed to be in the upper left corner of the image (sectioning along the first dimension), the "ij" convention. This means that when plotting meshes and points using cartesian systems, you might encounter confusing behaviors coming from the fact that in cartesian plots one axis is inverted with respect to ij coordinates (vertical axis increases going up, image row indexes increase going down). To make things as consistent as possible, in `bg-atlasapi` the 0 of the meshes coordinates is assumed to coincide with the 0 index of the images stack, and meshes coordinates increase following the direction stack indexes increase. -To deal with transformations between your data space and `bg-atlasapi`, you might find the [brainglobe-space](https://github.com/brainglobe/brainglobe-space) package helpful. +### Note on coordinates in `brainglobe-atlasapi` + +Working with both image coordinates and cartesian coordinates in the same space can be confusing! +In `brainglobe-atlasapi`, the origin is always assumed to be in the upper left corner of the image (sectioning along the first dimension), the "ij" convention. +This means that when plotting meshes and points using cartesian systems, you might encounter confusing behaviors coming from the fact that in cartesian plots one axis is inverted with respect to ij coordinates (vertical axis increases going up, image row indexes increase going down). +To make things as consistent as possible, in `brainglobe-atlasapi` the 0 of the meshes coordinates is assumed to coincide with the 0 index of the images stack, and meshes coordinates increase following the direction stack indexes increase. +To deal with transformations between your data space and `brainglobe-atlasapi`, you might find the [brainglobe-space](https://github.com/brainglobe/brainglobe-space) package helpful. + +## Contributing to brainglobe-atlasapi -# Contributing to bg-atlasapi **Contributors to bg-atlaspi are absolutely encouraged**, whether you want to fix bugs, add/request new features or simply ask questions. -If you would like to contribute to `bg-atlasapi` (or any of the downstream tools like [brainrender](https://github.com/brainglobe/brainrender) etc.) please get in touch by opening a new issue or pull request on [GitHub](https://github.com/brainglobe/bg-atlasapi). Please also see the [developers guide](https://brainglobe.info/developers/index.html). +If you would like to contribute to `brainglobe-atlasapi` (or any of the downstream tools like [brainrender](https://github.com/brainglobe/brainrender) etc.) please get in touch by opening a new issue or pull request on [GitHub](https://github.com/brainglobe/brainglobe-atlasapi). +Please also see the [developers guide](https://brainglobe.info/developers/index.html). -Someone might have already asked a question you might have, so if you're not sure where to start, check out the [issues](https://github.com/brainglobe/bg-atlasapi/issues) (and the issues of the other repositories). +Someone might have already asked a question you might have, so if you're not sure where to start, check out the [issues](https://github.com/brainglobe/brainglobe-atlasapi/issues) (and the issues of the other repositories). ## Citation + If you find the BrainGlobe Atlas API useful, please cite the paper in your work: >Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668, https://doi.org/10.21105/joss.02668 **Don't forget to cite the developers of the atlas that you used!** + +--- + +# Atlas Generation and Adding a New Atlas + +For full instructions to add a new BrainGlobe atlas, please see [here](https://brainglobe.info/documentation/brainglobe_atlasapi/adding-a-new-atlas.html). + +The `brainglobe_atlasapi.atlas_generation` submodule contains code for the generation of cleaned-up data, for the main `brainglobe_atlasapi` module. +This code was previously the `bg-atlasgen` module. + +## To contribute + +1. Fork this repo +2. Clone your repo +3. Run `git clone https://github.com/brainglobe/brainglobe-atlasapi` +4. Install an editable version of the package; by running `pip install -e .` within the cloned directory +5. Create a script to package your atlas, and place into `brainglobe_atlasapi/atlas_generation/atlas_scripts`. Please see other scripts for examples. + +Your script should contain everything required to run. +The raw data should be hosted on a publicly accessible repository so that anyone can run the script to recreate the atlas. + +If you need to add any dependencies, please add them as an extra in the `pyproject.toml` file, e.g.: + +```python +[project.optional-dependencies] +allenmouse = ["allensdk"] +newatlas = ["dependency_1", "dependency_2"] +``` diff --git a/bg_atlasapi/__init__.py b/bg_atlasapi/__init__.py deleted file mode 100644 index b8433a59..00000000 --- a/bg_atlasapi/__init__.py +++ /dev/null @@ -1,22 +0,0 @@ -from warnings import warn - -warn( - "This package has been renamed. " - "To continue receiving updates, please use brainglobe-atlasapi instead of this package. " - "https://github.com/brainglobe/brainglobe-atlasapi", - DeprecationWarning, -) - -from importlib.metadata import PackageNotFoundError, metadata - -try: - __version__ = metadata("bg-atlasapi")["Version"] - __author__ = metadata("bg-atlasapi")["Author"] - del metadata -except PackageNotFoundError: - # package is not installed - pass - - -from bg_atlasapi.bg_atlas import BrainGlobeAtlas -from bg_atlasapi.list_atlases import show_atlases diff --git a/brainglobe_atlasapi/__init__.py b/brainglobe_atlasapi/__init__.py new file mode 100644 index 00000000..d36b0416 --- /dev/null +++ b/brainglobe_atlasapi/__init__.py @@ -0,0 +1,13 @@ +from importlib.metadata import PackageNotFoundError, metadata + +try: + __version__ = metadata("brainglobe-atlasapi")["Version"] + __author__ = metadata("brainglobe-atlasapi")["Author"] + del metadata +except PackageNotFoundError: + # package is not installed + pass + + +from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas +from brainglobe_atlasapi.list_atlases import show_atlases diff --git a/brainglobe_atlasapi/atlas_generation/__init__.py b/brainglobe_atlasapi/atlas_generation/__init__.py new file mode 100644 index 00000000..fb935ef5 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/__init__.py @@ -0,0 +1,5 @@ +__version__ = "1" # will set major version of all atlases + +from rich.traceback import install + +install() diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/__init__.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py new file mode 100644 index 00000000..de923763 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py @@ -0,0 +1,401 @@ +__version__ = "0" + +import dataclasses +import json +import multiprocessing as mp +import time +import zipfile +from os import listdir, path +from pathlib import Path +from typing import Tuple + +import numpy as np +import pandas as pd +from rich.progress import track +from skimage import io + +from brainglobe_atlasapi import utils +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + +PARALLEL = True + + +def download_atlas_files(download_dir_path, atlas_file_url, ATLAS_NAME): + utils.check_internet_connection() + + atlas_files_dir = download_dir_path / ATLAS_NAME + try: + download_name = ATLAS_NAME + "_atlas.zip" + except TypeError: + download_name = ATLAS_NAME / "_atlas.zip" + destination_path = download_dir_path / download_name + utils.retrieve_over_http(atlas_file_url, destination_path) + + with zipfile.ZipFile(destination_path, "r") as zip_ref: + zip_ref.extractall(atlas_files_dir) + + return atlas_files_dir + + +def parse_structures(structures_file, root_id): + df = pd.read_csv(structures_file) + df = df.rename(columns={"Parent": "parent_structure_id"}) + df = df.rename(columns={"Region": "id"}) + df = df.rename(columns={"RegionName": "name"}) + df = df.rename(columns={"RegionAbbr": "acronym"}) + df = df.drop(columns=["Level"]) + # get length of labels so as to generate rgb values + no_items = df.shape[0] + # Random values for RGB + # could use this instead? + rgb_list = [ + [ + np.random.randint(0, 255), + np.random.randint(0, 255), + np.random.randint(0, 255), + ] + for i in range(no_items) + ] + rgb_list = pd.DataFrame(rgb_list, columns=["red", "green", "blue"]) + + df["rgb_triplet"] = rgb_list.apply( + lambda x: [x.red.item(), x.green.item(), x.blue.item()], axis=1 + ) + df["structure_id_path"] = df.apply(lambda x: [x.id], axis=1) + structures = df.to_dict("records") + structures = create_structure_hierarchy(structures, df, root_id) + return structures + + +def create_structure_hierarchy(structures, df, root_id): + for structure in structures: + if structure["id"] != root_id: + parent_id = structure["parent_structure_id"] + while True: + structure["structure_id_path"] = [parent_id] + structure[ + "structure_id_path" + ] + if parent_id != root_id: + parent_id = int( + df[df["id"] == parent_id]["parent_structure_id"] + ) + else: + break + else: + structure["name"] = "root" + structure["acronym"] = "root" + + del structure["parent_structure_id"] + + return structures + + +def create_meshes(download_dir_path, structures, annotated_volume, root_id): + meshes_dir_path = download_dir_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + tree = get_structures_tree(structures) + + labels = np.unique(annotated_volume).astype(np.int32) + + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + node.data = Region(is_label) + + # Mesh creation + closing_n_iters = 2 + decimate_fraction = 0.2 + smooth = False # smooth meshes after creation + start = time.time() + if PARALLEL: + pool = mp.Pool(mp.cpu_count() - 2) + + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + root_id, + closing_n_iters, + decimate_fraction, + smooth, + ) + for node in tree.nodes.values() + ], + ) + except mp.pool.MaybeEncodingError: + pass + else: + for node in track( + tree.nodes.values(), + total=tree.size(), + description="Creating meshes", + ): + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + root_id, + closing_n_iters, + decimate_fraction, + smooth, + ) + ) + + print( + "Finished mesh extraction in: ", + round((time.time() - start) / 60, 2), + " minutes", + ) + return meshes_dir_path + + +def create_mesh_dict(structures, meshes_dir_path): + meshes_dict = dict() + structures_with_mesh = [] + for s in structures: + # Check if a mesh was created + mesh_path = meshes_dir_path / f'{s["id"]}.obj' + if not mesh_path.exists(): + print(f"No mesh file exists for: {s}, ignoring it") + continue + else: + # Check that the mesh actually exists (i.e. not empty) + if mesh_path.stat().st_size < 512: + print(f"obj file for {s} is too small, ignoring it.") + continue + + structures_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structures_with_mesh)} " + "structures with mesh are kept" + ) + return meshes_dict, structures_with_mesh + + +@dataclasses.dataclass +class AtlasConfig: + """Data class to configure atlas creation.""" + + atlas_name: str + species: str + atlas_link: str + atlas_file_url: str + #: Input orientation in 3-letter notation using the NumPy system with + #: origin at top left corner of first plane. + #: Axis 0 = front to back, 1 = top to bottom, 2 = left to right. + #: Output orientation will be ASR. + orientation: str + #: Resolution to match the output orientation of ASR. + resolution: Tuple[float, float, float] + citation: str + root_id: int + atlas_packager: str + + +def create_atlas( + working_dir: Path = Path.home(), atlas_config: "AtlasConfig" = None +): + assert ( + len(atlas_config.orientation) == 3 + ), f"Orientation is not 3 characters, Got {atlas_config.orientation}" + assert ( + len(atlas_config.resolution) == 3 + ), f"Resolution is not correct, Got {atlas_config.resolution}" + assert ( + atlas_config.atlas_file_url + ), f"No download link provided for atlas in {atlas_config.atlas_file_url}" + if isinstance(working_dir, str): + working_dir = Path(working_dir) + # Generated atlas path: + working_dir = ( + working_dir / "brainglobe_workingdir" / atlas_config.atlas_name + ) + working_dir.mkdir(exist_ok=True, parents=True) + + download_dir_path = working_dir / "downloads" + download_dir_path.mkdir(exist_ok=True) + if path.isdir(atlas_config.atlas_file_url): + print("Setting atlas to directory: ", atlas_config.atlas_file_url) + atlas_files_dir = atlas_config.atlas_file_url + else: + # Download atlas files from link provided + print("Downloading atlas from link: ", atlas_config.atlas_file_url) + atlas_files_dir = download_atlas_files( + download_dir_path, + atlas_config.atlas_file_url, + atlas_config.atlas_name, + ) + ## Load files + + structures_file = atlas_files_dir / ( + [f for f in listdir(atlas_files_dir) if "region_ids_ADMBA" in f][0] + ) + + reference_file = atlas_files_dir / ( + [f for f in listdir(atlas_files_dir) if "atlasVolume.mhd" in f][0] + ) + + annotations_file = atlas_files_dir / ( + [f for f in listdir(atlas_files_dir) if "annotation.mhd" in f][0] + ) + # segments_file = atlas_files_dir / "Segments.csv" + + annotated_volume = io.imread(annotations_file) + template_volume = io.imread(reference_file) + + ## Parse structure metadata + structures = parse_structures(structures_file, atlas_config.root_id) + + # save regions list json: + with open(download_dir_path / "structures.json", "w") as f: + json.dump(structures, f) + + # Create meshes: + print(f"Saving atlas data at {download_dir_path}") + meshes_dir_path = create_meshes( + download_dir_path, structures, annotated_volume, atlas_config.root_id + ) + + meshes_dict, structures_with_mesh = create_mesh_dict( + structures, meshes_dir_path + ) + + # Wrap up, compress, and remove file: + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=atlas_config.atlas_name, + atlas_minor_version=__version__, + citation=atlas_config.citation, + atlas_link=atlas_config.atlas_link, + species=atlas_config.species, + resolution=atlas_config.resolution, + orientation=atlas_config.orientation, + root_id=atlas_config.root_id, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structures_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + atlas_packager=atlas_config.atlas_packager, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + scale_meshes=True, + ) + print("Done. Atlas generated at: ", output_filename) + return output_filename + + +if __name__ == "__main__": + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" + bg_root_dir.mkdir(exist_ok=True, parents=True) + + # set up E11.5 atlas settings and use as template for rest of brains + e11_5_config = AtlasConfig( + atlas_name="admba_3d_e11_5_mouse", + species="Mus musculus", + atlas_link="https://search.kg.ebrains.eu/instances/8ab25629-bdac-47d0-bc86-6f3aa3885f29", + atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000023_3Drecon-ADMBA-E11pt5_pub", + orientation="lsa", + resolution=(16, 16, 20), + citation="Young et al. 2021, https://doi.org/10.7554/eLife.61408", + root_id=15564, + atlas_packager="Pradeep Rajasekhar, WEHI, Australia, " + "rajasekhardotp@wehidotedudotau; David Young, UCSF, " + "United States, davedotyoung@ucsfdotedu", + ) + + # E13.5 atlas, with updated name and URLs + e13_5_config = dataclasses.replace( + e11_5_config, + atlas_name="admba_3d_e13_5_mouse", + atlas_link="https://search.kg.ebrains.eu/instances/bdb89f61-8dc4-4255-b4d5-50d470958b58", + atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000024_3Drecon-ADMBA-E13pt5_pub", + ) + + # E15.5 atlas + e15_5_config = dataclasses.replace( + e11_5_config, + atlas_name="admba_3d_e15_5_mouse", + atlas_link="https://search.kg.ebrains.eu/instances/Dataset/51a81ae5-d821-437a-a6d5-9b1f963cfe9b", + atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000025_3Drecon-ADMBA-E15pt5_pub", + ) + + # E18.5 atlas + e18_5_config = dataclasses.replace( + e11_5_config, + atlas_name="admba_3d_e18_5_mouse", + atlas_link="https://search.kg.ebrains.eu/instances/633b41be-867a-4611-8570-82271aebd516", + atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000026_3Drecon-ADMBA-E18pt5_pub", + ) + + # P4 atlas, which has different resolutions + p4_config = dataclasses.replace( + e11_5_config, + atlas_name="admba_3d_p4_mouse", + atlas_link="https://search.kg.ebrains.eu/instances/eea3589f-d74b-4988-8f4c-fd9ae8e3a4b3", + atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000027_3Drecon-ADMBA-P4_pub", + resolution=(16.752, 16.752, 20), + ) + + # P14 atlas, which has slightly different resolutions + p14_config = dataclasses.replace( + e11_5_config, + atlas_name="admba_3d_p14_mouse", + atlas_link="https://search.kg.ebrains.eu/instances/114e50aa-156c-4283-af73-11b7f03d287e", + atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000028_3Drecon-ADMBA-P14_pub", + resolution=(16.752, 16.752, 25), + ) + + # P28 atlas, which has same resolutions as P14 + p28_config = dataclasses.replace( + p14_config, + atlas_name="admba_3d_p28_mouse", + atlas_link="https://search.kg.ebrains.eu/instances/3a1153f0-6779-43bd-9f02-f92700a585a4", + atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000029_3Drecon-ADMBA-P28_pub", + ) + + # P56 atlas, which has different resolutions + p56_config = dataclasses.replace( + e11_5_config, + atlas_name="admba_3d_p56_mouse", + atlas_link="https://search.kg.ebrains.eu/instances/a7e99105-1ec2-42e2-a53a-7aa0f2b78135", + atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000030_3Drecon-ADMBA-P56_pub", + resolution=(25, 25, 25), + ) + + # atlases to create + configs = ( + e11_5_config, + e13_5_config, + e15_5_config, + e18_5_config, + p4_config, + p14_config, + p28_config, + p56_config, + ) + + # create each atlas + for config in configs: + create_atlas(bg_root_dir, config) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_cord.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_cord.py new file mode 100644 index 00000000..a2c80ea9 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_cord.py @@ -0,0 +1,298 @@ +__version__ = "1" + +import json +import multiprocessing as mp +import time +import zipfile +from pathlib import Path +from random import choices + +import numpy as np +import pandas as pd +import tifffile +from loguru import logger +from rich.progress import track + +# import sys +# sys.path.append("./") +from brainglobe_atlasapi import utils +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, + inspect_meshes_folder, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + +PARALLEL = True +TEST = False + + +def download_atlas_files(download_dir_path: Path, atlas_file_url: str) -> Path: + utils.check_internet_connection() + + atlas_files_dir = download_dir_path / "atlas_files" + + # only download data if they weren't already downloaded + if atlas_files_dir.exists(): + print("Not downloading atlas since it was downloaded already already") + return atlas_files_dir / "SC_P56_Atlas_10x10x20_v5_2020" + else: + print("Downloading atlas data") + + destination_path = download_dir_path / "atlas_download" + utils.retrieve_over_http(atlas_file_url, destination_path) + + with zipfile.ZipFile(destination_path, "r") as zip_ref: + zip_ref.extractall(atlas_files_dir) + + atlas_files_dir = atlas_files_dir / "SC_P56_Atlas_10x10x20_v5_2020" + return atlas_files_dir + + +def parse_structures(structures_file, root_id): + df = pd.read_csv(structures_file) + df = df.rename(columns={"parent_ID": "parent_structure_id"}) + df = df.drop( + columns=[ + "output_id", + "parent_acronym", + "children_acronym", + "children_IDs", + ] + ) + + df["rgb_triplet"] = df.apply(lambda x: [x.red, x.green, x.blue], axis=1) + df["structure_id_path"] = df.apply(lambda x: [x.id], axis=1) + + df = df.drop(columns=["red", "green", "blue"]) + + structures = df.to_dict("records") + structures = create_structure_hierarchy(structures, df, root_id) + return structures + + +def create_structure_hierarchy(structures, df, root_id): + for structure in structures: + if structure["id"] != root_id: + parent_id = structure["parent_structure_id"] + while True: + structure["structure_id_path"] = [parent_id] + structure[ + "structure_id_path" + ] + if parent_id != root_id: + parent_id = int( + df[df["id"] == parent_id]["parent_structure_id"] + ) + else: + break + else: + structure["name"] = "root" + structure["acronym"] = "root" + + del structure["parent_structure_id"] + + return structures + + +def create_meshes(download_dir_path, structures, annotated_volume, root_id): + meshes_dir_path = download_dir_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + tree = get_structures_tree(structures) + + labels = np.unique(annotated_volume).astype(np.int32) + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + + node.data = Region(is_label) + + # Mesh creation + closing_n_iters = 2 + decimate_fraction = 0.2 + smooth = False # smooth meshes after creation + start = time.time() + + # check how many regions to create the meshes for + nodes = list(tree.nodes.values()) + if TEST: + logger.info( + "Creating atlas in test mode: selecting 10 " + "random regions for mesh creation" + ) + nodes = choices(nodes, k=10) + + if PARALLEL: + print( + f"Creating {tree.size()} meshes in parallel with " + f"{mp.cpu_count() - 2} CPU cores" + ) + pool = mp.Pool(mp.cpu_count() - 2) + + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + root_id, + closing_n_iters, + decimate_fraction, + smooth, + ) + for node in nodes + ], + ) + except mp.pool.MaybeEncodingError: + pass + else: + print(f"Creating {len(nodes)} meshes") + for node in track( + nodes, + total=len(nodes), + description="Creating meshes", + ): + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + root_id, + closing_n_iters, + decimate_fraction, + smooth, + ) + ) + + print( + "Finished mesh extraction in: ", + round((time.time() - start) / 60, 2), + " minutes", + ) + + if TEST: + # create visualization of the various meshes + inspect_meshes_folder(meshes_dir_path) + + return meshes_dir_path + + +def create_mesh_dict(structures, meshes_dir_path): + meshes_dict = dict() + structures_with_mesh = [] + for s in structures: + # Check if a mesh was created + mesh_path = meshes_dir_path / f'{s["id"]}.obj' + if not mesh_path.exists(): + print(f"No mesh file exists for: {s}, ignoring it") + continue + else: + # Check that the mesh actually exists (i.e. not empty) + if mesh_path.stat().st_size < 512: + print(f"obj file for {s} is too small, ignoring it.") + continue + + structures_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structures_with_mesh)} " + "structures with mesh are kept" + ) + return meshes_dict, structures_with_mesh + + +def create_atlas(working_dir): + ATLAS_NAME = "allen_cord" + SPECIES = "Mus musculus" + ATLAS_LINK = "https://data.mendeley.com/datasets/4rrggzv5d5/1" + CITATION = ( + "Fiederling et al. 2021, https://doi.org/10.1101/2021.05.06.443008" + ) + ORIENTATION = "asr" + RESOLUTION = (20, 10, 10) + ROOT_ID = 250 + ATLAS_FILE_URL = ( + "https://md-datasets-cache-zipfiles-prod.s3.eu-west-1." + "amazonaws.com/4rrggzv5d5-1.zip" + ) + ATLAS_PACKAGER = "MetaCell LLC, Ltd." + + download_dir_path = working_dir / "downloads" + download_dir_path.mkdir(exist_ok=True) + + # Download atlas files from Mendeley + atlas_files_dir = download_atlas_files(download_dir_path, ATLAS_FILE_URL) + + # Load files + structures_file = atlas_files_dir / "Atlas_Regions.csv" + reference_file = atlas_files_dir / "Template.tif" + annotations_file = atlas_files_dir / "Annotation.tif" + segments_file = atlas_files_dir / "Segments.csv" + + annotated_volume = tifffile.imread(annotations_file) + template_volume = tifffile.imread(reference_file) + + atlas_segments = pd.read_csv(segments_file) + atlas_segments = dict(atlas_segments=atlas_segments.to_dict("records")) + + # Parse structure metadata + structures = parse_structures(structures_file, ROOT_ID) + + # save regions list json: + with open(download_dir_path / "structures.json", "w") as f: + json.dump(structures, f) + + # Create meshes: + print(f"Saving atlas data at {download_dir_path}") + meshes_dir_path = create_meshes( + download_dir_path, structures, annotated_volume, ROOT_ID + ) + meshes_dict, structures_with_mesh = create_mesh_dict( + structures, meshes_dir_path + ) + + # Wrap up, compress, and remove file: + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=RESOLUTION, + orientation=ORIENTATION, + root_id=ROOT_ID, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structures_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + atlas_packager=ATLAS_PACKAGER, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + scale_meshes=True, + additional_metadata=atlas_segments, + ) + + return output_filename + + +if __name__ == "__main__": + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" / "allen_cord_smooth" + bg_root_dir.mkdir(exist_ok=True, parents=True) + + # generate atlas + print(f'Creating atlas and saving it at "{bg_root_dir}"') + create_atlas(bg_root_dir) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_mouse.py new file mode 100644 index 00000000..cc28a2ef --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_mouse.py @@ -0,0 +1,115 @@ +__version__ = "2" + +from pathlib import Path + +from allensdk.api.queries.ontologies_api import OntologiesApi +from allensdk.api.queries.reference_space_api import ReferenceSpaceApi +from allensdk.core.reference_space_cache import ReferenceSpaceCache +from requests import exceptions +from tqdm import tqdm + +from brainglobe_atlasapi import descriptors +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data + + +def create_atlas(working_dir, resolution): + # Specify information about the atlas: + ATLAS_NAME = "allen_mouse" + SPECIES = "Mus musculus" + ATLAS_LINK = "http://www.brain-map.org" + CITATION = "Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007" + ORIENTATION = "asr" + + # Temporary folder for nrrd files download: + download_dir_path = working_dir / "downloading_path" + download_dir_path.mkdir(exist_ok=True) + + # Download annotated and template volume: + ######################################### + spacecache = ReferenceSpaceCache( + manifest=download_dir_path / "manifest.json", + # downloaded files are stored relative to here + resolution=resolution, + reference_space_key="annotation/ccf_2017", + # use the latest version of the CCF + ) + + # Download + annotated_volume, _ = spacecache.get_annotation_volume() + template_volume, _ = spacecache.get_template_volume() + print("Download completed...") + + # Download structures tree and meshes: + ###################################### + oapi = OntologiesApi() # ontologies + struct_tree = spacecache.get_structure_tree() # structures tree + + # Find id of set of regions with mesh: + select_set = ( + "Structures whose surfaces are represented by a precomputed mesh" + ) + + mesh_set_ids = [ + s["id"] + for s in oapi.get_structure_sets() + if s["description"] == select_set + ] + + structs_with_mesh = struct_tree.get_structures_by_set_id(mesh_set_ids) + + # Directory for mesh saving: + meshes_dir = working_dir / descriptors.MESHES_DIRNAME + + space = ReferenceSpaceApi() + meshes_dict = dict() + for s in tqdm(structs_with_mesh): + name = s["id"] + filename = meshes_dir / f"{name}.obj" + try: + space.download_structure_mesh( + structure_id=s["id"], + ccf_version="annotation/ccf_2017", + file_name=filename, + ) + meshes_dict[name] = filename + except (exceptions.HTTPError, ConnectionError): + print(s) + + # Loop over structures, remove entries not used: + for struct in structs_with_mesh: + [ + struct.pop(k) + for k in ["graph_id", "structure_set_ids", "graph_order"] + ] + + # Wrap up, compress, and remove file:0 + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(resolution,) * 3, + orientation=ORIENTATION, + root_id=997, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structs_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + ) + + return output_filename + + +if __name__ == "__main__": + RES_UM = 25 + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" / "allen_mouse" + bg_root_dir.mkdir(exist_ok=True) + + create_atlas(bg_root_dir, RES_UM) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/azba_zfish.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/azba_zfish.py new file mode 100644 index 00000000..b2e021db --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/azba_zfish.py @@ -0,0 +1,247 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Script to generate a Brainglobe compatible atlas object +for the Adult Zebrafish Brain Atlas (AZBA) + +@author: Kailyn Fields, kailyn.fields@wayne.edu +""" + +__version__ = "1" + +import csv +import multiprocessing as mp +import tarfile +import time +from pathlib import Path + +import numpy as np +import tifffile +from rich.progress import track + +from brainglobe_atlasapi import utils +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + +PARALLEL = False # Disable for debugging mesh creation + + +def create_atlas(working_dir, resolution): + # metadata + ATLAS_NAME = "azba_zfish" + SPECIES = "Danio rerio" + ATLAS_LINK = "http://www.azba.wayne.edu" + CITATION = "Kenney et al. 2021, https://doi.org/10.7554/elife.69988" + ATLAS_FILE_URL = "http://www.azba.wayne.edu/2021-08-22_AZBA.tar.gz" + ORIENTATION = "las" + ROOT_ID = 9999 + ATLAS_PACKAGER = "Kailyn Fields, kailyn.fields@wayne.edu" + ADDITIONAL_METADATA = {} + + # setup folder for downloading + working_dir = working_dir / ATLAS_NAME + working_dir.mkdir(exist_ok=True) + download_dir_path = working_dir / "downloads" + download_dir_path.mkdir(exist_ok=True) + atlas_path = download_dir_path / f"{ATLAS_NAME}" + + # download atlas files + utils.check_internet_connection() + destination_path = download_dir_path / "atlas_download" + utils.retrieve_over_http(ATLAS_FILE_URL, destination_path) + + # unpack the atlas download folder + tar = tarfile.open(destination_path) + tar.extractall(path=atlas_path) + tar.close() + destination_path.unlink() + + print("Atlas files download completed") + + # paths + structures_file = atlas_path / "2021-08-22_AZBA_labels.csv" + annotations_file = atlas_path / "2021-08-22_AZBA_segmentation.tif" + reference_topro = atlas_path / "20180219_AZBA_topro_average_2020.tif" + reference_file = atlas_path / "20180628_AZBA_AF_average.tif" + meshes_dir_path = atlas_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + # adding topro image as additional reference file, + # main reference file is autofl + topro = tifffile.imread(reference_topro) + ADDITIONAL_REFERENCES = {"TO-PRO": topro} + + # open structures.csv and prep for dictionary parsing + print("Creating structure tree") + zfishFile = open(structures_file) + zfishDictReader = csv.DictReader(zfishFile) + + # empty list to populate with dictionaries + hierarchy = [] + + # parse through csv file and populate hierarchy list + for row in zfishDictReader: + hierarchy.append(row) + + # make string to int and list of int conversions in + # 'id', 'structure_id_path', and 'rgb_triplet' key values + for i in range(0, len(hierarchy)): + hierarchy[i]["id"] = int(hierarchy[i]["id"]) + for j in range(0, len(hierarchy)): + hierarchy[j]["structure_id_path"] = list( + map(int, hierarchy[j]["structure_id_path"].split("/")) + ) + for k in range(0, len(hierarchy)): + try: + hierarchy[k]["rgb_triplet"] = list( + map(int, hierarchy[k]["rgb_triplet"].split("/")) + ) + except ValueError: + hierarchy[k]["rgb_triplet"] = [255, 255, 255] + + # remove clear label (id 0) from hierarchy. + # ITK-Snap uses this to label unlabeled areas, + # but this convention interferes with the root mask generation + # and is unnecessary for this application + hierarchy.remove(hierarchy[1]) + + # use tifffile to read annotated file + annotated_volume = tifffile.imread(annotations_file) + + print(f"Saving atlas data at {atlas_path}") + tree = get_structures_tree(hierarchy) + print( + f"Number of brain regions: {tree.size()}, " + f"max tree depth: {tree.depth()}" + ) + + # generate binary mask for mesh creation + labels = np.unique(annotated_volume).astype(np.int_) + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + + node.data = Region(is_label) + + # mesh creation + closing_n_iters = 2 + start = time.time() + + decimate_fraction = 0.3 + smooth = True + + if PARALLEL: + print("Multiprocessing mesh creation...") + pool = mp.Pool(int(mp.cpu_count() / 2)) + + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + ROOT_ID, + closing_n_iters, + ) + for node in tree.nodes.values() + ], + ) + except mp.pool.MaybeEncodingError: + pass + + else: + print("Multiprocessing disabled") + # nodes = list(tree.nodes.values()) + # nodes = choices(nodes, k=10) + for node in track( + tree.nodes.values(), + total=tree.size(), + description="Creating meshes", + ): + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + ) + + print( + "Finished mesh extraction in : ", + round((time.time() - start) / 60, 2), + " minutes", + ) + + # create meshes dict + meshes_dict = dict() + structures_with_mesh = [] + for s in hierarchy: + # check if a mesh was created + mesh_path = meshes_dir_path / f"{s['id']}.obj" + if not mesh_path.exists(): + print(f"No mesh file exists for: {s}, ignoring it.") + continue + else: + # check that the mesh actually exists and isn't empty + if mesh_path.stat().st_size < 512: + print(f"obj file for {s} is too small, ignoring it.") + continue + structures_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structures_with_mesh)} " + "structures with mesh are kept" + ) + + # import reference file with tifffile so + # it can be read in wrapup_atlas_from_data + reference = tifffile.imread(reference_file) + # inspect_meshes_folder(meshes_dir_path) + # wrap up atlas file + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(resolution,) * 3, + orientation=ORIENTATION, + root_id=ROOT_ID, + reference_stack=reference, + annotation_stack=annotations_file, + structures_list=hierarchy, + meshes_dict=meshes_dict, + working_dir=working_dir, + atlas_packager=ATLAS_PACKAGER, + additional_metadata=ADDITIONAL_METADATA, + additional_references=ADDITIONAL_REFERENCES, + ) + + return output_filename + + +if __name__ == "__main__": + resolution = 4 + + # generated atlas path + bg_root_dir = Path.home() / "brainglobe_workingdir" + bg_root_dir.mkdir(exist_ok=True, parents=True) + create_atlas(bg_root_dir, resolution) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/example_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/example_mouse.py new file mode 100644 index 00000000..447e08a4 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/example_mouse.py @@ -0,0 +1,114 @@ +__version__ = "2" + +from pathlib import Path + +from allensdk.api.queries.ontologies_api import OntologiesApi +from allensdk.api.queries.reference_space_api import ReferenceSpaceApi +from allensdk.core.reference_space_cache import ReferenceSpaceCache +from requests import exceptions +from tqdm import tqdm + +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data + + +def create_atlas(working_dir, resolution): + # Specify information about the atlas: + RES_UM = resolution # 100 + ATLAS_NAME = "example_mouse" + SPECIES = "Mus musculus" + ATLAS_LINK = "http://www.brain-map.org" + CITATION = "Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007" + ORIENTATION = "asr" + + # Temporary folder for nrrd files download: + download_dir_path = working_dir / "downloading_path" + download_dir_path.mkdir(exist_ok=True) + + # Download annotated and template volume: + ######################################### + spacecache = ReferenceSpaceCache( + manifest=download_dir_path / "manifest.json", + # downloaded files are stored relative to here + resolution=RES_UM, + reference_space_key="annotation/ccf_2017", + # use the latest version of the CCF + ) + + # Download + annotated_volume, _ = spacecache.get_annotation_volume() + template_volume, _ = spacecache.get_template_volume() + print("Download completed...") + + # Download structures tree and meshes: + ###################################### + oapi = OntologiesApi() # ontologies + struct_tree = spacecache.get_structure_tree() # structures tree + + # Find id of set of regions with mesh: + select_set = ( + "Structures whose surfaces are represented by a precomputed mesh" + ) + + mesh_set_ids = [ + s["id"] + for s in oapi.get_structure_sets() + if s["description"] == select_set + ] + + structs_with_mesh = struct_tree.get_structures_by_set_id(mesh_set_ids)[:3] + + # Directory for mesh saving: + meshes_dir = working_dir / "mesh_temp_download" + + space = ReferenceSpaceApi() + meshes_dict = dict() + for s in tqdm(structs_with_mesh): + name = s["id"] + filename = meshes_dir / f"{name}.obj" + try: + space.download_structure_mesh( + structure_id=s["id"], + ccf_version="annotation/ccf_2017", + file_name=filename, + ) + meshes_dict[name] = filename + except (exceptions.HTTPError, ConnectionError): + print(s) + + # Loop over structures, remove entries not used: + for struct in structs_with_mesh: + [ + struct.pop(k) + for k in ["graph_id", "structure_set_ids", "graph_order"] + ] + + # Wrap up, compress, and remove file: + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(RES_UM,) * 3, + orientation=ORIENTATION, + root_id=997, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structs_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + ) + + return output_filename + + +if __name__ == "__main__": + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" / "example" + bg_root_dir.mkdir(exist_ok=True) + + # create_atlas(working_dir, 100) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py new file mode 100644 index 00000000..a575bfa3 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py @@ -0,0 +1,302 @@ +import json +import multiprocessing as mp +import time +from pathlib import Path + +import numpy as np +import pandas as pd +import treelib +import urllib3 +from allensdk.core.structure_tree import StructureTree +from brainio import brainio +from rich.progress import track + +# import sys +# sys.path.append("./") +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, + inspect_meshes_folder, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + + +def prune_tree(tree): + nodes = tree.nodes.copy() + for key, node in nodes.items(): + if node.tag == "root": + continue + if node.data.has_label: + try: + children = tree.children(node.identifier) + except treelib.exceptions.NodeIDAbsentError: + continue + + if children: + for child in children: + try: + tree.remove_node(child.identifier) + except treelib.exceptions.NodeIDAbsentError: + pass + else: + # Remove if none of the children has mesh + try: + subtree = tree.subtree(node.identifier) + except treelib.exceptions.NodeIDAbsentError: + continue + else: + if not np.any( + [c.data.has_label for _, c in subtree.nodes.items()] + ): + tree.remove_node(node.identifier) + return tree + + +if __name__ == "__main__": + PARALLEL = False # disable parallel mesh extraction for easier debugging + TEST = False + + # ----------------- # + # PREP METADATA # + # ----------------- # + RES_UM = 500 + VERSION = 1 + ATLAS_NAME = "allen_human" + SPECIES = "Homo sapiens" + ATLAS_LINK = "http://download.alleninstitute.org/informatics-archive/allen_human_reference_atlas_3d_2020/version_1/" + CITATION = "Ding et al 2016, https://doi.org/10.1002/cne.24080" + ORIENTATION = "ipr" + + # ------------------ # + # PREP FILEPATHS # + # ------------------ # + + data_fld = Path( + r"D:\Dropbox (UCL - SWC)\Rotation_vte\Anatomy" + r"\Atlases\atlasesforbrainrender\AllenHuman" + ) + + annotations_image = data_fld / "annotation.nii" + anatomy_image = ( + data_fld + / "mni_icbm152_nlin_sym_09b" + / "mni_icbm152_pd_tal_nlin_sym_09b_hires.nii" + ) + + # Generated atlas path: + bg_root_dir = Path.home() / ".brainglobe" + bg_root_dir.mkdir(exist_ok=True) + + # Temporary folder for nrrd files download: + temp_path = Path(r"C:\Users\Federico\.brainglobe\humanev") + temp_path.mkdir(exist_ok=True) + + # Temporary folder for files before compressing: + uncompr_atlas_path = temp_path / ATLAS_NAME + uncompr_atlas_path.mkdir(exist_ok=True) + + # ---------------- # + # GET TEMPLATE # + # ---------------- # + annotation = brainio.load_any(annotations_image) # shape (394, 466, 378) + anatomy = brainio.load_any(anatomy_image) # shape (394, 466, 378) + + # Remove weird artefact + annotation = annotation[:200, :, :] + anatomy = anatomy[:200, :, :] + + # show(Volume(root_annotation), axes=1) + + # ------------------------ # + # STRUCTURES HIERARCHY # + # ------------------------ # + # Download structure tree + ######################### + + # RMA query to fetch structures for the structure graph + query_url = "http://api.brain-map.org/api/v2/data/query.json?criteria=model::Structure" + query_url += ",rma::criteria,[graph_id$eq%d]" % 16 + query_url += ( + ",rma::options[order$eq'structures.graph_order'][num_rows$eqall]" + ) + + http = urllib3.PoolManager() + r = http.request("GET", query_url) + data = json.loads(r.data.decode("utf-8"))["msg"] + structures = pd.read_json(json.dumps(data)) + + # Create empty list and collect all regions + # traversing the regions hierarchy: + regions_list = [] + + for i, region in structures.iterrows(): + if i == 0: + acronym = "root" + else: + acronym = region["acronym"] + + regions_list.append( + { + "name": region["name"], + "acronym": acronym, + "id": region["id"], + "rgb_triplet": StructureTree.hex_to_rgb( + region["color_hex_triplet"] + ), + "structure_id_path": StructureTree.path_to_list( + region["structure_id_path"] + ), + } + ) + ROOT_ID = regions_list[0]["id"] + + # ----------------- # + # CREATE MESHES # + # ----------------- # + print(f"Saving atlas data at {uncompr_atlas_path}") + meshes_dir_path = uncompr_atlas_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + tree = get_structures_tree(regions_list) + print( + f"Number of brain regions: {tree.size()}, " + f"max tree depth: {tree.depth()}" + ) + + # Mark which tree elements are in the annotation volume + labels = np.unique(annotation).astype(np.int32) + + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + + node.data = Region(is_label) + + # tree.show(data_property='has_label') + + # Remove nodes for which no mesh can be created + tree = prune_tree(tree) + print( + f"After pruning: # of brain regions: {tree.size()}, " + f"max tree depth: {tree.depth()}" + ) + + # Mesh creation + closing_n_iters = 2 + decimate_fraction = 0.2 + smooth = False # smooth meshes after creation + start = time.time() + if PARALLEL: + print("Starting mesh creation in parallel") + + pool = mp.Pool(mp.cpu_count() - 2) + + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + annotation, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + for node in tree.nodes.values() + ], + ) + except mp.pool.MaybeEncodingError: + # error with returning results from pool.map but we don't care + pass + else: + print("Starting mesh creation") + + for node in track( + tree.nodes.values(), + total=tree.size(), + description="Creating meshes", + ): + if node.tag == "root": + volume = annotation.copy() + volume[volume > 0] = node.identifier + else: + volume = annotation + + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + volume, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + ) + + print( + "Finished mesh extraction in: ", + round((time.time() - start) / 60, 2), + " minutes", + ) + + if TEST: + # create visualization of the various meshes + inspect_meshes_folder(meshes_dir_path) + + # Create meshes dict + meshes_dict = dict() + structures_with_mesh = [] + for s in regions_list: + # Check if a mesh was created + mesh_path = meshes_dir_path / f'{s["id"]}.obj' + if not mesh_path.exists(): + # print(f"No mesh file exists for: {s['name']}") + continue + else: + # Check that the mesh actually exists (i.e. not empty) + if mesh_path.stat().st_size < 512: + # print(f"obj file for {s['name']} is too small.") + continue + + structures_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structures_with_mesh)} " + "structures with mesh are kept" + ) + + # ----------- # + # WRAP UP # + # ----------- # + + # Wrap up, compress, and remove file: + print("Finalising atlas") + wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=VERSION, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(RES_UM,) * 3, + orientation=ORIENTATION, + root_id=ROOT_ID, + reference_stack=anatomy, + annotation_stack=annotation, + structures_list=structures_with_mesh, + meshes_dict=meshes_dict, + working_dir=bg_root_dir, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + ) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_developmental_ccf_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_developmental_ccf_mouse.py new file mode 100644 index 00000000..a02067cf --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_developmental_ccf_mouse.py @@ -0,0 +1,355 @@ +__version__ = "1" + +import json +import multiprocessing as mp +import time +import zipfile +from pathlib import Path + +import imio +import numpy as np +import pandas as pd +from rich.progress import track +from scipy.ndimage import zoom + +from brainglobe_atlasapi import utils +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + +PARALLEL = True # disable parallel mesh extraction for easier debugging + + +def clean_up_df_entries(df): + """ + Remove ' from string entries in the csv + """ + df["Acronym"] = df["Acronym"].apply(lambda x: x.replace("'", "")) + df["Name"] = df["Name"].apply(lambda x: x.replace("'", "")) + df["ID"] = df["ID"].apply( + lambda x: int(x) + ) # convert from numpy to int() for dumping as json + + ints = [int(ele) for ele in df["ID"]] + df["ID"] = ints + + +def get_structure_id_path_from_id(id, id_dict, root_id): + """ + Create the structure_id_path for a region + from a dict mapping id to parent_id + """ + structure_id_path = [id] + if id == root_id: + return structure_id_path + + while True: + parent = int(id_dict[id]) + structure_id_path.insert(0, parent) + + if parent == root_id: + break + + id = parent + + return structure_id_path + + +def create_atlas( + working_dir, + resolution, + reference_key, + reference_filename, + mesh_creation, + existing_mesh_dir_path=None, +): + """""" + ATLAS_NAME = f"kim_dev_mouse_{reference_key}" + SPECIES = "Mus musculus" + ATLAS_LINK = "https://data.mendeley.com/datasets/2svx788ddf/1" + CITATION = ( + "Kim, Yongsoo (2022), “KimLabDevCCFv001”, Mendeley Data, " + "V1, doi: 10.17632/2svx788ddf.1" + ) + ORIENTATION = "asl" + ROOT_ID = 99999999 + ANNOTATIONS_RES_UM = 10 + ATLAS_FILE_URL = "https://prod-dcd-datasets-cache-zipfiles.s3.eu-west-1.amazonaws.com/2svx788ddf-1.zip" + + # Temporary folder for download: + download_dir_path = working_dir / "downloads" + download_dir_path.mkdir(exist_ok=True) + atlas_files_dir = download_dir_path / "atlas_files" + + utils.check_internet_connection() + + destination_path = download_dir_path / "atlas_download" + + utils.retrieve_over_http(ATLAS_FILE_URL, destination_path) + + with zipfile.ZipFile(download_dir_path / "atlas_download", "r") as zip_ref: + zip_ref.extractall(atlas_files_dir) + + destination_path.unlink() + + # Set paths to volumes + structures_file = ( + atlas_files_dir + / "KimLabDevCCFv001" + / "KimLabDevCCFv001_MouseOntologyStructure.csv" + ) + annotations_file = ( + atlas_files_dir + / "KimLabDevCCFv001" + / "10um" + / "KimLabDevCCFv001_Annotations_ASL_Oriented_10um.nii.gz" + ) + template_file = ( + atlas_files_dir / "KimLabDevCCFv001" / "10um" / reference_filename + ) + + # ---------------- # + # GET TEMPLATE # + # ---------------- # + + # Load (and possibly downsample) annotated volume: + scaling = ANNOTATIONS_RES_UM / resolution + + annotated_volume = imio.load_nii(annotations_file, as_array=True) + template_volume = imio.load_nii(template_file, as_array=True) + + annotated_volume = zoom( + annotated_volume, (scaling, scaling, scaling), order=0, prefilter=False + ) + + # ------------------------ # + # STRUCTURES HIERARCHY # + # ------------------------ # + + # Parse region names & hierarchy + df = pd.read_csv(structures_file) + clean_up_df_entries(df) + + df.loc[len(df)] = ["root", ROOT_ID, "root", ROOT_ID] + df.append(["root", ROOT_ID, "root", ROOT_ID]) + + id_dict = dict(zip(df["ID"], df["Parent ID"])) + + assert id_dict[15564] == "[]" + id_dict[15564] = ROOT_ID + + structures = [] + for row in range(df.shape[0]): + entry = { + "acronym": df["Acronym"][row], + "id": int(df["ID"][row]), # from np.int for JSON serialization + "name": df["Name"][row], + "structure_id_path": get_structure_id_path_from_id( + int(df["ID"][row]), id_dict, ROOT_ID + ), + "rgb_triplet": [255, 255, 255], + } + + structures.append(entry) + + # save regions list json: + with open(download_dir_path / "structures.json", "w") as f: + json.dump(structures, f) + + # ----------------- # + # Create Meshes # + # ----------------- # + + print(f"Saving atlas data at {download_dir_path}") + + if mesh_creation == "copy": + meshes_dir_path = Path(existing_mesh_dir_path) + else: + meshes_dir_path = download_dir_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + tree = get_structures_tree(structures) + + rotated_annotations = np.rot90(annotated_volume, axes=(0, 2)) + + labels = np.unique(rotated_annotations).astype(np.int32) + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + + node.data = Region(is_label) + + if mesh_creation == "generate": + closing_n_iters = 2 + decimate_fraction = 0.04 + smooth = False # smooth meshes after creation + + start = time.time() + + if PARALLEL: + pool = mp.Pool(mp.cpu_count() - 2) + + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + rotated_annotations, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + for node in tree.nodes.values() + ], + ) + except mp.pool.MaybeEncodingError: + # error with returning results from pool.map but we don't care + pass + else: + for node in track( + tree.nodes.values(), + total=tree.size(), + description="Creating meshes", + ): + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + rotated_annotations, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + ) + + print( + "Finished mesh extraction in: ", + round((time.time() - start) / 60, 2), + " minutes", + ) + + # Create meshes dict + meshes_dict = dict() + structures_with_mesh = [] + for s in structures: + # Check if a mesh was created + mesh_path = meshes_dir_path / f'{s["id"]}.obj' + if not mesh_path.exists(): + print(f"No mesh file exists for: {s}, ignoring it") + continue + else: + # Check that the mesh actually exists (i.e. not empty) + if mesh_path.stat().st_size < 512: + print(f"obj file for {s} is too small, ignoring it.") + continue + + structures_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structures_with_mesh)} " + "structures with mesh are kept" + ) + + # ----------- # + # WRAP UP # + # ----------- # + + # Wrap up, compress, and remove file: + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(resolution,) * 3, + orientation=ORIENTATION, + root_id=ROOT_ID, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structures_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + scale_meshes=True, + ) + + return output_filename + + +if __name__ == "__main__": + """ + This atlas is too large to package into a single atlas. + Hence it is split with one atlas per reference. + To avoid re-generating the meshes for each creation, + the script should be run once with mesh_creation = 'generate'. + This will generate the standard template atlas with the meshes. + For the rest of the references, use mesh_creation = 'copy', + and set the existing_mesh_dir_path to the previously-generated meshes. + + Note the decimate fraction is set to 0.04 + to further reduce size of this large atlas. + """ + resolution = 10 # some resolution, in microns (10, 25, 50, 100) + + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" / "kim_mouse" + bg_root_dir.mkdir(exist_ok=True, parents=True) + + # First create the standard template, including all meshes + + create_atlas( + bg_root_dir, + resolution, + reference_key="stp", + reference_filename="CCFv3_average_template_ASL_Oriented_u16_10um.nii.gz", + mesh_creation="generate", + ) + + # Now get the mesh path from the previously generated atlas and use this + # for all other atlases + + additional_references = { + "idisco": "KimLabDevCCFv001_iDiscoLSFM2CCF_" + "avgTemplate_ASL_Oriented_10um.nii.gz", + "mri_a0": "KimLabDevCCFv001_P56_MRI-a02CCF_" + "avgTemplate_ASL_Oriented_10um.nii.gz", + "mri_adc": "KimLabDevCCFv001_P56_MRI-adc2CCF_" + "avgTemplate_ASL_Oriented_10um.nii.gz", + "mri_dwi": "KimLabDevCCFv001_P56_MRI-dwi2CCF_" + "avgTemplate_ASL_Oriented_10um.nii.gz", + "mri_fa": "KimLabDevCCFv001_P56_MRI-fa2CCF_" + "avgTemplate_ASL_Oriented_10um.nii.gz", + "mri_mtr": "KimLabDevCCFv001_P56_MRI-MTR2CCF_" + "avgTemplate_ASL_Oriented_10um.nii.gz", + "mri_t2": "KimLabDevCCFv001_P56_MRI-T22CCF_" + "avgTemplate_ASL_Oriented_10um.nii.gz", + } + + existing_mesh_dir_path = bg_root_dir / "downloads" / "meshes" + + for reference_key, reference_filename in additional_references.items(): + create_atlas( + bg_root_dir, + resolution, + reference_key, + reference_filename, + mesh_creation="copy", + existing_mesh_dir_path=existing_mesh_dir_path, + ) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_mouse.py new file mode 100644 index 00000000..b1e39778 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_mouse.py @@ -0,0 +1,245 @@ +__version__ = "1" + +import json +import multiprocessing as mp +import tarfile +import time +from pathlib import Path + +import numpy as np +import pandas as pd +import tifffile +from allensdk.core.reference_space_cache import ReferenceSpaceCache +from rich.progress import track +from scipy.ndimage import zoom + +# import sys +# sys.path.append("./") +from brainglobe_atlasapi import utils +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + +PARALLEL = False # disable parallel mesh extraction for easier debugging + + +def create_atlas(working_dir, resolution): + ATLAS_NAME = "kim_mouse" + SPECIES = "Mus musculus" + ATLAS_LINK = "https://kimlab.io/brain-map/atlas/" + CITATION = "Chon et al. 2019, https://doi.org/10.1038/s41467-019-13057-w" + ORIENTATION = "asr" + ROOT_ID = 997 + ANNOTATIONS_RES_UM = 10 + ATLAS_FILE_URL = "https://gin.g-node.org/brainglobe/kim_atlas_materials/raw/master/kim_atlas_materials.tar.gz" + + # Temporary folder for download: + download_dir_path = working_dir / "downloads" + download_dir_path.mkdir(exist_ok=True) + atlas_files_dir = download_dir_path / "atlas_files" + + # Download atlas_file + utils.check_internet_connection() + + destination_path = download_dir_path / "atlas_download" + utils.retrieve_over_http(ATLAS_FILE_URL, destination_path) + + tar = tarfile.open(destination_path) + tar.extractall(path=atlas_files_dir) + tar.close() + + destination_path.unlink() + + structures_file = atlas_files_dir / "kim_atlas" / "structures.csv" + annotations_file = atlas_files_dir / "kim_atlas" / "annotation.tiff" + + # ---------------- # + # GET TEMPLATE # + # ---------------- # + + # Load (and possibly downsample) annotated volume: + scaling = ANNOTATIONS_RES_UM / resolution + + annotated_volume = tifffile.imread(annotations_file) + annotated_volume = zoom( + annotated_volume, (scaling, scaling, scaling), order=0, prefilter=False + ) + + # Download annotated and template volume: + ######################################### + spacecache = ReferenceSpaceCache( + manifest=download_dir_path / "manifest.json", + # downloaded files are stored relative to here + resolution=resolution, + reference_space_key="annotation/ccf_2017", + # use the latest version of the CCF + ) + + # Download + template_volume, _ = spacecache.get_template_volume() + print("Download completed...") + + # ------------------------ # + # STRUCTURES HIERARCHY # + # ------------------------ # + + # Parse region names & hierarchy + # ############################## + df = pd.read_csv(structures_file) + df = df.drop(columns=["Unnamed: 0", "parent_id", "parent_acronym"]) + + # split by "/" and convert list of strings to list of ints + df["structure_id_path"] = ( + df["structure_id_path"] + .str.split(pat="/") + .map(lambda x: [int(i) for i in x]) + ) + + structures = df.to_dict("records") + + for structure in structures: + structure.update({"rgb_triplet": [255, 255, 255]}) + # root doesn't have a parent + if structure["id"] != 997: + structure["structure_id_path"].append(structure["id"]) + + # save regions list json: + with open(download_dir_path / "structures.json", "w") as f: + json.dump(structures, f) + + # Create meshes: + print(f"Saving atlas data at {download_dir_path}") + meshes_dir_path = download_dir_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + tree = get_structures_tree(structures) + + rotated_annotations = np.rot90(annotated_volume, axes=(0, 2)) + + labels = np.unique(rotated_annotations).astype(np.int32) + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + + node.data = Region(is_label) + + # Mesh creation + closing_n_iters = 2 + decimate_fraction = 0.2 + smooth = False # smooth meshes after creation + + start = time.time() + if PARALLEL: + pool = mp.Pool(mp.cpu_count() - 2) + + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + rotated_annotations, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + for node in tree.nodes.values() + ], + ) + except mp.pool.MaybeEncodingError: + # error with returning results from pool.map but we don't care + pass + else: + for node in track( + tree.nodes.values(), + total=tree.size(), + description="Creating meshes", + ): + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + rotated_annotations, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + ) + + print( + "Finished mesh extraction in: ", + round((time.time() - start) / 60, 2), + " minutes", + ) + + # Create meshes dict + meshes_dict = dict() + structures_with_mesh = [] + for s in structures: + # Check if a mesh was created + mesh_path = meshes_dir_path / f'{s["id"]}.obj' + if not mesh_path.exists(): + print(f"No mesh file exists for: {s}, ignoring it") + continue + else: + # Check that the mesh actually exists (i.e. not empty) + if mesh_path.stat().st_size < 512: + print(f"obj file for {s} is too small, ignoring it.") + continue + + structures_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structures_with_mesh)} " + "structures with mesh are kept" + ) + + # ----------- # + # WRAP UP # + # ----------- # + + # Wrap up, compress, and remove file: + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(resolution,) * 3, + orientation=ORIENTATION, + root_id=ROOT_ID, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structures_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + scale_meshes=True, + ) + + return output_filename + + +if __name__ == "__main__": + resolution = 10 # some resolution, in microns (10, 25, 50, 100) + + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" / "kim_mouse" + bg_root_dir.mkdir(exist_ok=True, parents=True) + create_atlas(bg_root_dir, resolution) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/mpin_zfish.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/mpin_zfish.py new file mode 100644 index 00000000..a2558aa5 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/mpin_zfish.py @@ -0,0 +1,266 @@ +__version__ = "1" + +import tarfile +import warnings +import zipfile +from pathlib import Path + +import numpy as np +import requests +from allensdk.core.structure_tree import StructureTree +from scipy.ndimage import binary_dilation, binary_erosion, binary_fill_holes +from tifffile import imread + +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.utils import retrieve_over_http + +BASE_URL = r"https://fishatlas.neuro.mpg.de" + + +def download_line_stack(bg_root_dir, tg_line_name): + """Utility function to download a line from its name.""" + reference_url = ( + f"{BASE_URL}/media/brain_browser/Lines/" + f"{tg_line_name}/AverageData/Tiff_File/" + f"Average_{tg_line_name}.zip" + ) + out_file_path = bg_root_dir / f"{tg_line_name}.zip" + retrieve_over_http(reference_url, out_file_path) + with zipfile.ZipFile(out_file_path, "r") as zip_ref: + zip_ref.extractall(bg_root_dir) + + return imread(str(next(bg_root_dir.glob(f"*{tg_line_name}*.tif")))) + + +def add_path_inplace(parent): + """Recursively traverse hierarchy of regions and append for each region + the full path of substructures in brainglobe standard list. + + Parameters + ---------- + parent : dict + node parsed from fishatlas website containing a "sub_regions" key + + """ + for ch in parent["sub_regions"]: + new_root = parent["structure_id_path"] + [ + ch["id"], + ] + + ch["structure_id_path"] = new_root + + add_path_inplace(ch) + + +def collect_all_inplace( + node, + traversing_list, + download_path, + mesh_dict, +): + """Recursively traverse a region hierarchy, download meshes, and append + regions to a list inplace. + + Parameters + ---------- + node + traversing_list + download_path + mesh_dict + + + """ + + # Append clean dictionary with brainglobe standard info: + traversing_list.append( + { + "name": node["name"], + "acronym": node["name"], + "id": node["id"], + "rgb_triplet": StructureTree.hex_to_rgb(node["color"]), + "structure_id_path": node["structure_id_path"], + } + ) + + # Url for the mesh: + mesh_url = ( + BASE_URL + node["files"]["file_3D"][:-4].replace("\\", "/") + ".stl" + ) + + # Try download, if mesh does not exist region is removed: + try: + filename = download_path / "{}.stl".format(node["id"]) + retrieve_over_http(mesh_url, filename) + + mesh_dict[node["id"]] = filename + except requests.exceptions.ConnectionError: + # Pop region from list: + message = "No mesh found for {}".format(traversing_list.pop()["name"]) + warnings.warn(message) + + for region in node["sub_regions"]: + collect_all_inplace(region, traversing_list, download_path, mesh_dict) + + +def create_atlas(working_dir, resolution): + # Specify fixed information about the atlas: + RES_UM = resolution + ATLAS_NAME = "mpin_zfish" + SPECIES = "Danio rerio" + ATLAS_LINK = "http://fishatlas.neuro.mpg.de" + CITATION = "Kunst et al 2019, https://doi.org/10.1016/j.neuron.2019.04.034" + ORIENTATION = "lai" + ATLAS_PACKAGER = "Luigi Petrucco, luigi.petrucco@gmail.com" + + # Download reference: + ##################### + reference_stack = download_line_stack(working_dir, "HuCGCaMP5G") + + # Download accessory references: + ################################ + additional_references = dict() + for line in ["H2BGCaMP", "GAD1b"]: + additional_references[line] = download_line_stack(working_dir, line) + + # Download annotation and hemispheres from GIN repo: + gin_url = "https://gin.g-node.org/brainglobe/mpin_zfish/raw/master/mpin_zfish_annotations_meshes.tar.gz" + compressed_zip_path = working_dir / "annotations.tar" + retrieve_over_http(gin_url, compressed_zip_path) + + tar = tarfile.open(compressed_zip_path) + tar.extractall(path=working_dir) + + extracted_dir = working_dir / "mpin_zfish_annotations" + + annotation_stack = imread(str(extracted_dir / "mpin_zfish_annotation.tif")) + + # Pad 1 voxel around the whole annotation: + annotation_stack[[0, -1], :, :] = 0 + annotation_stack[:, [0, -1], :] = 0 + annotation_stack[:, :, [0, -1]] = 0 + + hemispheres_stack = imread( + str(extracted_dir / "mpin_zfish_hemispheres.tif") + ) + + # meshes from the website and stacks do not have the same orientation. + # Therefore, flip axes of the stacks so that brainglobe-space + # reorientation is used on the meshes: + annotation_stack = annotation_stack.swapaxes(0, 2) + hemispheres_stack = hemispheres_stack.swapaxes(0, 2) + reference_stack = reference_stack.swapaxes(0, 2) + additional_references = { + k: v.swapaxes(0, 2) for k, v in additional_references.items() + } + + # Improve the annotation by defining a region that encompasses + # the whole brain but not the eyes. + # This will be aside from the official hierarchy: + BRAIN_ID = 2 # add this as not defined in the source + + # Ugly padding required not to have border + # artefacts in the binary operations: + + shape_stack = list(annotation_stack.shape) + pad = 100 + shape_stack[2] = shape_stack[2] + pad * 2 + brain_mask = np.zeros(shape_stack, dtype=np.uint8) + + # Exclude eyes from brain mask: + brain_mask[:, :, pad:-pad][ + (annotation_stack > 0) & (annotation_stack != 808) + ] = 255 + + # Perform binary operations: + brain_mask = binary_dilation(brain_mask, iterations=50) + brain_mask = binary_erosion(brain_mask, iterations=50) + brain_mask = binary_fill_holes(brain_mask) + + # Remove padding: + brain_mask = brain_mask[:, :, pad:-pad] + + annotation_stack[(annotation_stack == 0) & (brain_mask > 0)] = BRAIN_ID + + # Download structures tree and meshes: + ###################################### + regions_url = f"{BASE_URL}/neurons/get_brain_regions" + + meshes_dir_path = working_dir / "meshes_temp_download" + meshes_dir_path.mkdir(exist_ok=True) + + # Download structures hierarchy: + structures = requests.get(regions_url).json()["brain_regions"] + + # Initiate dictionary with root info: + ROOT_ID = 1 # add this as not defined in the source + structures_dict = { + "name": "root", + "id": ROOT_ID, + "sub_regions": structures.copy(), + "structure_id_path": [ROOT_ID], + "acronym": "root", + "files": { + "file_3D": "/media/Neurons_database/Brain_and_regions" + "/Brains/Outline/Outline_new.txt" + }, + "color": "#ffffff", + } + + # Go through the regions hierarchy and create the structure path entry: + add_path_inplace(structures_dict) + + # Create empty list and collect all regions + # traversing the regions hierarchy: + structures_list = [] + meshes_dict = {} + collect_all_inplace( + structures_dict, structures_list, meshes_dir_path, meshes_dict + ) + + # Artificially add entry for brain region: + brain_struct_entry = { + "name": "brain", + "id": BRAIN_ID, + "structure_id_path": [ROOT_ID, BRAIN_ID], + "acronym": "brain", + "rgb_triplet": [255, 255, 255], + } + structures_list.append(brain_struct_entry) + + # Use recalculated meshes that are smoothed + # with Blender and uploaded in G-Node: + for sid in [ROOT_ID, BRAIN_ID]: + meshes_dict[sid] = extracted_dir / f"{sid}.stl" + + # Wrap up, compress, and remove file:0 + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(RES_UM,) * 3, + orientation=ORIENTATION, + root_id=1, + reference_stack=reference_stack, + annotation_stack=annotation_stack, + structures_list=structures_list, + meshes_dict=meshes_dict, + working_dir=working_dir, + hemispheres_stack=hemispheres_stack, + cleanup_files=False, + compress=True, + additional_references=additional_references, + atlas_packager=ATLAS_PACKAGER, + ) + + return output_filename + + +if __name__ == "__main__": + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" / "fish" + bg_root_dir.mkdir(exist_ok=True, parents=True) + + create_atlas(bg_root_dir, 1) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/osten_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/osten_mouse.py new file mode 100644 index 00000000..d5254623 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/osten_mouse.py @@ -0,0 +1,242 @@ +__version__ = "0" + +import json +import multiprocessing as mp +import tarfile +import time +from pathlib import Path + +import numpy as np +import pandas as pd +import tifffile +from allensdk.core.reference_space_cache import ReferenceSpaceCache +from rich.progress import track +from scipy.ndimage import zoom + +from brainglobe_atlasapi import utils +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + +PARALLEL = False # disable parallel mesh extraction for easier debugging + + +def create_atlas(working_dir, resolution): + ATLAS_NAME = "osten_mouse" + SPECIES = "Mus musculus" + ATLAS_LINK = "https://doi.org/10.1016/j.celrep.2014.12.014" + CITATION = "Kim et al. 2015, https://doi.org/10.1016/j.celrep.2014.12.014" + ORIENTATION = "asr" + ROOT_ID = 997 + ANNOTATIONS_RES_UM = 10 + ATLAS_FILE_URL = "https://gin.g-node.org/brainglobe/osten_atlas_materials/raw/master/osten_atlas_materials.tar.gz" + + # Temporary folder for download: + download_dir_path = working_dir / "downloads" + download_dir_path.mkdir(exist_ok=True) + atlas_files_dir = download_dir_path / "atlas_files" + + # Download atlas_file + utils.check_internet_connection() + + destination_path = download_dir_path / "atlas_download" + utils.retrieve_over_http(ATLAS_FILE_URL, destination_path) + + tar = tarfile.open(destination_path) + tar.extractall(path=atlas_files_dir) + tar.close() + + destination_path.unlink() + + structures_file = atlas_files_dir / "osten_atlas" / "structures.csv" + annotations_file = atlas_files_dir / "osten_atlas" / "annotation.tiff" + + # ---------------- # + # GET TEMPLATE # + # ---------------- # + + # Load (and possibly downsample) annotated volume: + scaling = ANNOTATIONS_RES_UM / resolution + + annotated_volume = tifffile.imread(annotations_file) + annotated_volume = zoom( + annotated_volume, (scaling, scaling, scaling), order=0, prefilter=False + ) + + # Download annotated and template volume: + ######################################### + spacecache = ReferenceSpaceCache( + manifest=download_dir_path / "manifest.json", + # downloaded files are stored relative to here + resolution=resolution, + reference_space_key="annotation/ccf_2017", + # use the latest version of the CCF + ) + + # Download + template_volume, _ = spacecache.get_template_volume() + print("Download completed...") + + # ------------------------ # + # STRUCTURES HIERARCHY # + # ------------------------ # + + # Parse region names & hierarchy + # ############################## + df = pd.read_csv(structures_file) + df = df.drop(columns=["parent_id"]) + + # split by "/" and convert list of strings to list of ints + df["structure_id_path"] = ( + df["structure_id_path"] + .str.split(pat="/") + .map(lambda x: [int(i) for i in x]) + ) + df["structure_id_path"] = df["structure_id_path"].map(lambda x: x[:-1]) + structures = df.to_dict("records") + structures[0000]["structure_id_path"] = [997] + for structure in structures: + structure.update({"rgb_triplet": [255, 255, 255]}) + # root doesn't have a parent + if structure["id"] != 997: + structure["structure_id_path"].append(structure["id"]) + + # save regions list json: + with open(download_dir_path / "structures.json", "w") as f: + json.dump(structures, f) + + # Create meshes: + print(f"Saving atlas data at {download_dir_path}") + meshes_dir_path = download_dir_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + tree = get_structures_tree(structures) + + rotated_annotations = np.rot90(annotated_volume, axes=(0, 2)) + + labels = np.unique(rotated_annotations).astype(np.int32) + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + + node.data = Region(is_label) + + # Mesh creation + closing_n_iters = 2 + decimate_fraction = 0.2 + smooth = False # smooth meshes after creation + start = time.time() + if PARALLEL: + pool = mp.Pool(mp.cpu_count() - 2) + + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + rotated_annotations, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + for node in tree.nodes.values() + ], + ) + except mp.pool.MaybeEncodingError: + # error with returning results from pool.map but we don't care + pass + else: + for node in track( + tree.nodes.values(), + total=tree.size(), + description="Creating meshes", + ): + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + rotated_annotations, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + ) + + print( + "Finished mesh extraction in: ", + round((time.time() - start) / 60, 2), + " minutes", + ) + + # Create meshes dict + meshes_dict = dict() + structures_with_mesh = [] + for s in structures: + # Check if a mesh was created + mesh_path = meshes_dir_path / f'{s["id"]}.obj' + if not mesh_path.exists(): + print(f"No mesh file exists for: {s}, ignoring it") + continue + else: + # Check that the mesh actually exists (i.e. not empty) + if mesh_path.stat().st_size < 512: + print(f"obj file for {s} is too small, ignoring it.") + continue + + structures_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structures_with_mesh)} " + "structures with mesh are kept" + ) + + # ----------- # + # WRAP UP # + # ----------- # + + # Wrap up, compress, and remove file: + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(resolution,) * 3, + orientation=ORIENTATION, + root_id=ROOT_ID, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structures_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + scale_meshes=True, + ) + + return output_filename + + +if __name__ == "__main__": + resolution = 100 # some resolution, in microns + + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" / "osten_mouse" + bg_root_dir.mkdir(exist_ok=True, parents=True) + create_atlas(bg_root_dir, resolution) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_lsfm_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_lsfm_mouse.py new file mode 100644 index 00000000..0037afd9 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_lsfm_mouse.py @@ -0,0 +1,357 @@ +__version__ = "0" + +import json +import multiprocessing as mp +import tarfile +import time +from pathlib import Path + +import numpy as np +import pandas as pd +import SimpleITK as sitk +from rich.progress import track + +# from allensdk.core.reference_space_cache import ReferenceSpaceCache +from brainglobe_atlasapi import utils +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + +PARALLEL = False # disable parallel mesh extraction for easier debugging + + +### Additional functions ##################################################### + + +############################################################################## +def get_id_from_acronym(df, acronym): + """ + Get Allen's brain atlas ID from brain region acronym(s) + + Call: + get_id_from_acronym(df, acronym) + + Args: + df (pandas dataframe): + atlas table file [see atlas.load_table()] + acronym (string or list of strings): brain region acronym(s) + + Returns: + ID (int or list of ints): + brain region ID(s) corresponding to input acronym(s) + """ + + # create as list if necessary + if not isinstance(acronym, list): + acronym = [acronym] + + if len(acronym) > 1: + ID_list = [] + for acro in acronym: + ID = df["id"][df["acronym"] == acro].item() + ID_list.append(ID) + return ID_list + else: + return df["id"][df["acronym"] == acronym[0]].item() + + # return df['id'][df['acronym'] == acronym].item() # OLD VERSION + + +def get_acronym_from_id(df, ID): + """ + Get Allen's brain atlas acronym from brain region ID(s) + + Call: + get_acronym_from_ID(df, acronym) + + Args: + df (pandas dataframe): atlas table dataframe [see atlas.load_table()] + ID (int or list of int): brain region ID(s) + + Returns: + acronym (string or list of strings): + brain region acronym(s) corresponding to input ID(s) + """ + + # create as list if necessary + if not isinstance(ID, list): + ID = [ID] + + if len(ID) > 1: + acronym_list = [] + for id in ID: + acronym = df["acronym"][df["id"] == id].item() + acronym_list.append(acronym) + return acronym_list + else: + return df["acronym"][df["id"] == ID[0]].item() + + +def tree_traverse_child2parent(df, child_id, ids): + parent = df["parent_id"][df["id"] == child_id].item() + + if not np.isnan(parent): + id = df["id"][df["id"] == parent].item() + ids.append(id) + tree_traverse_child2parent(df, parent, ids) + return ids + else: + return ids + + +def get_all_parents(df, key): + """ + Get all parent IDs/acronyms in Allen's brain atlas hierarchical structure' + + Call: + get_all_children(df, key) + + Args: + df (pandas dataframe) : atlas table dataframe [see atlas.load_table()] + key (int/string) : atlas region ID/acronym + + Returns: + parents (list) : brain region acronym corresponding to input ID + """ + + if isinstance(key, str): # if input is acronym convert to ID + list_parent_ids = tree_traverse_child2parent( + df, get_id_from_acronym(df, key), [] + ) + elif isinstance(key, int): + list_parent_ids = tree_traverse_child2parent(df, key, []) + + if isinstance(key, str): # if input is acronym convert IDs to acronyms + parents = [] + for id in list_parent_ids: + parents.append(get_acronym_from_id(df, id)) + elif isinstance(key, int): + parents = list_parent_ids.copy() + + return parents + + +############################################################################## + +############################################################################## +# %% + + +def create_atlas(working_dir, resolution): + ATLAS_NAME = "perens_lsfm_mouse" + SPECIES = "Mus musculus" + ATLAS_LINK = "https://github.com/Gubra-ApS/LSFM-mouse-brain-atlas" + CITATION = "Perens et al. 2021, https://doi.org/10.1007/s12021-020-09490-8" + ORIENTATION = "rai" + ROOT_ID = 997 + ATLAS_FILE_URL = "https://github.com/Gubra-ApS/LSFM-mouse-brain-atlas/archive/master.tar.gz" + + # Temporary folder for download: + download_dir_path = working_dir / "downloads" + download_dir_path.mkdir(exist_ok=True) + atlas_files_dir = download_dir_path / "atlas_files" + + ## Download atlas_file + utils.check_internet_connection() + + destination_path = download_dir_path / "atlas_download.tar.gz" + utils.retrieve_over_http(ATLAS_FILE_URL, destination_path) + + tar = tarfile.open(destination_path) + tar.extractall(path=atlas_files_dir) + tar.close() + + destination_path.unlink() + + structures_file = ( + atlas_files_dir + / "LSFM-mouse-brain-atlas-master" + / "LSFM_atlas_files" + / "ARA2_annotation_info_avail_regions.csv" + ) + annotations_file = ( + atlas_files_dir + / "LSFM-mouse-brain-atlas-master" + / "LSFM_atlas_files" + / "gubra_ano_olf.nii.gz" + ) + reference_file = ( + atlas_files_dir + / "LSFM-mouse-brain-atlas-master" + / "LSFM_atlas_files" + / "gubra_template_olf.nii.gz" + ) + + annotated_volume = sitk.GetArrayFromImage( + sitk.ReadImage(str(annotations_file)) + ) + template_volume = sitk.GetArrayFromImage( + sitk.ReadImage(str(reference_file)) + ) + annotated_volume = np.rot90(annotated_volume, axes=(0, 2)) + template_volume = np.rot90(template_volume, axes=(0, 2)) + + print("Download completed...") + + # ------------------------ # + # STRUCTURES HIERARCHY # + # ------------------------ # + + # Parse region names & hierarchy + # ############################## + df = pd.read_csv(structures_file) + + # Make region hierarchy and gather colors to one list + parents = [] + rgb = [] + for index, row in df.iterrows(): + temp_id = row["id"] + temp_parents = get_all_parents(df, temp_id) + parents.append(temp_parents[::-1]) + + temp_rgb = [row["red"], row["green"], row["blue"]] + rgb.append(temp_rgb) + + df = df.drop(columns=["parent_id", "red", "green", "blue"]) + df = df.assign(structure_id_path=parents) + df = df.assign(rgb_triplet=rgb) + df.loc[0, "structure_id_path"] = [997] + + structures = df.to_dict("records") + + for structure in structures: + # root doesn't have a parent + if structure["id"] != 997: + structure["structure_id_path"].append(structure["id"]) + + # save regions list json: + with open(download_dir_path / "structures.json", "w") as f: + json.dump(structures, f) + + # Create meshes: + print(f"Saving atlas data at {download_dir_path}") + meshes_dir_path = download_dir_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + tree = get_structures_tree(structures) + + labels = np.unique(annotated_volume).astype(np.int32) + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + + node.data = Region(is_label) + + # Mesh creation + closing_n_iters = 2 + start = time.time() + if PARALLEL: + pool = mp.Pool(mp.cpu_count() - 2) + + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + ROOT_ID, + closing_n_iters, + ) + for node in tree.nodes.values() + ], + ) + except mp.pool.MaybeEncodingError: + # error with returning results from pool.map but we don't care + pass + else: + for node in track( + tree.nodes.values(), + total=tree.size(), + description="Creating meshes", + ): + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + ROOT_ID, + closing_n_iters, + ) + ) + + print( + "Finished mesh extraction in: ", + round((time.time() - start) / 60, 2), + " minutes", + ) + + # Create meshes dict + meshes_dict = dict() + structures_with_mesh = [] + for s in structures: + # Check if a mesh was created + mesh_path = meshes_dir_path / f'{s["id"]}.obj' + if not mesh_path.exists(): + print(f"No mesh file exists for: {s}, ignoring it") + continue + else: + # Check that the mesh actually exists (i.e. not empty) + if mesh_path.stat().st_size < 512: + print(f"obj file for {s} is too small, ignoring it.") + continue + + structures_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structures_with_mesh)} " + "structures with mesh are kept" + ) + + # ----------- # + # WRAP UP # + # ----------- # + + # Wrap up, compress, and remove file: + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(resolution,) * 3, + orientation=ORIENTATION, + root_id=ROOT_ID, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structures_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + scale_meshes=True, + ) + + return output_filename + + +if __name__ == "__main__": + resolution = 20 # some resolution, in microns + + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" / "perens_lsfm_mouse" + bg_root_dir.mkdir(exist_ok=True, parents=True) + create_atlas(bg_root_dir, resolution) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/princeton_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/princeton_mouse.py new file mode 100644 index 00000000..35c7c59b --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/princeton_mouse.py @@ -0,0 +1,246 @@ +__version__ = "0" +__atlas__ = "princeton_mouse" + +import json +import multiprocessing as mp +import os.path +import time +from pathlib import Path + +import numpy as np +import pandas as pd +import tifffile +from rich.progress import track +from scipy.ndimage import zoom + +from brainglobe_atlasapi import utils +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + +PARALLEL = False + + +def create_atlas(working_dir, resolution): + # Specify information about the atlas: + ATLAS_NAME = __atlas__ + SPECIES = "Mus musculus" + ATLAS_LINK = "https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links/" + CITATION = ( + "Pisano et al 2021, https://doi.org/10.1016/j.celrep.2021.109721" + ) + ORIENTATION = "las" + ROOT_ID = 997 + ATLAS_RES = 20 + PACKAGER = "Sam Clothier. sam.clothier.18@ucl.ac.uk" + + # Download the atlas tissue and annotation TIFFs: + ###################################### + + reference_download_url = "https://brainmaps.princeton.edu/pma_tissue" + annotation_download_url = "https://brainmaps.princeton.edu/pma_annotations" + + # Temporary folder for nrrd files download: + download_dir_path = working_dir / "downloads" + download_dir_path.mkdir(exist_ok=True) + + utils.check_internet_connection() + reference_dest_path = download_dir_path / "reference_download.tif" + annotation_dest_path = download_dir_path / "annotation_download.tif" + + if not os.path.isfile(reference_dest_path): + print("Downloading tissue volume...") + utils.retrieve_over_http(reference_download_url, reference_dest_path) + if not os.path.isfile(annotation_dest_path): + print("Downloading annotation stack...") + utils.retrieve_over_http(annotation_download_url, annotation_dest_path) + print("Download complete.") + + template_volume = tifffile.imread(reference_dest_path) + template_volume = np.array(template_volume) + annotated_volume = tifffile.imread(annotation_dest_path) + annotated_volume = np.array(annotated_volume) + + scaling = ATLAS_RES / resolution + annotated_volume = zoom( + annotated_volume, (scaling, scaling, scaling), order=0, prefilter=False + ) + + # Download structures tree and define regions: + ###################################### + + structures_download_url = "https://brainmaps.princeton.edu/pma_id_table" + structures_dest_path = download_dir_path / "structures_download.csv" + if not os.path.isfile(structures_dest_path): + utils.retrieve_over_http(structures_download_url, structures_dest_path) + + structures = pd.read_csv(structures_dest_path) + structures = structures.drop( + columns=["parent_name", "parent_acronym", "voxels_in_structure"] + ) + + # create structure_id_path column + def get_inheritance_list_from(id_val): + inheritance_list = [id_val] + + def add_parent_id(child_id): + if child_id != 997: # don't look for the parent of the root area + parent_id = structures.loc[ + structures["id"] == child_id, "parent_structure_id" + ].values[0] + inheritance_list.insert(0, int(parent_id)) + add_parent_id(parent_id) + + add_parent_id(id_val) + return inheritance_list + + structures["structure_id_path"] = structures["id"].map( + lambda x: get_inheritance_list_from(x) + ) + + # create rgb_triplet column + structures["rgb_triplet"] = "[255, 255, 255]" + structures["rgb_triplet"] = structures["rgb_triplet"].map( + lambda x: json.loads(x) + ) + + # order dataframe and convert to list of dictionaries + # specifying parameters for each area + structures = structures[ + ["acronym", "id", "name", "structure_id_path", "rgb_triplet"] + ] + structs_dict = structures.to_dict(orient="records") + print(structs_dict) + + # save regions list json: + with open(download_dir_path / "structures.json", "w") as f: + json.dump(structs_dict, f) + + # Create region meshes: + ###################################### + + print(f"Saving atlas data at {download_dir_path}") + meshes_dir_path = download_dir_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + tree = get_structures_tree(structs_dict) + rotated_annotations = np.rot90(annotated_volume, axes=(0, 2)) + + labels = np.unique(rotated_annotations).astype(np.int32) + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + node.data = Region(is_label) + + # Mesh creation + closing_n_iters = 2 + decimate_fraction = 0.2 + smooth = False # smooth meshes after creation + start = time.time() + if PARALLEL: + pool = mp.Pool(mp.cpu_count() - 2) + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + rotated_annotations, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + for node in tree.nodes.values() + ], + ) + except mp.pool.MaybeEncodingError: + # Error with returning results from pool.map, but we don't care + pass + else: + for node in track( + tree.nodes.values(), + total=tree.size(), + description="Creating meshes", + ): + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + rotated_annotations, + ROOT_ID, + closing_n_iters, + decimate_fraction, + smooth, + ) + ) + print( + "Finished mesh extraction in: ", + round((time.time() - start) / 60, 2), + " minutes", + ) + + # Create meshes dict + meshes_dict = dict() + structs_with_mesh = [] + for s in structs_dict: + # Check if a mesh was created + mesh_path = meshes_dir_path / f'{s["id"]}.obj' + if not mesh_path.exists(): + print(f"No mesh file exists for: {s}, ignoring it") + continue + else: + # Check that the mesh actually exists (i.e. not empty) + if mesh_path.stat().st_size < 512: + print(f"obj file for {s} is too small, ignoring it.") + continue + + structs_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structs_with_mesh)} structures with mesh are kept" + ) + + # Wrap up, compress, and remove file: + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(resolution,) * 3, + orientation=ORIENTATION, + root_id=997, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structs_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + atlas_packager=PACKAGER, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + ) + + return output_filename + + +if __name__ == "__main__": + RES_UM = 20 + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" / __atlas__ + bg_root_dir.mkdir(exist_ok=True, parents=True) + + create_atlas(bg_root_dir, RES_UM) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/template_script.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/template_script.py new file mode 100644 index 00000000..9b9229a7 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/template_script.py @@ -0,0 +1,75 @@ +"""Template script for the generation of an atlas. Note that the script +has to be renamed to match the name of the atlas (e.g. allen_mouse.py) +""" + +__version__ = "0" # will be used to set minor version of the atlas + +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data + + +def create_atlas(working_dir, resolution): + """Function to generate source data for an atlas. + + Parameters + ---------- + working_dir : Path object + Path where atlas will be created. + resolution : + Resolution of the atlas, in um. + + Returns + ------- + Path object + Path to the final compressed atlas file. + + """ + + ATLAS_NAME = "" + SPECIES = "" + ATLAS_LINK = "" + CITATION = "" + ORIENTATION = "" + + # do stuff to create the atlas + template_volume = None # volume with reference + annotated_volume = None # volume with structures annotations + structures_list = None # list of valid structure dictionaries + meshes_dict = None # dictionary of files with region meshes + root_id = None # id of the root structure + + # Put here additional reference stacks + # (different genotypes, filtered volumes, etc) + additional_references = dict() + + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=(resolution,) * 3, # if isotropic - highly recommended + orientation=ORIENTATION, + root_id=root_id, + reference_stack=template_volume, + annotation_stack=annotated_volume, + structures_list=structures_list, + meshes_dict=meshes_dict, + working_dir=working_dir, + additional_references=additional_references, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + ) + + return output_filename + + +# To test stuff locally: +if __name__ == "__main__": + resolution = 100 # some resolution, in microns + + # Generated atlas path: + bg_root_dir = "/path/to/some/dir" + bg_root_dir.mkdir(exist_ok=True) + + create_atlas(bg_root_dir, resolution) diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/whs_sd_rat.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/whs_sd_rat.py new file mode 100644 index 00000000..dcf8a3e3 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/whs_sd_rat.py @@ -0,0 +1,318 @@ +__version__ = "0" + +import json +import multiprocessing as mp +import time +import zipfile +from pathlib import Path + +import imio +import numpy as np +import xmltodict +from rich.progress import track + +from brainglobe_atlasapi import utils +from brainglobe_atlasapi.atlas_generation.mesh_utils import ( + Region, + create_region_mesh, +) +from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + +PARALLEL = True + + +def download_atlas_files(download_dir_path, atlas_file_url, ATLAS_NAME): + atlas_files_dir = download_dir_path / ATLAS_NAME + + if atlas_files_dir.exists(): + return atlas_files_dir + + utils.check_internet_connection() + + download_name = ATLAS_NAME + "_atlas.zip" + destination_path = download_dir_path / download_name + utils.retrieve_over_http(atlas_file_url, destination_path) + + with zipfile.ZipFile(destination_path, "r") as zip_ref: + zip_ref.extractall(atlas_files_dir) + + return atlas_files_dir + + +def parse_structures_xml(root, path=None, structures=None): + structures = structures or [] + path = path or [] + + rgb_triplet = tuple(int(root["@color"][i : i + 2], 16) for i in (1, 3, 5)) + id = int(root["@id"]) + struct = { + "name": root["@name"], + "acronym": root["@abbreviation"], + "id": int(root["@id"]), + "structure_id_path": path + [id], + "rgb_triplet": rgb_triplet, + } + structures.append(struct) + + if "label" in root: + if isinstance(root["label"], list): + for label in root["label"]: + parse_structures_xml( + label, path=path + [id], structures=structures + ) + else: + parse_structures_xml( + root["label"], path=path + [id], structures=structures + ) + + return structures + + +def parse_structures(structures_file: Path): + root = xmltodict.parse(structures_file.read_text())["milf"]["structure"] + root["@abbreviation"] = "root" + root["@color"] = "#ffffff" + root["@id"] = "10000" + root["@name"] = "Root" + + structures = parse_structures_xml(root) + return structures + + +def create_structure_hierarchy(structures, df, root_id): + for structure in structures: + if structure["id"] != root_id: + parent_id = structure["parent_structure_id"] + while True: + structure["structure_id_path"] = [parent_id] + structure[ + "structure_id_path" + ] + if parent_id != root_id: + parent_id = int( + df[df["id"] == parent_id]["parent_structure_id"] + ) + else: + break + else: + structure["name"] = "root" + structure["acronym"] = "root" + + del structure["parent_structure_id"] + + return structures + + +def create_meshes(download_dir_path, tree, annotated_volume, labels, root_id): + meshes_dir_path = download_dir_path / "meshes" + meshes_dir_path.mkdir(exist_ok=True) + + for key, node in tree.nodes.items(): + if key in labels: + is_label = True + else: + is_label = False + node.data = Region(is_label) + + # Mesh creation + closing_n_iters = 2 + decimate_fraction = 0.2 + smooth = False # smooth meshes after creation + start = time.time() + if PARALLEL: + pool = mp.Pool(min(mp.cpu_count() - 2, 16)) + + try: + pool.map( + create_region_mesh, + [ + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + root_id, + closing_n_iters, + decimate_fraction, + smooth, + ) + for node in tree.nodes.values() + ], + ) + except mp.pool.MaybeEncodingError: + pass + else: + for node in track( + tree.nodes.values(), + total=tree.size(), + description="Creating meshes", + ): + create_region_mesh( + ( + meshes_dir_path, + node, + tree, + labels, + annotated_volume, + root_id, + closing_n_iters, + decimate_fraction, + smooth, + ) + ) + + print( + "Finished mesh extraction in: ", + round((time.time() - start) / 60, 2), + " minutes", + ) + return meshes_dir_path + + +def create_mesh_dict(structures, meshes_dir_path): + meshes_dict = dict() + structures_with_mesh = [] + for s in structures: + # Check if a mesh was created + mesh_path = meshes_dir_path / f'{s["id"]}.obj' + if not mesh_path.exists(): + print(f"No mesh file exists for: {s}, ignoring it") + continue + else: + # Check that the mesh actually exists (i.e. not empty) + if mesh_path.stat().st_size < 512: + print(f"obj file for {s} is too small, ignoring it.") + continue + + structures_with_mesh.append(s) + meshes_dict[s["id"]] = mesh_path + + print( + f"In the end, {len(structures_with_mesh)} " + "structures with mesh are kept" + ) + return meshes_dict, structures_with_mesh + + +def create_atlas(working_dir): + ATLAS_NAME = "whs_sd_rat" + SPECIES = "Rattus norvegicus" + ATLAS_LINK = "https://www.nitrc.org/projects/whs-sd-atlas" + CITATION = ( + "Papp et al 2014, https://doi.org/10.1016/j.neuroimage.2014.04.001" + ) + ORIENTATION = "lpi" + RESOLUTION = (39, 39, 39) + ROOT_ID = 10000 + ATLAS_FILE_URL = "https://www.nitrc.org/frs/download.php/12263/MBAT_WHS_SD_rat_atlas_v4_pack.zip" + ATLAS_PACKAGER = ( + "Ben Kantor, Tel Aviv University, Israel, benkantor@mail.tau.ac.il" + ) + + assert len(ORIENTATION) == 3, ( + "Orientation is not 3 characters, Got" + ORIENTATION + ) + assert len(RESOLUTION) == 3, "Resolution is not correct, Got " + RESOLUTION + assert ( + ATLAS_FILE_URL + ), "No download link provided for atlas in ATLAS_FILE_URL" + + # Generated atlas path: + working_dir = working_dir / ATLAS_NAME + working_dir.mkdir(exist_ok=True, parents=True) + + download_dir_path = working_dir / "downloads" + download_dir_path.mkdir(exist_ok=True) + + # Download atlas files from link provided + print("Downloading atlas from link: ", ATLAS_FILE_URL) + atlas_files_dir = download_atlas_files( + download_dir_path, ATLAS_FILE_URL, ATLAS_NAME + ) + atlas_files_dir = atlas_files_dir / "MBAT_WHS_SD_rat_atlas_v4_pack/Data" + + # Parse structure metadata + structures = parse_structures( + atlas_files_dir / "WHS_SD_rat_atlas_v4_labels.ilf" + ) + + # Load files + annotation_stack = imio.load_any( + atlas_files_dir / "WHS_SD_rat_atlas_v4.nii.gz", as_numpy=True + ).astype(np.int64) + reference_stack = imio.load_any( + atlas_files_dir / "WHS_SD_rat_T2star_v1.01.nii.gz", as_numpy=True + ) + + # Remove structure with missing annotations + tree = get_structures_tree(structures) + labels = set(np.unique(annotation_stack).astype(np.int32)) + existing_structures = [] + for structure in structures: + stree = tree.subtree(structure["id"]) + ids = set(stree.nodes.keys()) + matched_labels = ids & labels + if matched_labels: + existing_structures.append(structure) + else: + node = tree.nodes[structure["id"]] + print( + f"{node.tag} not found in annotation volume, " + "removing from list of structures..." + ) + structures = existing_structures + tree = get_structures_tree(structures) + + # Clean junk from reference file + reference_stack *= annotation_stack > 0 + + # Create hemispheres stack + hemispheres_stack = np.full(reference_stack.shape, 2, dtype=np.uint8) + hemispheres_stack[:244] = 1 + + # save regions list json: + with open(download_dir_path / "structures.json", "w") as f: + json.dump(structures, f) + + # Create meshes: + print(f"Saving atlas data at {download_dir_path}") + meshes_dir_path = create_meshes( + download_dir_path, tree, annotation_stack, labels, ROOT_ID + ) + + meshes_dict, structures_with_mesh = create_mesh_dict( + structures, meshes_dir_path + ) + + # Wrap up, compress, and remove file: + print("Finalising atlas") + output_filename = wrapup_atlas_from_data( + atlas_name=ATLAS_NAME, + atlas_minor_version=__version__, + citation=CITATION, + atlas_link=ATLAS_LINK, + species=SPECIES, + resolution=RESOLUTION, + orientation=ORIENTATION, + root_id=ROOT_ID, + reference_stack=reference_stack, + annotation_stack=annotation_stack, + structures_list=structures_with_mesh, + meshes_dict=meshes_dict, + working_dir=working_dir, + atlas_packager=ATLAS_PACKAGER, + hemispheres_stack=hemispheres_stack, + cleanup_files=False, + compress=True, + scale_meshes=True, + ) + + return output_filename + + +if __name__ == "__main__": + # Generated atlas path: + bg_root_dir = Path.home() / "brainglobe_workingdir" + bg_root_dir.mkdir(exist_ok=True, parents=True) + create_atlas(bg_root_dir) diff --git a/brainglobe_atlasapi/atlas_generation/main_script.py b/brainglobe_atlasapi/atlas_generation/main_script.py new file mode 100644 index 00000000..b76d47c8 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/main_script.py @@ -0,0 +1,138 @@ +import configparser +import errno +import os +import shutil +import stat +from importlib import import_module +from pathlib import Path + +from git import Repo +from git.exc import GitCommandError + +import brainglobe_atlasapi.atlas_generation +from brainglobe_atlasapi.utils import ( + atlas_name_from_repr, + atlas_repr_from_name, +) + +# Main dictionary specifying which atlases to generate +# and with which resolutions: +GENERATION_DICT = dict( + mpin_zfish=[1], + allen_mouse=[10, 25, 50, 100], + kim_mouse=[10, 25, 50, 100], + osten_mouse=[10, 25, 50, 100], + example_mouse=[100], +) + + +CWD = Path.home() / "bg_auto" + + +def handleRemoveReadonly(func, path, exc): + excvalue = exc[1] + if func in (os.rmdir, os.remove) and excvalue.errno == errno.EACCES: + os.chmod(path, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO) # 0777 + func(path) + else: + raise + + +def delete_folder(path): + shutil.rmtree(path, ignore_errors=False, onerror=handleRemoveReadonly) + + +CWD.mkdir(exist_ok=True) + + +if __name__ == "__main__": + repo_path = CWD / "atlas_repo" + if repo_path.exists(): + repo = Repo(repo_path) + repo.git.pull() + else: + repo_path.mkdir(exist_ok=True) + + print("Cloning atlases repo...") + repo = Repo.clone_from( + "https://gin.g-node.org/brainglobe/atlases", repo_path + ) + # us = input("GIN-GNode user: ") + # pw = input("GIN-GNode password: ") + + # Read last versions from conf file: + conf = configparser.ConfigParser() + conf.read(repo_path / "last_versions.conf") + + # Find all atlases representation given the names in the conf: + atlases_repr = dict() + for k in conf["atlases"].keys(): + repr = atlas_repr_from_name(k) + # Read versions from conf: + repr["major_vers"], repr["minor_vers"] = conf["atlases"][k].split(".") + # Add as entries in a dict: + atlases_repr[repr.pop("name")] = repr + + # Major version is given by version of the atlas_gen module: + brainglobe_atlasapi.atlas_generation_version = ( + brainglobe_atlasapi.atlas_generation.__version__ + ) + + # Path to the scripts to generate the atlases: + atlas_gen_path = Path(__file__).parent + scripts_path = atlas_gen_path / "atlas_scripts" + + # Loop over the entries from the GENERATION_DICT configuration dict + commit_log = "Updated: " + for name, resolutions in GENERATION_DICT.items(): + status = atlases_repr[name] + module = import_module( + f"brainglobe_atlasapi.atlas_generation.atlas_scripts.{name}" + ) + script_version = module.__version__ + + if brainglobe_atlasapi.atlas_generation_version > status[ + "major_vers" + ] or ( + brainglobe_atlasapi.atlas_generation_version + == status["major_vers"] + and script_version > status["minor_vers"] + ): + # Loop over all resolutions: + for resolution in resolutions: + print(f"Generating {name}, {resolution} um...") + + # Make working directory for atlas generation: + temp_dir = CWD / f"tempdir_{name}_{resolution}" + temp_dir.mkdir(exist_ok=True) + + # Create and compress atlas: + output_filename = module.create_atlas(temp_dir, resolution) + + # Move atlas to repo: + shutil.move(str(output_filename), repo_path) + # delete_folder(temp_dir) + + # Update config file with new version: + k = atlas_name_from_repr(name, resolution) + conf["brainglobe_atlasapi.atlas_generation"] = str( + f"{brainglobe_atlasapi.atlas_generation_version}.{script_version}" + ) + with open(repo_path / "last_versions.conf", "w") as f: + conf.write(f) + + # Update log for commit message: + commit_log += f"{output_filename.stem}, " + + # Commit and push: + try: + repo.git.add(".") + repo.git.commit("-m", commit_log) + except GitCommandError: + pass + + repo.git.push() + + # Clear folder: + repo.close() + # delete_folder(repo_path) diff --git a/brainglobe_atlasapi/atlas_generation/mesh_utils.py b/brainglobe_atlasapi/atlas_generation/mesh_utils.py new file mode 100644 index 00000000..3f5fc3dd --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/mesh_utils.py @@ -0,0 +1,311 @@ +try: + from vedo import Mesh, Volume, load, show, write + from vedo.applications import Browser, Slicer3DPlotter +except ModuleNotFoundError: + raise ModuleNotFoundError( + "Mesh generation with these utils requires vedo\n" + + ' please install with "pip install vedo -U"' + ) + +try: + import mcubes +except ModuleNotFoundError: + raise ModuleNotFoundError( + "Mesh generation with these utils requires PyMCubes\n" + + ' please install with "pip install PyMCubes -U"' + ) + +from pathlib import Path + +import numpy as np +import scipy +from loguru import logger + +from brainglobe_atlasapi.atlas_generation.volume_utils import ( + create_masked_array, +) + +# ----------------- # +# MESH CREATION # +# ----------------- # + + +def region_mask_from_annotation( + structure_id, + annotation, + structures_list, +): + """Generate mask for a structure from an annotation file + and a list of structures. + + Parameters + ---------- + structure_id : int + id of the structure + annotation : np.array + annotation stack for the atlas + structures_list : list + list of structure dictionaries + + Returns + ------- + + """ + + mask_stack = np.zeros(annotation.shape, np.uint8) + + for curr_structure in structures_list: + if structure_id in curr_structure["structure_id_path"]: + mask_stack[annotation == curr_structure["id"]] = 1 + + return mask_stack + + +def extract_mesh_from_mask( + volume, + obj_filepath=None, + threshold=0.5, + smooth: bool = False, + mcubes_smooth=False, + closing_n_iters=8, + decimate_fraction: float = 0.6, # keep 60% of original fertices + use_marching_cubes=False, + extract_largest=False, +): + """ + Returns a vedo mesh actor with just the outer surface of a + binary mask volume. It's faster though less accurate than + extract_mesh_from_mask + + + Parameters + ---------- + obj_filepath: str or Path object + path to where the .obj mesh file will be saved + volume: 3d np.ndarray + threshold: float + min value to threshold the volume for isosurface extraction + smooth: bool + if True the surface mesh is smoothed + use_marching_cubes: bool: + if true PyMCubes is used to extract the volume's surface + it's slower and less accurate than vedo though. + mcubes_smooth: bool, + if True mcubes.smooth is used before applying marching cubes + closing_n_iters: int + number of iterations of closing morphological operation. + set to None to avoid applying morphological operations + decimate_fraction: float in range [0, 1]. + What fraction of the original number of vertices is to be kept. + EG .5 means that 50% of the vertices are kept, + the others are removed. + tol: float + parameter for decimation, with larger values corresponding + to more aggressive decimation. + EG 0.02 -> points that are closer than 2% of the size of the mesh's + bounding box are identified and removed (only one is kept). + extract_largest: bool + If True only the largest region are extracted. It can cause issues for + bilateral regions as only one will remain + + """ + # check savepath argument + if obj_filepath is not None: + if isinstance(obj_filepath, str): + obj_filepath = Path(obj_filepath) + + if not obj_filepath.parents[0].exists(): + raise FileExistsError( + "The folder where the .obj file is to be saved doesn't exist" + + f"\n {str(obj_filepath)}" + ) + + # Check volume argument + if np.min(volume) > 0 or np.max(volume) < 1: + raise ValueError( + "Argument volume should be a binary mask with only " + "0s and 1s when passing a np.ndarray" + ) + + # Apply morphological transformations + if closing_n_iters is not None: + volume = scipy.ndimage.morphology.binary_fill_holes(volume).astype(int) + volume = scipy.ndimage.morphology.binary_closing( + volume, iterations=closing_n_iters + ).astype(int) + + if not use_marching_cubes: + # Use faster algorithm + volume = Volume(volume) + mesh = volume.clone().isosurface(value=threshold).cap() + else: + print( + "The marching cubes algorithm might be rotated " + "compared to your volume data" + ) + # Apply marching cubes and save to .obj + if mcubes_smooth: + smooth = mcubes.smooth(volume) + vertices, triangles = mcubes.marching_cubes(smooth, 0) + else: + vertices, triangles = mcubes.marching_cubes(volume, 0.5) + + # create mesh + mesh = Mesh((vertices, triangles)) + + # Cleanup and save + if extract_largest: + mesh = mesh.extractLargestRegion() + + # decimate + mesh.decimate(decimate_fraction, method="pro") + + if smooth: + mesh.smoothLaplacian() + + if obj_filepath is not None: + write(mesh, str(obj_filepath)) + + return mesh + + +def create_region_mesh(args): + """ + Automates the creation of a region's mesh. Given a volume of annotations + and a structures tree, it takes the volume's region corresponding to the + region of interest and all of it's children's labels and creates a mesh. + It takes a tuple of arguments to facilitaed parallel processing with + multiprocessing.pool.map + + Note, by default it avoids overwriting a structure's mesh if the + .obj file exists already. + + Parameters + ---------- + meshes_dir_path: pathlib Path object with folder where meshes are saved + tree: treelib.Tree with hierarchical structures information + node: tree's node corresponding to the region who's mesh is being created + labels: list of unique label annotations in annotated volume, + (list(np.unique(annotated_volume))) + annotated_volume: 3d numpy array with annotaed volume + ROOT_ID: int, + id of root structure (mesh creation is a bit more refined for that) + """ + # Split arguments + logger.debug(f"Creating mesh for region {args[1].identifier}") + meshes_dir_path = args[0] + node = args[1] + tree = args[2] + labels = args[3] + annotated_volume = args[4] + ROOT_ID = args[5] + closing_n_iters = args[6] + decimate_fraction = args[7] + smooth = args[8] + + # Avoid overwriting existing mesh + savepath = meshes_dir_path / f"{node.identifier}.obj" + # if savepath.exists(): + # logger.debug(f"Mesh file save path exists already, skipping.") + # return + + # Get lables for region and it's children + stree = tree.subtree(node.identifier) + ids = list(stree.nodes.keys()) + + # Keep only labels that are in the annotation volume + matched_labels = [i for i in ids if i in labels] + + if ( + not matched_labels + ): # it fails if the region and all of it's children are not in annotation + print(f"No labels found for {node.tag}") + return + else: + # Create mask and extract mesh + mask = create_masked_array(annotated_volume, ids) + + if not np.max(mask): + print(f"Empty mask for {node.tag}") + else: + if node.identifier == ROOT_ID: + extract_mesh_from_mask( + mask, + obj_filepath=savepath, + smooth=smooth, + decimate_fraction=decimate_fraction, + ) + else: + extract_mesh_from_mask( + mask, + obj_filepath=savepath, + smooth=smooth, + closing_n_iters=closing_n_iters, + decimate_fraction=decimate_fraction, + ) + + +class Region(object): + """ + Class used to add metadata to treelib.Tree during atlas creation. + Using this means that you can then filter tree nodes depending on + whether or not they have a mesh/label + """ + + def __init__(self, has_label): + self.has_label = has_label + + +# ------------------- # +# MESH INSPECTION # +# ------------------- # +def compare_mesh_and_volume(mesh, volume): + """ + Creates and interactive vedo + visualisation to look at a reference volume + and a mesh at the same time. Can be used to + assess the quality of the mesh extraction. + + Parameters: + ----------- + + mesh: vedo Mesh + volume: np.array or vtkvedoplotter Volume + """ + if isinstance(volume, np.ndarray): + volume = Volume(volume) + + vp = Slicer3DPlotter(volume, bg2="white", showHisto=False) + vp.add(mesh.alpha(0.5)) + vp.show() + + +def inspect_meshes_folder(folder): + """ + Used to create an interactive vedo visualisation + to scroll through all .obj files saved in a folder + + Parameters + ---------- + folder: str or Path object + path to folder with .obj files + """ + + if isinstance(folder, str): + folder = Path(folder) + + if not folder.exists(): + raise FileNotFoundError("The folder passed doesnt exist") + + mesh_files = folder.glob("*.obj") + + Browser([load(str(mf)).c("w").lw(0.25).lc("k") for mf in mesh_files]) + logger.debug("visualization ready") + show() + + +if __name__ == "__main__": + folder = ( + r"C:\Users\Federico\.brainglobe\temp\allen_human_500um_v0.1\meshes" + ) + inspect_meshes_folder(folder) diff --git a/brainglobe_atlasapi/atlas_generation/metadata_utils.py b/brainglobe_atlasapi/atlas_generation/metadata_utils.py new file mode 100644 index 00000000..66b84487 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/metadata_utils.py @@ -0,0 +1,146 @@ +""" + Automatic creation of + . structures.csv + . README.txt +""" + +import json +import re +from datetime import datetime + +import requests +from requests.exceptions import ConnectionError, InvalidURL, MissingSchema + +from brainglobe_atlasapi import descriptors +from brainglobe_atlasapi.atlas_generation.structure_json_to_csv import ( + convert_structure_json_to_csv, +) +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + + +def generate_metadata_dict( + name, + citation, + atlas_link, + species, + symmetric, + resolution, + orientation, + version, + shape, + transformation_mat, + additional_references, + atlas_packager, +): + # Name should be author_species + assert len(name.split("_")) >= 2 + + # Control version formatting: + assert re.match("[0-9]+\\.[0-9]+", version) + + # We ask for DOI and correct link only if atlas is published: + if citation != "unpublished": + assert "doi" in citation + + # Test url: + try: + _ = requests.get(atlas_link) + except (MissingSchema, InvalidURL, ConnectionError): + raise InvalidURL( + "Ensure that the url is valid and formatted correctly!" + ) + + # Enforce correct format for symmetric, resolution and shape: + assert isinstance(symmetric, bool) + assert len(resolution) == 3 + assert len(shape) == 3 + + resolution = tuple([float(v) for v in resolution]) + shape = tuple(int(v) for v in shape) + + assert isinstance(additional_references, list) + + return dict( + name=name, + citation=citation, + atlas_link=atlas_link, + species=species, + symmetric=symmetric, + resolution=resolution, + orientation=orientation, + version=version, + shape=shape, + trasform_to_bg=tuple([tuple(m) for m in transformation_mat]), + additional_references=additional_references, + atlas_packager=atlas_packager, + ) + + +def create_readme(uncompr_atlas_path, metadata_dict, structures): + readmepath = str(uncompr_atlas_path / "README.txt") + + # First write the structure tree + structuresTree = get_structures_tree(structures) + structuresTree.save2file(readmepath) + + # The prepend the header and info + with open(readmepath, "r") as original: + tree = original.read() + + with open(readmepath, "w") as out: + out.write("-- BRAINGLOBE ATLAS --\n") + + now = datetime.now() + out.write("Generated on: " + now.strftime("%d/%m/%Y") + "\n\n") + + out.write("------------------------------\n\n\n") + + for key, value in metadata_dict.items(): + out.write(f" {key}: {value}\n") + + out.write("\n\n\n") + out.write("------------------------------\n\n\n") + out.write("\n\n\n") + + out.write("-- BRAIN STRUCTURES TREE --\n") + + out.write(tree) + + +def create_structures_csv(uncompr_atlas_path, root): + """ + Converts an atlas structure json dictionary to csv. For cellfinder + compatibility and ease of browsing. + + Parameters + ---------- + uncompr_atlas_path : str or Path object + path to uncompressed atlas folder + """ + convert_structure_json_to_csv( + uncompr_atlas_path / "structures.json", root=root + ) + + +def create_metadata_files( + dest_dir, metadata_dict, structures, root_id, additional_metadata={} +): + """ + Automatic creation of + . structures.csv + . README.txt + from an atlas files. All Files are saved in the uncompressed atlas folder + awaiting compression and upload to GIN. + + :param uncompr_atlas_path: path to uncompressed atlas folder + :param metadata_dict: dict with atlas metadata + :param structures: list of dictionaries with structures hierarchical info + :param additional_metadata: Dict to add to atlas metadata + """ + # write metadata dict: + with open(dest_dir / descriptors.METADATA_FILENAME, "w") as f: + # only save additional metadata to json, don't include in readme + json.dump({**metadata_dict, **additional_metadata}, f) + + create_structures_csv(dest_dir, root_id) + create_readme(dest_dir, metadata_dict, structures) diff --git a/brainglobe_atlasapi/atlas_generation/stacks.py b/brainglobe_atlasapi/atlas_generation/stacks.py new file mode 100644 index 00000000..72bc630b --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/stacks.py @@ -0,0 +1,63 @@ +import tifffile + +from brainglobe_atlasapi import descriptors + + +def write_stack(stack, filename): + """ + Parameters + ---------- + stack + filename + + """ + tifffile.imsave(str(filename), stack) + + +def save_reference(stack, output_dir): + """ + Parameters + ---------- + stack + output_dir + """ + if stack.dtype != descriptors.REFERENCE_DTYPE: + stack = stack.astype(descriptors.REFERENCE_DTYPE) + write_stack(stack, output_dir / descriptors.REFERENCE_FILENAME) + + +def save_secondary_reference(stack, name, output_dir): + """ + Parameters + ---------- + stack + name + output_dir + """ + if stack.dtype != descriptors.REFERENCE_DTYPE: + stack = stack.astype(descriptors.REFERENCE_DTYPE) + write_stack(stack, output_dir / f"{name}.tiff") + + +def save_annotation(stack, output_dir): + """ + Parameters + ---------- + stack + output_dir + """ + if stack.dtype != descriptors.ANNOTATION_DTYPE: + stack = stack.astype(descriptors.ANNOTATION_DTYPE) + write_stack(stack, output_dir / descriptors.ANNOTATION_FILENAME) + + +def save_hemispheres(stack, output_dir): + """ + Parameters + ---------- + stack + output_dir + """ + if stack.dtype != descriptors.HEMISPHERES_DTYPE: + stack = stack.astype(descriptors.HEMISPHERES_DTYPE) + write_stack(stack, output_dir / descriptors.HEMISPHERES_FILENAME) diff --git a/brainglobe_atlasapi/atlas_generation/structure_json_to_csv.py b/brainglobe_atlasapi/atlas_generation/structure_json_to_csv.py new file mode 100644 index 00000000..3021f3fd --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/structure_json_to_csv.py @@ -0,0 +1,84 @@ +from pathlib import Path + +import pandas as pd + + +def structure_id_path_to_string(structure_id_path): + """ + Given a path (as a list of structure ids) to a specific structure, + return as a string of "/" separated structure ids + Parameters + ---------- + structure_id_path : list + list of ints defining the path to a region (which is the last element) + + Returns + ------- + str: + "/" separated string of structure ids + + """ + + path_string = "/" + for element in structure_id_path: + path_string = path_string + str(element) + "/" + return path_string + + +def get_parent_id(structure_id_path, root=997): + """ + Given a path (as a list of structure ids) to a specific structure, + return the id of the parent structure + + Parameters + ---------- + structure_id_path : list + list of ints defining the path to a region (which is the last element) + + root : int (optional) + Value for the root (whole brain) structure that has no parent. + + Returns + ------- + int or None : + id of the parent structure (or None if no parent) + """ + + if structure_id_path == [root]: + return None + else: + return int(structure_id_path[-2]) + + +def convert_structure_json_to_csv( + structure_json_path, destination_path=None, root=997 +): + """ + Converts an atlas structure json dictionary to csv. For cellfinder + compatibility and ease of browsing. + + Parameters + ---------- + structure_json_path : str or Path object + path to the json file + destination_path : str or Path object (optional) + Where to save the resulting csv file. Defaults to the same directory + as the json file. + """ + + structure_json_path = Path(structure_json_path) + + df = pd.read_json(structure_json_path) + df = df.drop(columns=["rgb_triplet"]) + df["parent_structure_id"] = df["structure_id_path"].apply( + get_parent_id, root=root + ) + df["structure_id_path"] = df["structure_id_path"].apply( + structure_id_path_to_string + ) + df = df.sort_values("name") + + if destination_path is None: + destination_path = structure_json_path.with_suffix(".csv") + + df.to_csv(destination_path, index=False) diff --git a/brainglobe_atlasapi/atlas_generation/structures.py b/brainglobe_atlasapi/atlas_generation/structures.py new file mode 100644 index 00000000..1abb2b89 --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/structures.py @@ -0,0 +1,116 @@ +from brainglobe_atlasapi.descriptors import STRUCTURE_TEMPLATE as STEMPLATE +from brainglobe_atlasapi.structure_tree_util import get_structures_tree + + +def check_struct_consistency(structures): + """Ensures internal consistency of the structures list + Parameters + ---------- + structures + + Returns + ------- + + """ + assert isinstance(structures, list) + assert isinstance(structures[0], dict) + + # Check that all structures have the correct keys and value types: + for struct in structures: + try: + assert struct.keys() == STEMPLATE.keys() + assert [ + isinstance(v, type(STEMPLATE[k])) for k, v in struct.items() + ] + except AssertionError: + raise AssertionError( + f"Inconsistencies found for structure {struct}" + ) + + +def get_structure_children(structures, region, use_tree=False): + """ + Given a list of dictionaries with structures data, + and a structure from the list, this function returns + the structures in the list that are children of + the given structure (region). + If use_tree is true it creates a StructureTree and uses that. + """ + if not isinstance(structures, list): + raise ValueError("structures should be a list") + if not isinstance(structures[0], dict): + raise ValueError("structures should be a list of dictionaries") + if not isinstance(region, dict): + raise ValueError( + "region should be a dictionary with a structures data" + ) + + if "id" not in region.keys() or "structure_id_path" not in region.keys(): + raise ValueError( + "Incomplete structures dicts, " + "need both 'id' and 'structure_id_path'" + ) + + if not use_tree: + sub_region_ids = [] + for subregion in structures: + if region["id"] in subregion["structure_id_path"]: + sub_region_ids.append(subregion["id"]) + else: + tree = get_structures_tree(structures) + sub_region_ids = [ + n.identifier for k, n in tree.subtree(region["id"]).nodes.items() + ] + + if sub_region_ids == []: + print(f'{region["acronym"]} doesnt seem to contain any other regions') + return None + else: + return sub_region_ids + + +def get_structure_terminal_nodes(structures, region): + """ + Given a list of dictionaries with structures data, + and a structure from the list, this function returns + the structures in the list that are children of + the given structure (region) that are leafs of the + struture tree + """ + + tree = get_structures_tree(structures) + + sub_region_ids = [ + n.identifier for n in tree.subtree(region["id"]).leaves() + ] + + if not sub_region_ids: + print(f'{region["acronym"]} doesnt seem to contain any other regions') + return None + else: + return sub_region_ids + + +# Used by show_which_structures_have_mesh +class Region(object): + def __init__(self, has_mesh): + self.has_mesh = has_mesh + + +def show_which_structures_have_mesh(structures, meshes_dir): + """ + It prints out a tree visualisation with + True for the regions that a mesh and false for the others + + """ + tree = get_structures_tree(structures) + + for idx, node in tree.nodes.items(): + savepath = meshes_dir / f"{idx}.obj" + if savepath.exists(): + has_mesh = True + else: + has_mesh = False + node.data = Region(has_mesh) + + tree.show(data_property="has_mesh") diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py new file mode 100644 index 00000000..c3adfe4f --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py @@ -0,0 +1,246 @@ +"""Script to validate atlases""" + +import json +import os +from pathlib import Path + +import numpy as np + +from brainglobe_atlasapi import BrainGlobeAtlas +from brainglobe_atlasapi.config import get_brainglobe_dir +from brainglobe_atlasapi.list_atlases import ( + get_all_atlases_lastversions, + get_atlases_lastversions, + get_local_atlas_version, +) +from brainglobe_atlasapi.update_atlases import update_atlas + + +def validate_atlas_files(atlas: BrainGlobeAtlas): + """Checks if basic files exist in the atlas folder""" + + atlas_path = ( + Path(get_brainglobe_dir()) + / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}" + ) + assert atlas_path.is_dir(), f"Atlas path {atlas_path} not found" + expected_files = [ + "annotation.tiff", + "reference.tiff", + "metadata.json", + "structures.json", + ] + for expected_file_name in expected_files: + expected_path = Path(atlas_path / expected_file_name) + assert ( + expected_path.is_file() + ), f"Expected file not found at {expected_path}" + + meshes_path = atlas_path / "meshes" + assert meshes_path.is_dir(), f"Meshes path {meshes_path} not found" + return True + + +def _assert_close(mesh_coord, annotation_coord, pixel_size, diff_tolerance=10): + """ + Helper function to check if the mesh and the annotation coordinate + are closer to each other than an arbitrary tolerance value + times the pixel size. + + The default tolerance value is 10. + """ + assert abs(mesh_coord - annotation_coord) <= diff_tolerance * pixel_size, ( + f"Mesh coordinate {mesh_coord} and " + f"annotation coordinate {annotation_coord}", + f"differ by more than {diff_tolerance} " + f"times pixel size {pixel_size}", + ) + return True + + +def validate_mesh_matches_image_extents(atlas: BrainGlobeAtlas): + """Checks if the mesh and the image extents are similar""" + + root_mesh = atlas.mesh_from_structure("root") + annotation_image = atlas.annotation + resolution = atlas.resolution + + # minimum and maximum values of the annotation image (z, y, x) + z_range, y_range, x_range = np.nonzero(annotation_image) + z_min, z_max = np.min(z_range), np.max(z_range) + y_min, y_max = np.min(y_range), np.max(y_range) + x_min, x_max = np.min(x_range), np.max(x_range) + + # minimum and maximum values of the annotation image + # scaled by the atlas resolution + z_min_scaled, z_max_scaled = z_min * resolution[0], z_max * resolution[0] + y_min_scaled, y_max_scaled = y_min * resolution[1], y_max * resolution[1] + x_min_scaled, x_max_scaled = x_min * resolution[2], x_max * resolution[2] + + # z, y and x coordinates of the root mesh (extent of the whole object) + mesh_points = root_mesh.points + z_coords, y_coords, x_coords = ( + mesh_points[:, 0], + mesh_points[:, 1], + mesh_points[:, 2], + ) + + # minimum and maximum coordinates of the root mesh + z_min_mesh, z_max_mesh = np.min(z_coords), np.max(z_coords) + y_min_mesh, y_max_mesh = np.min(y_coords), np.max(y_coords) + x_min_mesh, x_max_mesh = np.min(x_coords), np.max(x_coords) + + # checking if root mesh and image are on the same scale + _assert_close(z_min_mesh, z_min_scaled, resolution[0]) + _assert_close(z_max_mesh, z_max_scaled, resolution[0]) + _assert_close(y_min_mesh, y_min_scaled, resolution[1]) + _assert_close(y_max_mesh, y_max_scaled, resolution[1]) + _assert_close(x_min_mesh, x_min_scaled, resolution[2]) + _assert_close(x_max_mesh, x_max_scaled, resolution[2]) + + return True + + +def open_for_visual_check(atlas: BrainGlobeAtlas): + # implement visual checks later + pass + + +def validate_checksum(atlas: BrainGlobeAtlas): + # implement later + pass + + +def check_additional_references(atlas: BrainGlobeAtlas): + # check additional references are different, but have same dimensions + pass + + +def catch_missing_mesh_files(atlas: BrainGlobeAtlas): + """ + Checks if all the structures in the atlas have a corresponding mesh file + """ + + ids_from_bg_atlas_api = list(atlas.structures.keys()) + + atlas_path = ( + Path(get_brainglobe_dir()) + / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}" + ) + obj_path = Path(atlas_path / "meshes") + + ids_from_mesh_files = [ + int(Path(file).stem) + for file in os.listdir(obj_path) + if file.endswith(".obj") + ] + + in_bg_not_mesh = [] + for id in ids_from_bg_atlas_api: + if id not in ids_from_mesh_files: + in_bg_not_mesh.append(id) + + if len(in_bg_not_mesh) != 0: + raise AssertionError( + f"Structures with IDs {in_bg_not_mesh} are in the atlas, " + "but don't have a corresponding mesh file." + ) + + +def catch_missing_structures(atlas: BrainGlobeAtlas): + """ + Checks if all the mesh files in the atlas folder + are listed as a structure in the atlas. + """ + + ids_from_bg_atlas_api = list(atlas.structures.keys()) + + atlas_path = ( + Path(get_brainglobe_dir()) + / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}" + ) + obj_path = Path(atlas_path / "meshes") + + ids_from_mesh_files = [ + int(Path(file).stem) + for file in os.listdir(obj_path) + if file.endswith(".obj") + ] + + in_mesh_not_bg = [] + for id in ids_from_mesh_files: + if id not in ids_from_bg_atlas_api: + in_mesh_not_bg.append(id) + + if len(in_mesh_not_bg) != 0: + raise AssertionError( + f"Structures with IDs {in_mesh_not_bg} have a mesh file, " + "but are not accessible through the atlas." + ) + + +def validate_atlas(atlas_name, version, validation_functions): + """Validates the latest version of a given atlas""" + + print(atlas_name, version) + BrainGlobeAtlas(atlas_name) + updated = get_atlases_lastversions()[atlas_name]["updated"] + if not updated: + update_atlas(atlas_name) + + validation_results = {atlas_name: []} + + for i, validation_function in enumerate(validation_functions): + try: + validation_function(BrainGlobeAtlas(atlas_name)) + validation_results[atlas_name].append( + (validation_function.__name__, None, str("Pass")) + ) + except AssertionError as error: + validation_results[atlas_name].append( + (validation_function.__name__, str(error), str("Fail")) + ) + + return validation_results + + +if __name__ == "__main__": + # list to store the validation functions + all_validation_functions = [ + validate_atlas_files, + validate_mesh_matches_image_extents, + open_for_visual_check, + validate_checksum, + check_additional_references, + catch_missing_mesh_files, + catch_missing_structures, + ] + + valid_atlases = [] + invalid_atlases = [] + validation_results = {} + + for atlas_name, version in get_all_atlases_lastversions().items(): + temp_validation_results = validate_atlas( + atlas_name, version, all_validation_functions + ) + validation_results.update(temp_validation_results) + + print("Validation has been completed") + print("Find validation_results.json in ~/.brainglobe/atlases/validation/") + + # Get the directory path + output_dir_path = str(get_brainglobe_dir() / "atlases/validation") + + # Create the directory if it doesn't exist + if not os.path.exists(output_dir_path): + os.makedirs(output_dir_path) + + # Open a file for writing (will overwrite any files from previous runs!) + with open( + str( + get_brainglobe_dir() / "atlases/validation/validation_results.json" + ), + "w", + ) as file: + json.dump(validation_results, file) diff --git a/brainglobe_atlasapi/atlas_generation/volume_utils.py b/brainglobe_atlasapi/atlas_generation/volume_utils.py new file mode 100644 index 00000000..af4904ad --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/volume_utils.py @@ -0,0 +1,108 @@ +""" + Code useful for dealing with volumetric data + (e.g. allen annotation volume for the mouse atlas) + extracting surfaces from volumetric data .... +""" + +try: + from vedo import Volume +except ModuleNotFoundError: + raise ModuleNotFoundError( + "Mesh generation with these utils requires vedo\n" + + ' please install with "pip install vedo -U"' + ) + +import os + +import imio +import numpy as np + + +def create_masked_array(volume, label, greater_than=False): + """ + Given a 2d o 3d numpy array and a + label value, creates a masked binary + array which is 1 when volume == label + and 0 otherwise + + Parameters + ---------- + volume: np.ndarray + (2d or 3d array) + label: int, float or list of int. + the masked array will be 1 where volume == label + greater_than: bool + if True, all voxels with value > label will be set to 1 + """ + if not isinstance(volume, np.ndarray): + raise ValueError( + f"Argument volume should be a numpy array not {type(volume)}" + ) + + arr = np.zeros_like(volume) + + if not isinstance(label, list) and not np.all(np.isin(label, volume)): + print(f"Label {label} is not in the array, returning empty mask") + return arr + # elif isinstance(label, list): + # if not np.any(np.isin(volume, label)): + # print(f"Label is not in the array, returning empty mask") + # return arr + + if not greater_than: + if not isinstance(label, list): + arr[volume == label] = 1 + else: + arr[np.isin(volume, label)] = 1 + else: + arr[volume > label] = 1 + return arr + + +# ----------------------------- vedo utils ----------------------------- # +# This stuff is outdated, use the functions in mesh_utils.py +# to extract meshes from volumes + + +def load_labelled_volume(data, vmin=0, alpha=1, **kwargs): + """ + Load volume image from .nrrd file. + + Assume that voxels with value = 0 are empty while voxels with values > 0 + are labels. + (EG to indicate the location of a brain region in a reference atlas) + + :param data: str, path to file with volume data or 3d numpy array. + :param vmin: float, values below this number will be assigned an alpha=0 + and not be visualized. + :param **kwargs: kwargs to pass to the Volume class from vedo. + :param alpha: float in [0,1], + transparency [for the part of volume with value > vmin]. + """ + # Load/check volumetric data + if isinstance(data, str): # load from file + if not os.path.isfile(data): + raise FileNotFoundError(f"Volume data file {data} not found") + + try: + data = imio.load_any(data) + except Exception as e: + raise ValueError( + f"Could not load volume data from file: {data} - {e}" + ) + + elif not isinstance(data, np.ndarray): + raise ValueError( + f"Data should be a filepath or np array, not: {data.__type__}" + ) + + # Create volume and set transparency range + vol = Volume(data, alpha=alpha, **kwargs) + + otf = vol.GetProperty().GetScalarOpacity() + otf.RemoveAllPoints() + otf.AddPoint(vmin, 0) # set to transparent + otf.AddPoint(vmin + 0.1, alpha) # set to opaque + otf.AddPoint(data.max(), alpha) + + return vol diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py new file mode 100644 index 00000000..ef0f9f6d --- /dev/null +++ b/brainglobe_atlasapi/atlas_generation/wrapup.py @@ -0,0 +1,229 @@ +import json +import shutil +import tarfile +from pathlib import Path + +import brainglobe_space as bgs +import meshio as mio +import tifffile + +import brainglobe_atlasapi.atlas_generation +from brainglobe_atlasapi import descriptors +from brainglobe_atlasapi.atlas_generation.metadata_utils import ( + create_metadata_files, + generate_metadata_dict, +) +from brainglobe_atlasapi.atlas_generation.stacks import ( + save_annotation, + save_hemispheres, + save_reference, + save_secondary_reference, +) +from brainglobe_atlasapi.atlas_generation.structures import ( + check_struct_consistency, +) +from brainglobe_atlasapi.utils import atlas_name_from_repr + +# This should be changed every time we make changes in the atlas +# structure: +ATLAS_VERSION = brainglobe_atlasapi.atlas_generation.__version__ + + +def wrapup_atlas_from_data( + atlas_name, + atlas_minor_version, + citation, + atlas_link, + species, + resolution, + orientation, + root_id, + reference_stack, + annotation_stack, + structures_list, + meshes_dict, + working_dir, + atlas_packager=None, + hemispheres_stack=None, + cleanup_files=False, + compress=True, + scale_meshes=False, + additional_references={}, + additional_metadata={}, +): + """ + Finalise an atlas with truly consistent format from all the data. + + Parameters + ---------- + atlas_name : str + Atlas name in the form author_species. + atlas_minor_version : int or str + Minor version number for this particular atlas. + citation : str + Citation for the atlas, if unpublished specify "unpublished". + atlas_link : str + Valid URL for the atlas. + species : str + Species name formatted as "CommonName (Genus species)". + resolution : tuple + Three elements tuple, resolution on three axes + orientation : + Orientation of the original atlas + (tuple describing origin for BGSpace). + root_id : + Id of the root element of the atlas. + reference_stack : str or Path or numpy array + Reference stack for the atlas. + If str or Path, will be read with tifffile. + annotation_stack : str or Path or numpy array + Annotation stack for the atlas. + If str or Path, will be read with tifffile. + structures_list : list of dict + List of valid dictionary for structures. + meshes_dict : dict + dict of meshio-compatible mesh file paths in the form + {sruct_id: meshpath} + working_dir : str or Path obj + Path where the atlas folder and compressed file will be generated. + atlas_packager : str or None + Credit for those responsible for converting the atlas + into the BrainGlobe format. + hemispheres_stack : str or Path or numpy array, optional + Hemisphere stack for the atlas. + If str or Path, will be read with tifffile. + If none is provided, atlas is assumed to be symmetric. + cleanup_files : bool, optional + (Default value = False) + compress : bool, optional + (Default value = True) + scale_meshes: bool, optional + (Default values = False). + If True the meshes points are scaled by the resolution + to ensure that they are specified in microns, + regardless of the atlas resolution. + additional_references: dict, optional + (Default value = empty dict). + Dictionary with secondary reference stacks. + additional_metadata: dict, optional + (Default value = empty dict). + Additional metadata to write to metadata.json + """ + + # If no hemisphere file is given, assume the atlas is symmetric: + symmetric = hemispheres_stack is None + + # Instantiate BGSpace obj, using original stack size in um as meshes + # are un um: + original_shape = reference_stack.shape + volume_shape = tuple(res * s for res, s in zip(resolution, original_shape)) + space_convention = bgs.AnatomicalSpace(orientation, shape=volume_shape) + + # Check consistency of structures .json file: + check_struct_consistency(structures_list) + + atlas_dir_name = atlas_name_from_repr( + atlas_name, resolution[0], ATLAS_VERSION, atlas_minor_version + ) + dest_dir = Path(working_dir) / atlas_dir_name + + # exist_ok would be more permissive but error-prone here as there might + # be old files + dest_dir.mkdir() + + stack_list = [reference_stack, annotation_stack] + saving_fun_list = [save_reference, save_annotation] + + # If the atlas is not symmetric, we are also providing an hemisphere stack: + if not symmetric: + stack_list += [ + hemispheres_stack, + ] + saving_fun_list += [ + save_hemispheres, + ] + + # write tiff stacks: + for stack, saving_function in zip(stack_list, saving_fun_list): + if isinstance(stack, str) or isinstance(stack, Path): + stack = tifffile.imread(stack) + + # Reorient stacks if required: + stack = space_convention.map_stack_to( + descriptors.ATLAS_ORIENTATION, stack, copy=False + ) + shape = stack.shape + + saving_function(stack, dest_dir) + + for k, stack in additional_references.items(): + stack = space_convention.map_stack_to( + descriptors.ATLAS_ORIENTATION, stack, copy=False + ) + save_secondary_reference(stack, k, output_dir=dest_dir) + + # Reorient vertices of the mesh. + mesh_dest_dir = dest_dir / descriptors.MESHES_DIRNAME + mesh_dest_dir.mkdir() + + for mesh_id, meshfile in meshes_dict.items(): + mesh = mio.read(meshfile) + + if scale_meshes: + # Scale the mesh to the desired resolution, BEFORE transforming: + mesh.points *= resolution + + # Reorient points: + mesh.points = space_convention.map_points_to( + descriptors.ATLAS_ORIENTATION, mesh.points + ) + + # Save in meshes dir: + mio.write(mesh_dest_dir / f"{mesh_id}.obj", mesh) + + transformation_mat = space_convention.transformation_matrix_to( + descriptors.ATLAS_ORIENTATION + ) + + # save regions list json: + with open(dest_dir / descriptors.STRUCTURES_FILENAME, "w") as f: + json.dump(structures_list, f) + + # Finalize metadata dictionary: + metadata_dict = generate_metadata_dict( + name=atlas_name, + citation=citation, + atlas_link=atlas_link, + species=species, + symmetric=symmetric, + resolution=resolution, + orientation=descriptors.ATLAS_ORIENTATION, + version=f"{ATLAS_VERSION}.{atlas_minor_version}", + shape=shape, + transformation_mat=transformation_mat, + additional_references=[k for k in additional_references.keys()], + atlas_packager=atlas_packager, + ) + + # Create human readable .csv and .txt files: + create_metadata_files( + dest_dir, + metadata_dict, + structures_list, + root_id, + additional_metadata=additional_metadata, + ) + + # Compress if required: + if compress: + output_filename = dest_dir.parent / f"{dest_dir.name}.tar.gz" + print(f"Saving compressed atlas data at: {output_filename}") + with tarfile.open(output_filename, "w:gz") as tar: + tar.add(dest_dir, arcname=dest_dir.name) + + # Cleanup if required: + if cleanup_files: + # Clean temporary directory and remove it: + shutil.rmtree(dest_dir) + + return output_filename diff --git a/bg_atlasapi/bg_atlas.py b/brainglobe_atlasapi/bg_atlas.py similarity index 96% rename from bg_atlasapi/bg_atlas.py rename to brainglobe_atlasapi/bg_atlas.py index cab2d152..34b80032 100644 --- a/bg_atlasapi/bg_atlas.py +++ b/brainglobe_atlasapi/bg_atlas.py @@ -6,8 +6,8 @@ from rich import print as rprint from rich.console import Console -from bg_atlasapi import config, core, descriptors, utils -from bg_atlasapi.utils import _rich_atlas_metadata +from brainglobe_atlasapi import config, core, descriptors, utils +from brainglobe_atlasapi.utils import _rich_atlas_metadata COMPRESSED_FILENAME = "atlas.tar.gz" @@ -82,7 +82,7 @@ def __init__( raise ValueError(f"{atlas_name} is not a valid atlas name!") rprint( - f"[magenta2]bg_atlasapi: {self.atlas_name} " + f"[magenta2]brainglobe_atlasapi: {self.atlas_name} " "not found locally. Downloading...[magenta2]" ) self.download_extract_file() @@ -188,7 +188,7 @@ def check_latest_version(self): if local != online: rprint( - f"[b][magenta2]bg_atlasapi[/b]: " + f"[b][magenta2]brainglobe_atlasapi[/b]: " f"[b]{self.atlas_name}[/b] version [b]{local}[/b]" f"is not the latest available ([b]{online}[/b]). " "To update the atlas run in the terminal:[/magenta2]\n" diff --git a/bg_atlasapi/cli.py b/brainglobe_atlasapi/cli.py similarity index 91% rename from bg_atlasapi/cli.py rename to brainglobe_atlasapi/cli.py index c699789a..e8687809 100644 --- a/bg_atlasapi/cli.py +++ b/brainglobe_atlasapi/cli.py @@ -1,8 +1,8 @@ import click -from bg_atlasapi.config import cli_modify_config -from bg_atlasapi.list_atlases import show_atlases -from bg_atlasapi.update_atlases import install_atlas, update_atlas +from brainglobe_atlasapi.config import cli_modify_config +from brainglobe_atlasapi.list_atlases import show_atlases +from brainglobe_atlasapi.update_atlases import install_atlas, update_atlas @click.command(context_settings={"help_option_names": ["-h", "--help"]}) diff --git a/bg_atlasapi/config.py b/brainglobe_atlasapi/config.py similarity index 100% rename from bg_atlasapi/config.py rename to brainglobe_atlasapi/config.py diff --git a/bg_atlasapi/core.py b/brainglobe_atlasapi/core.py similarity index 98% rename from bg_atlasapi/core.py rename to brainglobe_atlasapi/core.py index c1475b58..a24dd2a8 100644 --- a/bg_atlasapi/core.py +++ b/brainglobe_atlasapi/core.py @@ -6,7 +6,7 @@ import pandas as pd from brainglobe_space import AnatomicalSpace -from bg_atlasapi.descriptors import ( +from brainglobe_atlasapi.descriptors import ( ANNOTATION_FILENAME, HEMISPHERES_FILENAME, MESHES_DIRNAME, @@ -14,8 +14,8 @@ REFERENCE_FILENAME, STRUCTURES_FILENAME, ) -from bg_atlasapi.structure_class import StructuresDict -from bg_atlasapi.utils import read_json, read_tiff +from brainglobe_atlasapi.structure_class import StructuresDict +from brainglobe_atlasapi.utils import read_json, read_tiff class Atlas: diff --git a/bg_atlasapi/descriptors.py b/brainglobe_atlasapi/descriptors.py similarity index 95% rename from bg_atlasapi/descriptors.py rename to brainglobe_atlasapi/descriptors.py index c3fdd64c..06def75d 100644 --- a/bg_atlasapi/descriptors.py +++ b/brainglobe_atlasapi/descriptors.py @@ -3,7 +3,7 @@ # Base url of the gin repository: remote_url_base = "https://gin.g-node.org/brainglobe/atlases/raw/master/{}" -# Major version of atlases used by current bg-atlasapi release: +# Major version of atlases used by current brainglobe-atlasapi release: ATLAS_MAJOR_V = 0 # Entries and types from this template will be used to check atlas info diff --git a/bg_atlasapi/list_atlases.py b/brainglobe_atlasapi/list_atlases.py similarity index 98% rename from bg_atlasapi/list_atlases.py rename to brainglobe_atlasapi/list_atlases.py index e4ff7ff2..92760d89 100644 --- a/bg_atlasapi/list_atlases.py +++ b/brainglobe_atlasapi/list_atlases.py @@ -6,7 +6,7 @@ from rich.panel import Panel from rich.table import Table -from bg_atlasapi import config, descriptors, utils +from brainglobe_atlasapi import config, descriptors, utils def get_downloaded_atlases(): diff --git a/bg_atlasapi/structure_class.py b/brainglobe_atlasapi/structure_class.py similarity index 96% rename from bg_atlasapi/structure_class.py rename to brainglobe_atlasapi/structure_class.py index 53c4b839..4d09c620 100644 --- a/bg_atlasapi/structure_class.py +++ b/brainglobe_atlasapi/structure_class.py @@ -3,7 +3,7 @@ import meshio as mio -from bg_atlasapi.structure_tree_util import get_structures_tree +from brainglobe_atlasapi.structure_tree_util import get_structures_tree class Structure(UserDict): diff --git a/bg_atlasapi/structure_tree_util.py b/brainglobe_atlasapi/structure_tree_util.py similarity index 100% rename from bg_atlasapi/structure_tree_util.py rename to brainglobe_atlasapi/structure_tree_util.py diff --git a/bg_atlasapi/update_atlases.py b/brainglobe_atlasapi/update_atlases.py similarity index 72% rename from bg_atlasapi/update_atlases.py rename to brainglobe_atlasapi/update_atlases.py index 57ba4f74..7a2b7f2a 100644 --- a/bg_atlasapi/update_atlases.py +++ b/brainglobe_atlasapi/update_atlases.py @@ -2,12 +2,15 @@ from rich import print as rprint -from bg_atlasapi.bg_atlas import BrainGlobeAtlas, _version_str_from_tuple -from bg_atlasapi.list_atlases import get_downloaded_atlases +from brainglobe_atlasapi.bg_atlas import ( + BrainGlobeAtlas, + _version_str_from_tuple, +) +from brainglobe_atlasapi.list_atlases import get_downloaded_atlases def update_atlas(atlas_name, force=False): - """Updates a bg_atlasapi atlas from the latest + """Updates a brainglobe_atlasapi atlas from the latest available version online. Arguments: @@ -25,7 +28,7 @@ def update_atlas(atlas_name, force=False): if not force: if atlas.check_latest_version(): rprint( - f"[b][magenta2]bg_atlasapi: {atlas.atlas_name} " + f"[b][magenta2]brainglobe_atlasapi: {atlas.atlas_name} " "is already updated " f"(version: {_version_str_from_tuple(atlas.local_version)})" "[/b]" @@ -34,7 +37,8 @@ def update_atlas(atlas_name, force=False): # Delete atlas folder rprint( - f"[b][magenta2]bg_atlasapi: updating {atlas.atlas_name}[/magenta2][/b]" + "[b][magenta2]brainglobe_atlasapi: " + f"updating {atlas.atlas_name}[/magenta2][/b]" ) fld = atlas.brainglobe_dir / atlas.local_full_name shutil.rmtree(fld) @@ -49,8 +53,9 @@ def update_atlas(atlas_name, force=False): # Check that everything went well rprint( - f"[b][magenta2]bg_atlasapi: {atlas.atlas_name} updated to version: " - + f"{_version_str_from_tuple(atlas.remote_version)}[/magenta2][/b]" + "[b][magenta2]brainglobe_atlasapi: " + f"{atlas.atlas_name} updated to version: " + f"{_version_str_from_tuple(atlas.remote_version)}[/magenta2][/b]" ) @@ -72,7 +77,7 @@ def install_atlas(atlas_name): available_atlases = get_downloaded_atlases() if atlas_name in available_atlases: rprint( - f"[b][magenta2]bg_atlasapi: installing {atlas_name}: " + f"[b][magenta2]brainglobe_atlasapi: installing {atlas_name}: " "atlas already installed![/magenta2][/b]" ) return diff --git a/bg_atlasapi/utils.py b/brainglobe_atlasapi/utils.py similarity index 100% rename from bg_atlasapi/utils.py rename to brainglobe_atlasapi/utils.py diff --git a/pyproject.toml b/pyproject.toml index 0153ebc0..786914d7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] -name = "bg-atlasapi" -description = "A lightweight python module to interact with atlases for systems neuroscience" +name = "brainglobe-atlasapi" +description = "A lightweight python module to interact with and generate atlases for systems neuroscience." readme = "README.md" license = { file = "LICENSE" } authors = [ @@ -19,43 +19,64 @@ classifiers = [ requires-python = ">=3.9" dependencies = [ "brainglobe-space >= 1.0.0", + "brainglobe-utils >= 0.4.0", "click", + "loguru", "meshio", + "meshio", + "numpy", "numpy", "pandas", "pyarrow", + "PyMCubes", "requests", "rich >= 9.0.0", + "rich", + "SimpleITK", "tifffile", + "tqdm>=4.46.1", "treelib", + "vedo", + "xmltodict", ] dynamic = ["version"] [project.urls] -"Homepage" = "https://brainglobe.info/documentation/bg-atlasapi/index.html" -"Source Code" = "https://github.com/brainglobe/bg-atlasapi" -"Bug Tracker" = "https://github.com/brainglobe/bg-atlasapi/issues" -"Documentation" = "https://brainglobe.info/documentation/bg-atlasapi/index.html" +"Homepage" = "https://brainglobe.info/documentation/brainglobe-atlasapi/index.html" +"Source Code" = "https://github.com/brainglobe/brainglobe-atlasapi" +"Bug Tracker" = "https://github.com/brainglobe/brainglobe-atlasapi/issues" +"Documentation" = "https://brainglobe.info/documentation/brainglobe-atlasapi/index.html" [project.optional-dependencies] -dev = ["check-manifest", "pre-commit", "pytest", "pytest-cov"] +dev = [ + "black", + "check-manifest", + "coverage", + "mypy", + "pre-commit", + "pytest-cov", + "pytest-mock", + "pytest", + "ruff", + "setuptools_scm", + "tox", +] + +allenmouse = ["allensdk"] [build-system] requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"] build-backend = "setuptools.build_meta" -[project.scripts] -brainglobe = "bg_atlasapi.cli:bg_cli" - [tool.setuptools] include-package-data = true [tool.setuptools.packages.find] -include = ["bg_atlasapi*"] +include = ["brainglobe_atlasapi*"] exclude = ["tests*"] [tool.pytest.ini_options] -addopts = "--cov=bg_atlasapi" +addopts = "--cov=brainglobe_atlasapi" filterwarnings = ["error"] markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"] @@ -66,26 +87,18 @@ line-length = 79 [tool.setuptools_scm] -[tool.check-manifest] -ignore = [ - "*.yaml", - "tox.ini", - "tests/*", - "tests/test_unit/*", - "tests/test_integration/*", -] - [tool.ruff] line-length = 79 exclude = ["__init__.py", "build", ".eggs"] -select = ["I", "E", "F"] fix = true +[tool.ruff.lint] +select = ["I", "E", "F"] + [tool.tox] legacy_tox_ini = """ -# For more information about tox, see https://tox.readthedocs.io/en/latest/ [tox] -envlist = py{38,39,310,311} +envlist = py{39,310,311} [gh-actions] python = @@ -96,5 +109,5 @@ python = [testenv] extras = dev -commands = pytest -v --color=yes --cov=bg_atlasapi --cov-report=xml -W ignore::DeprecationWarning +commands = pytest -v --color=yes --cov=brainglobe_atlasapi --cov-report=xml """ diff --git a/tests/atlasapi/__init__.py b/tests/atlasapi/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tests/test_bg_atlas.py b/tests/atlasapi/test_bg_atlas.py similarity index 93% rename from tests/test_bg_atlas.py rename to tests/atlasapi/test_bg_atlas.py index 449ecf96..7d200159 100644 --- a/tests/test_bg_atlas.py +++ b/tests/atlasapi/test_bg_atlas.py @@ -3,7 +3,7 @@ import pytest -from bg_atlasapi.bg_atlas import BrainGlobeAtlas +from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas def test_versions(atlas): diff --git a/tests/test_cli.py b/tests/atlasapi/test_cli.py similarity index 96% rename from tests/test_cli.py rename to tests/atlasapi/test_cli.py index 31b037da..462582c6 100644 --- a/tests/test_cli.py +++ b/tests/atlasapi/test_cli.py @@ -1,6 +1,6 @@ from click.testing import CliRunner -from bg_atlasapi import cli, config +from brainglobe_atlasapi import cli, config # This testing of the command line application does not really diff --git a/tests/test_config_file.py b/tests/atlasapi/test_config_file.py similarity index 92% rename from tests/test_config_file.py rename to tests/atlasapi/test_config_file.py index 33723006..2e7e202d 100644 --- a/tests/test_config_file.py +++ b/tests/atlasapi/test_config_file.py @@ -5,7 +5,7 @@ import pytest from click.testing import CliRunner -from bg_atlasapi import bg_atlas, cli, config +from brainglobe_atlasapi import bg_atlas, cli, config @pytest.fixture() @@ -27,7 +27,7 @@ def test_config_creation(conf_path): # Ugly test zone: here we use the terminal commands, which edit the config -# file in the bg_atlasapi repo from which the tests are being run. +# file in the brainglobe_atlasapi repo from which the tests are being run. # This is not the cleanest way, the alternative would be to run this test in # a new env. @pytest.mark.slow diff --git a/tests/test_core_atlas.py b/tests/atlasapi/test_core_atlas.py similarity index 98% rename from tests/test_core_atlas.py rename to tests/atlasapi/test_core_atlas.py index 6c60df83..a8b6cb94 100644 --- a/tests/test_core_atlas.py +++ b/tests/atlasapi/test_core_atlas.py @@ -6,7 +6,7 @@ import pytest import tifffile -from bg_atlasapi.core import AdditionalRefDict +from brainglobe_atlasapi.core import AdditionalRefDict def test_initialization(atlas): diff --git a/tests/test_list_atlases.py b/tests/atlasapi/test_list_atlases.py similarity index 95% rename from tests/test_list_atlases.py rename to tests/atlasapi/test_list_atlases.py index 7030b76d..afa7b581 100644 --- a/tests/test_list_atlases.py +++ b/tests/atlasapi/test_list_atlases.py @@ -1,4 +1,4 @@ -from bg_atlasapi.list_atlases import ( +from brainglobe_atlasapi.list_atlases import ( get_atlases_lastversions, get_downloaded_atlases, get_local_atlas_version, diff --git a/tests/test_structure_dict.py b/tests/atlasapi/test_structure_dict.py similarity index 91% rename from tests/test_structure_dict.py rename to tests/atlasapi/test_structure_dict.py index cd6c627b..211e87d3 100644 --- a/tests/test_structure_dict.py +++ b/tests/atlasapi/test_structure_dict.py @@ -1,9 +1,9 @@ import meshio as mio import pytest -from bg_atlasapi import descriptors -from bg_atlasapi.structure_class import StructuresDict -from bg_atlasapi.utils import read_json +from brainglobe_atlasapi import descriptors +from brainglobe_atlasapi.structure_class import StructuresDict +from brainglobe_atlasapi.utils import read_json structures_list = [ { diff --git a/tests/test_update_atlas.py b/tests/atlasapi/test_update_atlas.py similarity index 88% rename from tests/test_update_atlas.py rename to tests/atlasapi/test_update_atlas.py index 433f6e86..abfc1ee2 100644 --- a/tests/test_update_atlas.py +++ b/tests/atlasapi/test_update_atlas.py @@ -1,6 +1,6 @@ import pytest -from bg_atlasapi import update_atlases +from brainglobe_atlasapi import update_atlases def test_update(): diff --git a/tests/test_utils.py b/tests/atlasapi/test_utils.py similarity index 98% rename from tests/test_utils.py rename to tests/atlasapi/test_utils.py index 1d194872..e09279d9 100644 --- a/tests/test_utils.py +++ b/tests/atlasapi/test_utils.py @@ -4,7 +4,7 @@ import requests from requests import HTTPError -from bg_atlasapi import utils +from brainglobe_atlasapi import utils test_url = "https://gin.g-node.org/BrainGlobe/atlases/raw/master/example_mouse_100um_v1.2.tar.gz" diff --git a/tests/atlasgen/test_validation.py b/tests/atlasgen/test_validation.py new file mode 100644 index 00000000..46d7b944 --- /dev/null +++ b/tests/atlasgen/test_validation.py @@ -0,0 +1,123 @@ +import os + +import numpy as np +import pytest + +from brainglobe_atlasapi import BrainGlobeAtlas +from brainglobe_atlasapi.atlas_generation.validate_atlases import ( + _assert_close, + catch_missing_mesh_files, + catch_missing_structures, + validate_atlas_files, + validate_mesh_matches_image_extents, +) +from brainglobe_atlasapi.config import get_brainglobe_dir + + +@pytest.fixture +def atlas(): + """A fixture providing a low-res Allen Mouse atlas for testing. + Tests assume this atlas is valid""" + return BrainGlobeAtlas("allen_mouse_100um") + + +@pytest.fixture +def atlas_with_bad_reference_file(): + """A fixture providing an invalid version of Allen Mouse atlas for testing. + The atlas will have a misnamed template file that won't be found by the API + This fixture also does the clean-up after the test has run + """ + good_name = get_brainglobe_dir() / "allen_mouse_100um_v1.2/reference.tiff" + bad_name = ( + get_brainglobe_dir() / "allen_mouse_100um_v1.2/reference_bad.tiff" + ) + os.rename(good_name, bad_name) + yield BrainGlobeAtlas("allen_mouse_100um") + os.rename(bad_name, good_name) + + +@pytest.fixture +def atlas_with_missing_structure(): + atlas = BrainGlobeAtlas("osten_mouse_100um") + modified_structures = atlas.structures.copy() + modified_structures.pop(688) + + modified_atlas = BrainGlobeAtlas("osten_mouse_100um") + modified_atlas.structures = modified_structures + return modified_atlas + + +def test_validate_mesh_matches_image_extents(atlas): + assert validate_mesh_matches_image_extents(atlas) + + +def test_validate_mesh_matches_image_extents_negative(mocker, atlas): + flipped_annotation_image = np.transpose(atlas.annotation) + mocker.patch( + "brainglobe_atlasapi.BrainGlobeAtlas.annotation", + new_callable=mocker.PropertyMock, + return_value=flipped_annotation_image, + ) + with pytest.raises( + AssertionError, match="differ by more than 10 times pixel size" + ): + validate_mesh_matches_image_extents(atlas) + + +def test_valid_atlas_files(atlas): + assert validate_atlas_files(atlas) + + +def test_invalid_atlas_path(atlas_with_bad_reference_file): + with pytest.raises(AssertionError, match="Expected file not found"): + validate_atlas_files(atlas_with_bad_reference_file) + + +def test_assert_close(): + assert _assert_close(99.5, 8, 10) + + +def test_assert_close_negative(): + with pytest.raises( + AssertionError, match="differ by more than 10 times pixel size" + ): + _assert_close(99.5, 30, 2) + + +def test_catch_missing_mesh_files(atlas): + """ + Tests if catch_missing_mesh_files function raises an error, + when there is at least one structure in the atlas that doesn't have + a corresponding obj file. + + Expected behaviour: + True for "allen_mouse_10um" (structure 545 doesn't have an obj file): + fails the validation function, + raises an error --> no output from this test function + """ + + with pytest.raises( + AssertionError, + match=r"Structures with IDs \[.*?\] are in the atlas, " + "but don't have a corresponding mesh file.", + ): + catch_missing_mesh_files(atlas) + + +def test_catch_missing_structures(atlas_with_missing_structure): + """ + Tests if catch_missing_structures function raises an error, + when there is at least one orphan obj file (doesn't have a + corresponding structure in the atlas) + + Expected behaviour: + Currently no atlas fails the validation function this way so the + [] is always empty --> this test function should always raise an error + """ + + with pytest.raises( + AssertionError, + match=r"Structures with IDs \[.*?\] have a mesh file, " + "but are not accessible through the atlas.", + ): + catch_missing_structures(atlas_with_missing_structure) diff --git a/tests/conftest.py b/tests/conftest.py index d7d58161..41f197da 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -4,7 +4,7 @@ import pytest -from bg_atlasapi.bg_atlas import BrainGlobeAtlas +from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas @pytest.fixture() diff --git a/tutorials/Atlas API usage.ipynb b/tutorials/Atlas API usage.ipynb index 38d9d376..5bbfe1c3 100644 --- a/tutorials/Atlas API usage.ipynb +++ b/tutorials/Atlas API usage.ipynb @@ -1,1715 +1,1715 @@ { - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Introduction to the `BrainGlobeAtlas` class" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## 0. Creating a `BrainGlobeAtlas` object and list availabe options" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "To instantiate a `BrainGlobeAtlas` object, we need to instantiate it with the atlas name. The first time we use it, a version of this atlas files will be downloaded from the [remote GIN repository](http://gin.g-node.org/brainglobe/atlases) and stored on your local machine (by default, in .../Users/username/.brainglobe):" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "allen mouse atlas (res. 100um)\n", - "From: http://www.brain-map.org (Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007 )\n" - ] - } - ], - "source": [ - "import numpy as np\n", - "from bg_atlasapi import BrainGlobeAtlas\n", - "from pprint import pprint\n", - "\n", - "bg_atlas = BrainGlobeAtlas(\"allen_mouse_100um\", check_latest=False)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "To know what atlases are available through BrainGlobe, we can use the `show_atlases` function (we need to be online):" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
                                                                                  \n",
-       "                                                                                  \n",
-       "                                Brainglobe Atlases                                \n",
-       "╭──────────────────────────────────┬────────────┬───────────────┬────────────────╮\n",
-       "│ Name                             │ Downloaded │ Local version │ Latest version │\n",
-       "├──────────────────────────────────┼────────────┼───────────────┼────────────────┤\n",
-       "│ whs_sd_rat_39um                  │     ✔      │      1.0      │      1.0       │\n",
-       "│ allen_mouse_25um                 │     ✔      │      1.2      │      1.2       │\n",
-       "│ allen_mouse_100um                │     ✔      │      1.2      │      1.2       │\n",
-       "│ allen_mouse_50um                 │     ✔      │      1.2      │      1.2       │\n",
-       "│ example_mouse_100um              │    ---     │      ---      │      1.2       │\n",
-       "│ allen_mouse_10um                 │    ---     │      ---      │      1.2       │\n",
-       "│ mpin_zfish_1um                   │    ---     │      ---      │      1.0       │\n",
-       "│ allen_human_500um                │    ---     │      ---      │      0.1       │\n",
-       "│ kim_mouse_10um                   │    ---     │      ---      │      1.0       │\n",
-       "│ kim_mouse_25um                   │    ---     │      ---      │      1.0       │\n",
-       "│ kim_mouse_50um                   │    ---     │      ---      │      1.0       │\n",
-       "│ kim_mouse_100um                  │    ---     │      ---      │      1.0       │\n",
-       "│ osten_mouse_10um                 │    ---     │      ---      │      1.1       │\n",
-       "│ osten_mouse_25um                 │    ---     │      ---      │      1.1       │\n",
-       "│ osten_mouse_50um                 │    ---     │      ---      │      1.1       │\n",
-       "│ osten_mouse_100um                │    ---     │      ---      │      1.1       │\n",
-       "│ allen_cord_20um                  │    ---     │      ---      │      1.0       │\n",
-       "│ azba_zfish_4um                   │    ---     │      ---      │      1.1       │\n",
-       "│ perens_lsfm_mouse_20um           │    ---     │      ---      │      1.0       │\n",
-       "│ admba_3d_e11_5_mouse_16um        │    ---     │      ---      │      1.0       │\n",
-       "│ admba_3d_e13_5_mouse_16um        │    ---     │      ---      │      1.0       │\n",
-       "│ admba_3d_e15_5_mouse_16um        │    ---     │      ---      │      1.0       │\n",
-       "│ admba_3d_e18_5_mouse_16um        │    ---     │      ---      │      1.0       │\n",
-       "│ admba_3d_p4_mouse_16.752um       │    ---     │      ---      │      1.0       │\n",
-       "│ admba_3d_p14_mouse_16.752um      │    ---     │      ---      │      1.0       │\n",
-       "│ admba_3d_p28_mouse_16.752um      │    ---     │      ---      │      1.0       │\n",
-       "│ admba_3d_p56_mouse_25um          │    ---     │      ---      │      1.0       │\n",
-       "╰──────────────────────────────────┴────────────┴───────────────┴────────────────╯\n",
-       "
\n" - ], - "text/plain": [ - "\u001b[3m \u001b[0m\n", - "\u001b[3m \u001b[0m\n", - "\u001b[3m Brainglobe Atlases \u001b[0m\n", - "╭──────────────────────────────────┬────────────┬───────────────┬────────────────╮\n", - "│\u001b[1;32m \u001b[0m\u001b[1;32mName \u001b[0m\u001b[1;32m \u001b[0m│\u001b[1;32m \u001b[0m\u001b[1;32mDownloaded\u001b[0m\u001b[1;32m \u001b[0m│\u001b[1;32m \u001b[0m\u001b[1;32mLocal version\u001b[0m\u001b[1;32m \u001b[0m│\u001b[1;32m \u001b[0m\u001b[1;32mLatest version\u001b[0m\u001b[1;32m \u001b[0m│\n", - "├──────────────────────────────────┼────────────┼───────────────┼────────────────┤\n", - "│ \u001b[1mwhs_sd_rat_39um\u001b[0m │ \u001b[32m✔\u001b[0m │ 1.0 │ 1.0 │\n", - "│ \u001b[1mallen_mouse_25um\u001b[0m │ \u001b[32m✔\u001b[0m │ 1.2 │ 1.2 │\n", - "│ \u001b[1mallen_mouse_100um\u001b[0m │ \u001b[32m✔\u001b[0m │ 1.2 │ 1.2 │\n", - "│ \u001b[1mallen_mouse_50um\u001b[0m │ \u001b[32m✔\u001b[0m │ 1.2 │ 1.2 │\n", - "│ \u001b[1mexample_mouse_100um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.2 │\n", - "│ \u001b[1mallen_mouse_10um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.2 │\n", - "│ \u001b[1mmpin_zfish_1um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1mallen_human_500um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 0.1 │\n", - "│ \u001b[1mkim_mouse_10um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1mkim_mouse_25um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1mkim_mouse_50um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1mkim_mouse_100um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1mosten_mouse_10um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", - "│ \u001b[1mosten_mouse_25um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", - "│ \u001b[1mosten_mouse_50um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", - "│ \u001b[1mosten_mouse_100um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", - "│ \u001b[1mallen_cord_20um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1mazba_zfish_4um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", - "│ \u001b[1mperens_lsfm_mouse_20um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1madmba_3d_e11_5_mouse_16um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1madmba_3d_e13_5_mouse_16um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1madmba_3d_e15_5_mouse_16um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1madmba_3d_e18_5_mouse_16um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1madmba_3d_p4_mouse_16.752um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1madmba_3d_p14_mouse_16.752um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1madmba_3d_p28_mouse_16.752um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "│ \u001b[1madmba_3d_p56_mouse_25um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", - "╰──────────────────────────────────┴────────────┴───────────────┴────────────────╯\n" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "from bg_atlasapi import show_atlases\n", - "show_atlases()" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## 1. Using a `BrainGlobe` atlas" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "A BrainGlobe atlas is a convenient API for interacting with an anatomical atlas. BrainGlobe atlases contain:\n", - " * Metadata\n", - " * The reference anatomical stack used for the registration itself\n", - " * Region annotation stack (the segmented atlas image that occupies the same space as the reference stack)\n", - " * Hemisphere annotation stack which denotes left and right\n", - " * Description of the region hierarchy\n", - " * Meshes for the regions" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 1.0 Metadata" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "All atlases have a standard set of medatata describing their source, species, resolution, etc:" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'name': 'allen_mouse',\n", - " 'citation': 'Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007',\n", - " 'atlas_link': 'http://www.brain-map.org',\n", - " 'species': 'Mus musculus',\n", - " 'symmetric': True,\n", - " 'resolution': [100.0, 100.0, 100.0],\n", - " 'orientation': 'asr',\n", - " 'version': '1.2',\n", - " 'shape': [132, 80, 114],\n", - " 'trasform_to_bg': [[1.0, 0.0, 0.0, 0.0],\n", - " [0.0, 1.0, 0.0, 0.0],\n", - " [0.0, 0.0, 1.0, 0.0],\n", - " [0.0, 0.0, 0.0, 1.0]],\n", - " 'additional_references': []}" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "bg_atlas.metadata" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 1.1 Anatomical, annotation and hemispheres stack" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "from matplotlib import pyplot as plt" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Anatomical reference:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "space = bg_atlas.space\n", - "stack = bg_atlas.reference\n", - "\n", - "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", - "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", - " mid_index = stack.shape[i]//2\n", - " axs[i].imshow(np.moveaxis(stack,i,0)[mid_index,:,:], cmap=\"gray\",clim=(0,250))\n", - " axs[i].set_title(f\"{plane.capitalize()} view\")\n", - " axs[i].set_ylabel(labels[0])\n", - " axs[i].set_xlabel(labels[1])" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Annotations stack:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "space = bg_atlas.space\n", - "stack = bg_atlas.annotation\n", - "\n", - "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", - "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", - " mid_index = stack.shape[i]//2\n", - " axs[i].imshow(np.moveaxis(stack,i,0)[mid_index,:,:], cmap=\"gray\",clim=(0,1250))\n", - " axs[i].set_title(f\"{plane.capitalize()} view\")\n", - " axs[i].set_ylabel(labels[0])\n", - " axs[i].set_xlabel(labels[1])\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "space = bg_atlas.space\n", - "stack = bg_atlas.hemispheres\n", - "\n", - "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", - "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", - " axs[i].imshow(stack.max(i), cmap=\"gray\")\n", - " axs[i].set_title(f\"{plane.capitalize()} view\")\n", - " axs[i].set_ylabel(labels[0])\n", - " axs[i].set_xlabel(labels[1])" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 1.2 Regions hierarchy" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The atlas comes with the description of a hierarchy of brain structures. To have an overview:" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "root (997)\n", - "├── VS (73)\n", - "│ ├── AQ (140)\n", - "│ ├── V3 (129)\n", - "│ ├── V4 (145)\n", - "│ │ └── V4r (153)\n", - "│ ├── VL (81)\n", - "│ │ ├── SEZ (98)\n", - "│ │ └── chpl (108)\n", - "│ └── c (164)\n", - "├── fiber tracts (1009)\n", - "│ ├── cbf (960)\n", - "│ │ ├── arb (728)\n", - "│ │ ├── cbc (744)\n", - "│ │ └── cbp (752)\n", - "│ │ ├── icp (1123)\n", - "│ │ │ └── sctd (553)\n", - "│ │ ├── mcp (78)\n", - "│ │ └── scp (326)\n", - "│ │ ├── dscp (812)\n", - "│ │ ├── sctv (866)\n", - "│ │ └── uf (850)\n", - "│ ├── cm (967)\n", - "│ │ ├── IIIn (832)\n", - "│ │ │ ├── mlf (62)\n", - "│ │ │ └── pc (158)\n", - "│ │ ├── IIn (848)\n", - "│ │ │ ├── bsc (916)\n", - "│ │ │ ├── csc (336)\n", - "│ │ │ ├── och (117)\n", - "│ │ │ └── opt (125)\n", - "│ │ ├── IVn (911)\n", - "│ │ ├── In (840)\n", - "│ │ │ ├── aco (900)\n", - "│ │ │ ├── lotg (21)\n", - "│ │ │ │ ├── lot (665)\n", - "│ │ │ │ └── lotd (538)\n", - "│ │ │ └── onl (1016)\n", - "│ │ ├── VIIIn (933)\n", - "│ │ │ ├── cVIIIn (948)\n", - "│ │ │ │ ├── bic (482)\n", - "│ │ │ │ ├── cic (633)\n", - "│ │ │ │ ├── das (506)\n", - "│ │ │ │ ├── ll (658)\n", - "│ │ │ │ └── tb (841)\n", - "│ │ │ └── vVIIIn (413)\n", - "│ │ ├── VIIn (798)\n", - "│ │ │ └── gVIIn (1116)\n", - "│ │ ├── Vn (901)\n", - "│ │ │ ├── moV (93)\n", - "│ │ │ └── sV (229)\n", - "│ │ │ └── sptV (794)\n", - "│ │ ├── Xn (917)\n", - "│ │ │ └── ts (237)\n", - "│ │ ├── drt (792)\n", - "│ │ │ └── cett (932)\n", - "│ │ │ ├── dc (514)\n", - "│ │ │ │ └── cuf (380)\n", - "│ │ │ └── ml (697)\n", - "│ │ └── von (949)\n", - "│ ├── eps (1000)\n", - "│ │ ├── epsc (760)\n", - "│ │ │ └── nst (102)\n", - "│ │ ├── rust (863)\n", - "│ │ │ └── vtd (397)\n", - "│ │ └── tsp (877)\n", - "│ │ ├── dtd (1060)\n", - "│ │ ├── tspc (1043)\n", - "│ │ └── tspd (1051)\n", - "│ ├── lfbs (983)\n", - "│ │ ├── cc (776)\n", - "│ │ │ ├── ccb (484682516)\n", - "│ │ │ ├── ccg (1108)\n", - "│ │ │ ├── ccs (986)\n", - "│ │ │ ├── ee (964)\n", - "│ │ │ ├── fa (956)\n", - "│ │ │ │ └── ec (579)\n", - "│ │ │ └── fp (971)\n", - "│ │ ├── cst (784)\n", - "│ │ │ ├── cpd (924)\n", - "│ │ │ ├── int (6)\n", - "│ │ │ ├── py (190)\n", - "│ │ │ └── pyd (198)\n", - "│ │ └── lfbst (896)\n", - "│ │ ├── ar (484682524)\n", - "│ │ ├── em (1092)\n", - "│ │ └── or (484682520)\n", - "│ ├── mfbs (991)\n", - "│ │ ├── mfbc (768)\n", - "│ │ │ ├── act (908)\n", - "│ │ │ ├── amc (884)\n", - "│ │ │ ├── cing (940)\n", - "│ │ │ ├── fxs (1099)\n", - "│ │ │ │ ├── alv (466)\n", - "│ │ │ │ ├── df (530)\n", - "│ │ │ │ ├── fi (603)\n", - "│ │ │ │ ├── fxpo (737)\n", - "│ │ │ │ │ ├── fx (436)\n", - "│ │ │ │ │ └── mct (428)\n", - "│ │ │ │ └── hc (618)\n", - "│ │ │ │ ├── dhc (443)\n", - "│ │ │ │ └── vhc (449)\n", - "│ │ │ └── st (301)\n", - "│ │ │ └── stc (484682528)\n", - "│ │ └── mfsbshy (824)\n", - "│ │ ├── mfb (54)\n", - "│ │ ├── mfbse (1083)\n", - "│ │ │ ├── fr (595)\n", - "│ │ │ ├── hbc (611)\n", - "│ │ │ └── sm (802)\n", - "│ │ ├── mfbsma (46)\n", - "│ │ │ ├── mp (673)\n", - "│ │ │ ├── mtg (681)\n", - "│ │ │ ├── mtt (690)\n", - "│ │ │ └── pm (753)\n", - "│ │ └── sup (349)\n", - "│ └── scwm (484682512)\n", - "└── grey (8)\n", - " ├── BS (343)\n", - " │ ├── HB (1065)\n", - " │ │ ├── MY (354)\n", - " │ │ │ ├── MY-mot (370)\n", - " │ │ │ │ ├── ACVII (576)\n", - " │ │ │ │ ├── AMB (135)\n", - " │ │ │ │ │ ├── AMBd (939)\n", - " │ │ │ │ │ └── AMBv (143)\n", - " │ │ │ │ ├── DMX (839)\n", - " │ │ │ │ ├── GRN (1048)\n", - " │ │ │ │ ├── ICB (372)\n", - " │ │ │ │ ├── IO (83)\n", - " │ │ │ │ ├── IRN (136)\n", - " │ │ │ │ ├── ISN (106)\n", - " │ │ │ │ ├── LIN (203)\n", - " │ │ │ │ ├── LRN (235)\n", - " │ │ │ │ │ ├── LRNm (955)\n", - " │ │ │ │ │ └── LRNp (963)\n", - " │ │ │ │ ├── MARN (307)\n", - " │ │ │ │ ├── MDRN (395)\n", - " │ │ │ │ │ ├── MDRNd (1098)\n", - " │ │ │ │ │ └── MDRNv (1107)\n", - " │ │ │ │ ├── PARN (852)\n", - " │ │ │ │ ├── PAS (859)\n", - " │ │ │ │ ├── PGRN (938)\n", - " │ │ │ │ │ ├── PGRNd (970)\n", - " │ │ │ │ │ └── PGRNl (978)\n", - " │ │ │ │ ├── PHY (154)\n", - " │ │ │ │ │ ├── NR (177)\n", - " │ │ │ │ │ └── PRP (169)\n", - " │ │ │ │ ├── PPY (1069)\n", - " │ │ │ │ ├── VI (653)\n", - " │ │ │ │ ├── VII (661)\n", - " │ │ │ │ ├── VNC (701)\n", - " │ │ │ │ │ ├── LAV (209)\n", - " │ │ │ │ │ ├── MV (202)\n", - " │ │ │ │ │ ├── SPIV (225)\n", - " │ │ │ │ │ └── SUV (217)\n", - " │ │ │ │ ├── XII (773)\n", - " │ │ │ │ ├── x (765)\n", - " │ │ │ │ └── y (781)\n", - " │ │ │ ├── MY-sat (379)\n", - " │ │ │ │ ├── RM (206)\n", - " │ │ │ │ ├── RO (222)\n", - " │ │ │ │ └── RPA (230)\n", - " │ │ │ └── MY-sen (386)\n", - " │ │ │ ├── AP (207)\n", - " │ │ │ ├── CN (607)\n", - " │ │ │ │ ├── DCO (96)\n", - " │ │ │ │ └── VCO (101)\n", - " │ │ │ ├── DCN (720)\n", - " │ │ │ │ ├── CU (711)\n", - " │ │ │ │ └── GR (1039)\n", - " │ │ │ ├── ECU (903)\n", - " │ │ │ ├── NTB (642)\n", - " │ │ │ ├── NTS (651)\n", - " │ │ │ ├── Pa5 (589508451)\n", - " │ │ │ ├── SPVC (429)\n", - " │ │ │ ├── SPVI (437)\n", - " │ │ │ └── SPVO (445)\n", - " │ │ └── P (771)\n", - " │ │ ├── P-mot (987)\n", - " │ │ │ ├── Acs5 (549009219)\n", - " │ │ │ ├── B (280)\n", - " │ │ │ ├── DTN (880)\n", - " │ │ │ ├── I5 (549009227)\n", - " │ │ │ ├── P5 (549009215)\n", - " │ │ │ ├── PC5 (549009223)\n", - " │ │ │ ├── PCG (898)\n", - " │ │ │ ├── PDTg (599626927)\n", - " │ │ │ ├── PG (931)\n", - " │ │ │ ├── PRNc (1093)\n", - " │ │ │ ├── SG (318)\n", - " │ │ │ ├── SUT (534)\n", - " │ │ │ ├── TRN (574)\n", - " │ │ │ └── V (621)\n", - " │ │ ├── P-sat (1117)\n", - " │ │ │ ├── CS (679)\n", - " │ │ │ ├── LC (147)\n", - " │ │ │ ├── LDT (162)\n", - " │ │ │ ├── NI (604)\n", - " │ │ │ ├── PRNr (146)\n", - " │ │ │ ├── RPO (238)\n", - " │ │ │ ├── SLC (350)\n", - " │ │ │ └── SLD (358)\n", - " │ │ └── P-sen (1132)\n", - " │ │ ├── NLL (612)\n", - " │ │ ├── PB (867)\n", - " │ │ │ └── KF (123)\n", - " │ │ ├── PSV (7)\n", - " │ │ └── SOC (398)\n", - " │ │ ├── POR (122)\n", - " │ │ ├── SOCl (114)\n", - " │ │ └── SOCm (105)\n", - " │ ├── IB (1129)\n", - " │ │ ├── HY (1097)\n", - " │ │ │ ├── LZ (290)\n", - " │ │ │ │ ├── LHA (194)\n", - " │ │ │ │ ├── LPO (226)\n", - " │ │ │ │ ├── PST (356)\n", - " │ │ │ │ ├── PSTN (364)\n", - " │ │ │ │ ├── PeF (576073704)\n", - " │ │ │ │ ├── RCH (173)\n", - " │ │ │ │ ├── STN (470)\n", - " │ │ │ │ ├── TU (614)\n", - " │ │ │ │ └── ZI (797)\n", - " │ │ │ │ └── FF (804)\n", - " │ │ │ ├── ME (10671)\n", - " │ │ │ ├── MEZ (467)\n", - " │ │ │ │ ├── AHN (88)\n", - " │ │ │ │ ├── MBO (331)\n", - " │ │ │ │ │ ├── LM (210)\n", - " │ │ │ │ │ ├── MM (491)\n", - " │ │ │ │ │ │ ├── MMd (606826659)\n", - " │ │ │ │ │ │ ├── MMl (606826647)\n", - " │ │ │ │ │ │ ├── MMm (606826651)\n", - " │ │ │ │ │ │ ├── MMme (732)\n", - " │ │ │ │ │ │ └── MMp (606826655)\n", - " │ │ │ │ │ ├── SUM (525)\n", - " │ │ │ │ │ └── TM (557)\n", - " │ │ │ │ │ ├── TMd (1126)\n", - " │ │ │ │ │ └── TMv (1)\n", - " │ │ │ │ ├── MPN (515)\n", - " │ │ │ │ ├── PH (946)\n", - " │ │ │ │ ├── PMd (980)\n", - " │ │ │ │ ├── PMv (1004)\n", - " │ │ │ │ ├── PVHd (63)\n", - " │ │ │ │ └── VMH (693)\n", - " │ │ │ ├── PVR (141)\n", - " │ │ │ │ ├── ADP (72)\n", - " │ │ │ │ ├── AVP (263)\n", - " │ │ │ │ ├── AVPV (272)\n", - " │ │ │ │ ├── DMH (830)\n", - " │ │ │ │ ├── MEPO (452)\n", - " │ │ │ │ ├── MPO (523)\n", - " │ │ │ │ ├── OV (763)\n", - " │ │ │ │ ├── PD (914)\n", - " │ │ │ │ ├── PS (1109)\n", - " │ │ │ │ ├── PVp (126)\n", - " │ │ │ │ ├── PVpo (133)\n", - " │ │ │ │ ├── SBPV (347)\n", - " │ │ │ │ ├── SCH (286)\n", - " │ │ │ │ ├── SFO (338)\n", - " │ │ │ │ ├── VLPO (689)\n", - " │ │ │ │ └── VMPO (576073699)\n", - " │ │ │ └── PVZ (157)\n", - " │ │ │ ├── ARH (223)\n", - " │ │ │ ├── ASO (332)\n", - " │ │ │ ├── PVH (38)\n", - " │ │ │ ├── PVa (30)\n", - " │ │ │ ├── PVi (118)\n", - " │ │ │ └── SO (390)\n", - " │ │ └── TH (549)\n", - " │ │ ├── DORpm (856)\n", - " │ │ │ ├── ATN (239)\n", - " │ │ │ │ ├── AD (64)\n", - " │ │ │ │ ├── AM (127)\n", - " │ │ │ │ │ ├── AMd (1096)\n", - " │ │ │ │ │ └── AMv (1104)\n", - " │ │ │ │ ├── AV (255)\n", - " │ │ │ │ ├── IAD (1113)\n", - " │ │ │ │ ├── IAM (1120)\n", - " │ │ │ │ └── LD (155)\n", - " │ │ │ ├── EPI (958)\n", - " │ │ │ │ ├── LH (186)\n", - " │ │ │ │ └── MH (483)\n", - " │ │ │ ├── GENv (1014)\n", - " │ │ │ │ ├── IGL (27)\n", - " │ │ │ │ ├── IntG (563807439)\n", - " │ │ │ │ ├── LGv (178)\n", - " │ │ │ │ └── SubG (321)\n", - " │ │ │ ├── ILM (51)\n", - " │ │ │ │ ├── CL (575)\n", - " │ │ │ │ ├── CM (599)\n", - " │ │ │ │ ├── PCN (907)\n", - " │ │ │ │ ├── PF (930)\n", - " │ │ │ │ ├── PIL (560581563)\n", - " │ │ │ │ └── RH (189)\n", - " │ │ │ ├── LAT (138)\n", - " │ │ │ │ ├── Eth (560581551)\n", - " │ │ │ │ ├── LP (218)\n", - " │ │ │ │ ├── PO (1020)\n", - " │ │ │ │ ├── POL (1029)\n", - " │ │ │ │ └── SGN (325)\n", - " │ │ │ ├── MED (444)\n", - " │ │ │ │ ├── IMD (59)\n", - " │ │ │ │ ├── MD (362)\n", - " │ │ │ │ ├── PR (1077)\n", - " │ │ │ │ └── SMT (366)\n", - " │ │ │ ├── MTN (571)\n", - " │ │ │ │ ├── PT (15)\n", - " │ │ │ │ ├── PVT (149)\n", - " │ │ │ │ ├── RE (181)\n", - " │ │ │ │ └── Xi (560581559)\n", - " │ │ │ └── RT (262)\n", - " │ │ └── DORsm (864)\n", - " │ │ ├── GENd (1008)\n", - " │ │ │ ├── LGd (170)\n", - " │ │ │ │ ├── LGd-co (496345668)\n", - " │ │ │ │ ├── LGd-ip (496345672)\n", - " │ │ │ │ └── LGd-sh (496345664)\n", - " │ │ │ └── MG (475)\n", - " │ │ │ ├── MGd (1072)\n", - " │ │ │ ├── MGm (1088)\n", - " │ │ │ └── MGv (1079)\n", - " │ │ ├── PP (1044)\n", - " │ │ ├── SPA (609)\n", - " │ │ ├── SPF (406)\n", - " │ │ │ ├── SPFm (414)\n", - " │ │ │ └── SPFp (422)\n", - " │ │ └── VENT (637)\n", - " │ │ ├── PoT (563807435)\n", - " │ │ ├── VAL (629)\n", - " │ │ ├── VM (685)\n", - " │ │ └── VP (709)\n", - " │ │ ├── VPL (718)\n", - " │ │ ├── VPLpc (725)\n", - " │ │ ├── VPM (733)\n", - " │ │ └── VPMpc (741)\n", - " │ └── MB (313)\n", - " │ ├── MBmot (323)\n", - " │ │ ├── AT (231)\n", - " │ │ ├── CUN (616)\n", - " │ │ ├── DT (75)\n", - " │ │ ├── EW (975)\n", - " │ │ ├── III (35)\n", - " │ │ ├── IV (115)\n", - " │ │ ├── LT (66)\n", - " │ │ ├── MA3 (549009211)\n", - " │ │ ├── MRN (128)\n", - " │ │ ├── MT (58)\n", - " │ │ ├── PAG (795)\n", - " │ │ │ ├── INC (67)\n", - " │ │ │ ├── ND (587)\n", - " │ │ │ ├── PRC (50)\n", - " │ │ │ └── Su3 (614454277)\n", - " │ │ ├── PN (607344830)\n", - " │ │ ├── PRT (1100)\n", - " │ │ │ ├── APN (215)\n", - " │ │ │ ├── MPT (531)\n", - " │ │ │ ├── NOT (628)\n", - " │ │ │ ├── NPC (634)\n", - " │ │ │ ├── OP (706)\n", - " │ │ │ ├── PPT (1061)\n", - " │ │ │ └── RPF (549009203)\n", - " │ │ ├── Pa4 (606826663)\n", - " │ │ ├── RN (214)\n", - " │ │ ├── RR (246)\n", - " │ │ ├── SCm (294)\n", - " │ │ │ ├── SCdg (26)\n", - " │ │ │ ├── SCdw (42)\n", - " │ │ │ ├── SCig (10)\n", - " │ │ │ └── SCiw (17)\n", - " │ │ ├── SNr (381)\n", - " │ │ ├── VTA (749)\n", - " │ │ └── VTN (757)\n", - " │ ├── MBsen (339)\n", - " │ │ ├── IC (4)\n", - " │ │ │ ├── ICc (811)\n", - " │ │ │ ├── ICd (820)\n", - " │ │ │ └── ICe (828)\n", - " │ │ ├── MEV (460)\n", - " │ │ ├── NB (580)\n", - " │ │ ├── PBG (874)\n", - " │ │ ├── SAG (271)\n", - " │ │ ├── SCO (599626923)\n", - " │ │ └── SCs (302)\n", - " │ │ ├── SCop (851)\n", - " │ │ ├── SCsg (842)\n", - " │ │ └── SCzo (834)\n", - " │ └── MBsta (348)\n", - " │ ├── PPN (1052)\n", - " │ ├── RAmb (165)\n", - " │ │ ├── CLI (591)\n", - " │ │ ├── DR (872)\n", - " │ │ ├── IF (12)\n", - " │ │ ├── IPN (100)\n", - " │ │ │ ├── IPA (607344842)\n", - " │ │ │ ├── IPC (607344838)\n", - " │ │ │ ├── IPDL (607344858)\n", - " │ │ │ ├── IPDM (607344854)\n", - " │ │ │ ├── IPI (607344850)\n", - " │ │ │ ├── IPL (607344846)\n", - " │ │ │ ├── IPR (607344834)\n", - " │ │ │ └── IPRL (607344862)\n", - " │ │ └── RL (197)\n", - " │ └── SNc (374)\n", - " ├── CB (512)\n", - " │ ├── CBN (519)\n", - " │ │ ├── DN (846)\n", - " │ │ ├── FN (989)\n", - " │ │ ├── IP (91)\n", - " │ │ └── VeCB (589508455)\n", - " │ └── CBX (528)\n", - " │ ├── HEM (1073)\n", - " │ │ ├── AN (1017)\n", - " │ │ │ ├── ANcr1 (1056)\n", - " │ │ │ └── ANcr2 (1064)\n", - " │ │ ├── COPY (1033)\n", - " │ │ ├── FL (1049)\n", - " │ │ ├── PFL (1041)\n", - " │ │ ├── PRM (1025)\n", - " │ │ └── SIM (1007)\n", - " │ └── VERM (645)\n", - " │ ├── CENT (920)\n", - " │ │ ├── CENT2 (976)\n", - " │ │ └── CENT3 (984)\n", - " │ ├── CUL (928)\n", - " │ │ └── CUL4, 5 (1091)\n", - " │ ├── DEC (936)\n", - " │ ├── FOTU (944)\n", - " │ ├── LING (912)\n", - " │ ├── NOD (968)\n", - " │ ├── PYR (951)\n", - " │ └── UVU (957)\n", - " └── CH (567)\n", - " ├── CNU (623)\n", - " │ ├── PAL (803)\n", - " │ │ ├── PALc (809)\n", - " │ │ │ ├── BAC (287)\n", - " │ │ │ └── BST (351)\n", - " │ │ ├── PALd (818)\n", - " │ │ │ ├── GPe (1022)\n", - " │ │ │ └── GPi (1031)\n", - " │ │ ├── PALm (826)\n", - " │ │ │ ├── MSC (904)\n", - " │ │ │ │ ├── MS (564)\n", - " │ │ │ │ └── NDB (596)\n", - " │ │ │ └── TRS (581)\n", - " │ │ └── PALv (835)\n", - " │ │ ├── MA (298)\n", - " │ │ └── SI (342)\n", - " │ └── STR (477)\n", - " │ ├── LSX (275)\n", - " │ │ ├── LS (242)\n", - " │ │ │ ├── LSc (250)\n", - " │ │ │ ├── LSr (258)\n", - " │ │ │ └── LSv (266)\n", - " │ │ ├── SF (310)\n", - " │ │ └── SH (333)\n", - " │ ├── STRd (485)\n", - " │ │ └── CP (672)\n", - " │ ├── STRv (493)\n", - " │ │ ├── ACB (56)\n", - " │ │ ├── FS (998)\n", - " │ │ └── OT (754)\n", - " │ └── sAMY (278)\n", - " │ ├── AAA (23)\n", - " │ ├── BA (292)\n", - " │ ├── CEA (536)\n", - " │ │ ├── CEAc (544)\n", - " │ │ ├── CEAl (551)\n", - " │ │ └── CEAm (559)\n", - " │ ├── IA (1105)\n", - " │ └── MEA (403)\n", - " └── CTX (688)\n", - " ├── CTXpl (695)\n", - " │ ├── HPF (1089)\n", - " │ │ ├── HIP (1080)\n", - " │ │ │ ├── CA (375)\n", - " │ │ │ │ ├── CA1 (382)\n", - " │ │ │ │ ├── CA2 (423)\n", - " │ │ │ │ └── CA3 (463)\n", - " │ │ │ ├── DG (726)\n", - " │ │ │ │ ├── DG-mo (10703)\n", - " │ │ │ │ ├── DG-po (10704)\n", - " │ │ │ │ └── DG-sg (632)\n", - " │ │ │ ├── FC (982)\n", - " │ │ │ └── IG (19)\n", - " │ │ └── RHP (822)\n", - " │ │ ├── APr (484682508)\n", - " │ │ ├── ENT (909)\n", - " │ │ │ ├── ENTl (918)\n", - " │ │ │ │ ├── ENTl1 (1121)\n", - " │ │ │ │ ├── ENTl2 (20)\n", - " │ │ │ │ ├── ENTl3 (52)\n", - " │ │ │ │ ├── ENTl5 (139)\n", - " │ │ │ │ └── ENTl6a (28)\n", - " │ │ │ └── ENTm (926)\n", - " │ │ │ ├── ENTm1 (526)\n", - " │ │ │ ├── ENTm2 (543)\n", - " │ │ │ ├── ENTm3 (664)\n", - " │ │ │ ├── ENTm5 (727)\n", - " │ │ │ └── ENTm6 (743)\n", - " │ │ ├── HATA (589508447)\n", - " │ │ ├── PAR (843)\n", - " │ │ ├── POST (1037)\n", - " │ │ ├── PRE (1084)\n", - " │ │ ├── ProS (484682470)\n", - " │ │ └── SUB (502)\n", - " │ ├── Isocortex (315)\n", - " │ │ ├── ACA (31)\n", - " │ │ │ ├── ACAd (39)\n", - " │ │ │ │ ├── ACAd1 (935)\n", - " │ │ │ │ ├── ACAd2/3 (211)\n", - " │ │ │ │ ├── ACAd5 (1015)\n", - " │ │ │ │ ├── ACAd6a (919)\n", - " │ │ │ │ └── ACAd6b (927)\n", - " │ │ │ └── ACAv (48)\n", - " │ │ │ ├── ACAv1 (588)\n", - " │ │ │ ├── ACAv2/3 (296)\n", - " │ │ │ ├── ACAv5 (772)\n", - " │ │ │ ├── ACAv6a (810)\n", - " │ │ │ └── ACAv6b (819)\n", - " │ │ ├── AI (95)\n", - " │ │ │ ├── AId (104)\n", - " │ │ │ │ ├── AId1 (996)\n", - " │ │ │ │ ├── AId2/3 (328)\n", - " │ │ │ │ ├── AId5 (1101)\n", - " │ │ │ │ ├── AId6a (783)\n", - " │ │ │ │ └── AId6b (831)\n", - " │ │ │ ├── AIp (111)\n", - " │ │ │ │ ├── AIp1 (120)\n", - " │ │ │ │ ├── AIp2/3 (163)\n", - " │ │ │ │ ├── AIp5 (344)\n", - " │ │ │ │ ├── AIp6a (314)\n", - " │ │ │ │ └── AIp6b (355)\n", - " │ │ │ └── AIv (119)\n", - " │ │ │ ├── AIv1 (704)\n", - " │ │ │ ├── AIv2/3 (694)\n", - " │ │ │ ├── AIv5 (800)\n", - " │ │ │ ├── AIv6a (675)\n", - " │ │ │ └── AIv6b (699)\n", - " │ │ ├── AUD (247)\n", - " │ │ │ ├── AUDd (1011)\n", - " │ │ │ │ ├── AUDd1 (527)\n", - " │ │ │ │ ├── AUDd2/3 (600)\n", - " │ │ │ │ ├── AUDd4 (678)\n", - " │ │ │ │ ├── AUDd5 (252)\n", - " │ │ │ │ ├── AUDd6a (156)\n", - " │ │ │ │ └── AUDd6b (243)\n", - " │ │ │ ├── AUDp (1002)\n", - " │ │ │ │ ├── AUDp1 (735)\n", - " │ │ │ │ ├── AUDp2/3 (251)\n", - " │ │ │ │ ├── AUDp4 (816)\n", - " │ │ │ │ ├── AUDp5 (847)\n", - " │ │ │ │ ├── AUDp6a (954)\n", - " │ │ │ │ └── AUDp6b (1005)\n", - " │ │ │ ├── AUDpo (1027)\n", - " │ │ │ │ ├── AUDpo1 (696)\n", - " │ │ │ │ ├── AUDpo2/3 (643)\n", - " │ │ │ │ ├── AUDpo4 (759)\n", - " │ │ │ │ ├── AUDpo5 (791)\n", - " │ │ │ │ ├── AUDpo6a (249)\n", - " │ │ │ │ └── AUDpo6b (456)\n", - " │ │ │ └── AUDv (1018)\n", - " │ │ │ ├── AUDv1 (959)\n", - " │ │ │ ├── AUDv2/3 (755)\n", - " │ │ │ ├── AUDv4 (990)\n", - " │ │ │ ├── AUDv5 (1023)\n", - " │ │ │ ├── AUDv6a (520)\n", - " │ │ │ └── AUDv6b (598)\n", - " │ │ ├── ECT (895)\n", - " │ │ │ ├── ECT1 (836)\n", - " │ │ │ ├── ECT2/3 (427)\n", - " │ │ │ ├── ECT5 (988)\n", - " │ │ │ ├── ECT6a (977)\n", - " │ │ │ └── ECT6b (1045)\n", - " │ │ ├── FRP (184)\n", - " │ │ │ ├── FRP1 (68)\n", - " │ │ │ ├── FRP2/3 (667)\n", - " │ │ │ ├── FRP5 (526157192)\n", - " │ │ │ ├── FRP6a (526157196)\n", - " │ │ │ └── FRP6b (526322264)\n", - " │ │ ├── GU (1057)\n", - " │ │ │ ├── GU1 (36)\n", - " │ │ │ ├── GU2/3 (180)\n", - " │ │ │ ├── GU4 (148)\n", - " │ │ │ ├── GU5 (187)\n", - " │ │ │ ├── GU6a (638)\n", - " │ │ │ └── GU6b (662)\n", - " │ │ ├── ILA (44)\n", - " │ │ │ ├── ILA1 (707)\n", - " │ │ │ ├── ILA2/3 (556)\n", - " │ │ │ ├── ILA5 (827)\n", - " │ │ │ ├── ILA6a (1054)\n", - " │ │ │ └── ILA6b (1081)\n", - " │ │ ├── MO (500)\n", - " │ │ │ ├── MOp (985)\n", - " │ │ │ │ ├── MOp1 (320)\n", - " │ │ │ │ ├── MOp2/3 (943)\n", - " │ │ │ │ ├── MOp5 (648)\n", - " │ │ │ │ ├── MOp6a (844)\n", - " │ │ │ │ └── MOp6b (882)\n", - " │ │ │ └── MOs (993)\n", - " │ │ │ ├── MOs1 (656)\n", - " │ │ │ ├── MOs2/3 (962)\n", - " │ │ │ ├── MOs5 (767)\n", - " │ │ │ ├── MOs6a (1021)\n", - " │ │ │ └── MOs6b (1085)\n", - " │ │ ├── ORB (714)\n", - " │ │ │ ├── ORBl (723)\n", - " │ │ │ │ ├── ORBl1 (448)\n", - " │ │ │ │ ├── ORBl2/3 (412)\n", - " │ │ │ │ ├── ORBl5 (630)\n", - " │ │ │ │ ├── ORBl6a (440)\n", - " │ │ │ │ └── ORBl6b (488)\n", - " │ │ │ ├── ORBm (731)\n", - " │ │ │ │ ├── ORBm1 (484)\n", - " │ │ │ │ ├── ORBm2/3 (582)\n", - " │ │ │ │ ├── ORBm5 (620)\n", - " │ │ │ │ ├── ORBm6a (910)\n", - " │ │ │ │ └── ORBm6b (527696977)\n", - " │ │ │ └── ORBvl (746)\n", - " │ │ │ ├── ORBvl1 (969)\n", - " │ │ │ ├── ORBvl2/3 (288)\n", - " │ │ │ ├── ORBvl5 (1125)\n", - " │ │ │ ├── ORBvl6a (608)\n", - " │ │ │ └── ORBvl6b (680)\n", - " │ │ ├── PERI (922)\n", - " │ │ │ ├── PERI1 (540)\n", - " │ │ │ ├── PERI2/3 (888)\n", - " │ │ │ ├── PERI5 (692)\n", - " │ │ │ ├── PERI6a (335)\n", - " │ │ │ └── PERI6b (368)\n", - " │ │ ├── PL (972)\n", - " │ │ │ ├── PL1 (171)\n", - " │ │ │ ├── PL2/3 (304)\n", - " │ │ │ ├── PL5 (363)\n", - " │ │ │ ├── PL6a (84)\n", - " │ │ │ └── PL6b (132)\n", - " │ │ ├── PTLp (22)\n", - " │ │ │ ├── VISa (312782546)\n", - " │ │ │ │ ├── VISa1 (312782550)\n", - " │ │ │ │ ├── VISa2/3 (312782554)\n", - " │ │ │ │ ├── VISa4 (312782558)\n", - " │ │ │ │ ├── VISa5 (312782562)\n", - " │ │ │ │ ├── VISa6a (312782566)\n", - " │ │ │ │ └── VISa6b (312782570)\n", - " │ │ │ └── VISrl (417)\n", - " │ │ │ ├── VISrl1 (312782604)\n", - " │ │ │ ├── VISrl2/3 (312782608)\n", - " │ │ │ ├── VISrl4 (312782612)\n", - " │ │ │ ├── VISrl5 (312782616)\n", - " │ │ │ ├── VISrl6a (312782620)\n", - " │ │ │ └── VISrl6b (312782624)\n", - " │ │ ├── RSP (254)\n", - " │ │ │ ├── RSPagl (894)\n", - " │ │ │ │ ├── RSPagl1 (671)\n", - " │ │ │ │ ├── RSPagl2/3 (965)\n", - " │ │ │ │ ├── RSPagl5 (774)\n", - " │ │ │ │ ├── RSPagl6a (906)\n", - " │ │ │ │ └── RSPagl6b (279)\n", - " │ │ │ ├── RSPd (879)\n", - " │ │ │ │ ├── RSPd1 (442)\n", - " │ │ │ │ ├── RSPd2/3 (434)\n", - " │ │ │ │ ├── RSPd4 (545)\n", - " │ │ │ │ ├── RSPd5 (610)\n", - " │ │ │ │ ├── RSPd6a (274)\n", - " │ │ │ │ └── RSPd6b (330)\n", - " │ │ │ └── RSPv (886)\n", - " │ │ │ ├── RSPv1 (542)\n", - " │ │ │ ├── RSPv2/3 (430)\n", - " │ │ │ ├── RSPv5 (687)\n", - " │ │ │ ├── RSPv6a (590)\n", - " │ │ │ └── RSPv6b (622)\n", - " │ │ ├── SS (453)\n", - " │ │ │ ├── SSp (322)\n", - " │ │ │ │ ├── SSp-bfd (329)\n", - " │ │ │ │ │ ├── SSp-bfd1 (981)\n", - " │ │ │ │ │ ├── SSp-bfd2/3 (201)\n", - " │ │ │ │ │ ├── SSp-bfd4 (1047)\n", - " │ │ │ │ │ ├── SSp-bfd5 (1070)\n", - " │ │ │ │ │ ├── SSp-bfd6a (1038)\n", - " │ │ │ │ │ └── SSp-bfd6b (1062)\n", - " │ │ │ │ ├── SSp-ll (337)\n", - " │ │ │ │ │ ├── SSp-ll1 (1030)\n", - " │ │ │ │ │ ├── SSp-ll2/3 (113)\n", - " │ │ │ │ │ ├── SSp-ll4 (1094)\n", - " │ │ │ │ │ ├── SSp-ll5 (1128)\n", - " │ │ │ │ │ ├── SSp-ll6a (478)\n", - " │ │ │ │ │ └── SSp-ll6b (510)\n", - " │ │ │ │ ├── SSp-m (345)\n", - " │ │ │ │ │ ├── SSp-m1 (878)\n", - " │ │ │ │ │ ├── SSp-m2/3 (657)\n", - " │ │ │ │ │ ├── SSp-m4 (950)\n", - " │ │ │ │ │ ├── SSp-m5 (974)\n", - " │ │ │ │ │ ├── SSp-m6a (1102)\n", - " │ │ │ │ │ └── SSp-m6b (2)\n", - " │ │ │ │ ├── SSp-n (353)\n", - " │ │ │ │ │ ├── SSp-n1 (558)\n", - " │ │ │ │ │ ├── SSp-n2/3 (838)\n", - " │ │ │ │ │ ├── SSp-n4 (654)\n", - " │ │ │ │ │ ├── SSp-n5 (702)\n", - " │ │ │ │ │ ├── SSp-n6a (889)\n", - " │ │ │ │ │ └── SSp-n6b (929)\n", - " │ │ │ │ ├── SSp-tr (361)\n", - " │ │ │ │ │ ├── SSp-tr1 (1006)\n", - " │ │ │ │ │ ├── SSp-tr2/3 (670)\n", - " │ │ │ │ │ ├── SSp-tr4 (1086)\n", - " │ │ │ │ │ ├── SSp-tr5 (1111)\n", - " │ │ │ │ │ ├── SSp-tr6a (9)\n", - " │ │ │ │ │ └── SSp-tr6b (461)\n", - " │ │ │ │ ├── SSp-ul (369)\n", - " │ │ │ │ │ ├── SSp-ul1 (450)\n", - " │ │ │ │ │ ├── SSp-ul2/3 (854)\n", - " │ │ │ │ │ ├── SSp-ul4 (577)\n", - " │ │ │ │ │ ├── SSp-ul5 (625)\n", - " │ │ │ │ │ ├── SSp-ul6a (945)\n", - " │ │ │ │ │ └── SSp-ul6b (1026)\n", - " │ │ │ │ └── SSp-un (182305689)\n", - " │ │ │ │ ├── SSp-un1 (182305693)\n", - " │ │ │ │ ├── SSp-un2/3 (182305697)\n", - " │ │ │ │ ├── SSp-un4 (182305701)\n", - " │ │ │ │ ├── SSp-un5 (182305705)\n", - " │ │ │ │ ├── SSp-un6a (182305709)\n", - " │ │ │ │ └── SSp-un6b (182305713)\n", - " │ │ │ └── SSs (378)\n", - " │ │ │ ├── SSs1 (873)\n", - " │ │ │ ├── SSs2/3 (806)\n", - " │ │ │ ├── SSs4 (1035)\n", - " │ │ │ ├── SSs5 (1090)\n", - " │ │ │ ├── SSs6a (862)\n", - " │ │ │ └── SSs6b (893)\n", - " │ │ ├── TEa (541)\n", - " │ │ │ ├── TEa1 (97)\n", - " │ │ │ ├── TEa2/3 (1127)\n", - " │ │ │ ├── TEa4 (234)\n", - " │ │ │ ├── TEa5 (289)\n", - " │ │ │ ├── TEa6a (729)\n", - " │ │ │ └── TEa6b (786)\n", - " │ │ ├── VIS (669)\n", - " │ │ │ ├── VISal (402)\n", - " │ │ │ │ ├── VISal1 (1074)\n", - " │ │ │ │ ├── VISal2/3 (905)\n", - " │ │ │ │ ├── VISal4 (1114)\n", - " │ │ │ │ ├── VISal5 (233)\n", - " │ │ │ │ ├── VISal6a (601)\n", - " │ │ │ │ └── VISal6b (649)\n", - " │ │ │ ├── VISam (394)\n", - " │ │ │ │ ├── VISam1 (281)\n", - " │ │ │ │ ├── VISam2/3 (1066)\n", - " │ │ │ │ ├── VISam4 (401)\n", - " │ │ │ │ ├── VISam5 (433)\n", - " │ │ │ │ ├── VISam6a (1046)\n", - " │ │ │ │ └── VISam6b (441)\n", - " │ │ │ ├── VISl (409)\n", - " │ │ │ │ ├── VISl1 (421)\n", - " │ │ │ │ ├── VISl2/3 (973)\n", - " │ │ │ │ ├── VISl4 (573)\n", - " │ │ │ │ ├── VISl5 (613)\n", - " │ │ │ │ ├── VISl6a (74)\n", - " │ │ │ │ └── VISl6b (121)\n", - " │ │ │ ├── VISli (312782574)\n", - " │ │ │ │ ├── VISli1 (312782578)\n", - " │ │ │ │ ├── VISli2/3 (312782582)\n", - " │ │ │ │ ├── VISli4 (312782586)\n", - " │ │ │ │ ├── VISli5 (312782590)\n", - " │ │ │ │ ├── VISli6a (312782594)\n", - " │ │ │ │ └── VISli6b (312782598)\n", - " │ │ │ ├── VISp (385)\n", - " │ │ │ │ ├── VISp1 (593)\n", - " │ │ │ │ ├── VISp2/3 (821)\n", - " │ │ │ │ ├── VISp4 (721)\n", - " │ │ │ │ ├── VISp5 (778)\n", - " │ │ │ │ ├── VISp6a (33)\n", - " │ │ │ │ └── VISp6b (305)\n", - " │ │ │ ├── VISpl (425)\n", - " │ │ │ │ ├── VISpl1 (750)\n", - " │ │ │ │ ├── VISpl2/3 (269)\n", - " │ │ │ │ ├── VISpl4 (869)\n", - " │ │ │ │ ├── VISpl5 (902)\n", - " │ │ │ │ ├── VISpl6a (377)\n", - " │ │ │ │ └── VISpl6b (393)\n", - " │ │ │ ├── VISpm (533)\n", - " │ │ │ │ ├── VISpm1 (805)\n", - " │ │ │ │ ├── VISpm2/3 (41)\n", - " │ │ │ │ ├── VISpm4 (501)\n", - " │ │ │ │ ├── VISpm5 (565)\n", - " │ │ │ │ ├── VISpm6a (257)\n", - " │ │ │ │ └── VISpm6b (469)\n", - " │ │ │ └── VISpor (312782628)\n", - " │ │ │ ├── VISpor1 (312782632)\n", - " │ │ │ ├── VISpor2/3 (312782636)\n", - " │ │ │ ├── VISpor4 (312782640)\n", - " │ │ │ ├── VISpor5 (312782644)\n", - " │ │ │ ├── VISpor6a (312782648)\n", - " │ │ │ └── VISpor6b (312782652)\n", - " │ │ └── VISC (677)\n", - " │ │ ├── VISC1 (897)\n", - " │ │ ├── VISC2/3 (1106)\n", - " │ │ ├── VISC4 (1010)\n", - " │ │ ├── VISC5 (1058)\n", - " │ │ ├── VISC6a (857)\n", - " │ │ └── VISC6b (849)\n", - " │ └── OLF (698)\n", - " │ ├── AOB (151)\n", - " │ │ ├── AOBgl (188)\n", - " │ │ ├── AOBgr (196)\n", - " │ │ └── AOBmi (204)\n", - " │ ├── AON (159)\n", - " │ ├── COA (631)\n", - " │ │ ├── COAa (639)\n", - " │ │ └── COAp (647)\n", - " │ │ ├── COApl (655)\n", - " │ │ └── COApm (663)\n", - " │ ├── DP (814)\n", - " │ ├── MOB (507)\n", - " │ ├── NLOT (619)\n", - " │ │ ├── NLOT1 (260)\n", - " │ │ ├── NLOT2 (268)\n", - " │ │ └── NLOT3 (1139)\n", - " │ ├── PAA (788)\n", - " │ ├── PIR (961)\n", - " │ ├── TR (566)\n", - " │ └── TT (589)\n", - " │ ├── TTd (597)\n", - " │ └── TTv (605)\n", - " └── CTXsp (703)\n", - " ├── BLA (295)\n", - " │ ├── BLAa (303)\n", - " │ ├── BLAp (311)\n", - " │ └── BLAv (451)\n", - " ├── BMA (319)\n", - " │ ├── BMAa (327)\n", - " │ └── BMAp (334)\n", - " ├── CLA (583)\n", - " ├── EP (942)\n", - " │ ├── EPd (952)\n", - " │ └── EPv (966)\n", - " ├── LA (131)\n", - " └── PA (780)" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "bg_atlas.structures" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The structures attribute is a custom dictionary that can be queried by region number or acronym, and contains all the information for a given structure:" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{'acronym': 'root',\n", - " 'id': 997,\n", - " 'mesh': None,\n", - " 'mesh_filename': PosixPath('/home/rob/.brainglobe/allen_mouse_100um_v1.2/meshes/997.obj'),\n", - " 'name': 'root',\n", - " 'rgb_triplet': [255, 255, 255],\n", - " 'structure_id_path': [997]}\n" - ] - } - ], - "source": [ - "pprint(bg_atlas.structures[\"root\"])" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "In particular, the `structure_id_path` key contains a list description of the path in the hierarchy up to a particular region, and can be used for queries on the hierarchy." - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[997, 8, 567]" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "bg_atlas.structures[\"CH\"][\"structure_id_path\"]" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "We can use the `bg_atlas.get_structure_descendants` and `bg_atlas.get_structure_ancestors` methods to explore the hierarchy:" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['VISC1', 'VISC2/3', 'VISC4', 'VISC5', 'VISC6a', 'VISC6b']" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "bg_atlas.get_structure_descendants(\"VISC\")" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['root', 'grey', 'CH', 'CTX', 'CTXpl', 'Isocortex', 'VISC']" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "bg_atlas.get_structure_ancestors(\"VISC6a\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "---\n", - "**NOTE**: \n", - "the levels of the hierarchy depends on the underlying atlas, so we cannot ensure the goodness and consistency of their hierarchy three.\n", - "---" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "There is an higher level description of the structures hierarchy that is built using the [treelib](https://treelib.readthedocs.io/en/latest/) package, and is available as: " - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "bg_atlas.structures.tree" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "For most applications though the methods described above and the list path of each region should be enough to query the hierarchy without additional layers of complication." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 1.3 Region masks" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The `get_structure_mask` method returns a mask volume where all voxels belonging to an area or to the descendants of that area are non zero. All other voxels are zero. We will generate the structure mask for primary visual cortex to see how this works. \n", - "\n", - "Primary visual cortex (`VISp`) has an ID value of `385` but no voxels in the annotation image actually have that value:" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{'acronym': 'VISp',\n", - " 'id': 385,\n", - " 'mesh': None,\n", - " 'mesh_filename': PosixPath('/home/rob/.brainglobe/allen_mouse_100um_v1.2/meshes/385.obj'),\n", - " 'name': 'Primary visual area',\n", - " 'rgb_triplet': [8, 133, 140],\n", - " 'structure_id_path': [997, 8, 567, 688, 695, 315, 669, 385]}\n" - ] - } - ], - "source": [ - "pprint(bg_atlas.structures[\"VISp\"])" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# No voxels in the annotation volume are labelled as being VISp\n", - "(bg_atlas.annotation==385).sum()" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The reason no VISp voxels exist is because the annotation volume is segmented more finely. In this case `VISp` is divided into cortical layers and it is IDs associated with these layers that are present in the annotation volume." - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "['VISp1', 'VISp2/3', 'VISp4', 'VISp5', 'VISp6a', 'VISp6b']" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# The descendants (children) of VISp are cortical layers\n", - "bg_atlas.get_structure_descendants(\"VISp\")" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "VISp1\t593\n", - "VISp2/3\t821\n", - "VISp4\t721\n", - "VISp5\t778\n", - "VISp6a\t33\n", - "VISp6b\t305\n" - ] - } - ], - "source": [ - "# The IDs associated with each layer in primary visual cortex\n", - "layers = bg_atlas.get_structure_descendants(\"VISp\")\n", - "layer_ids = [bg_atlas.structures[this_layer]['id'] for this_layer in layers]\n", - "\n", - "for (this_layer, this_id) in zip(layers, layer_ids):\n", - " print(\"%s\\t%s\" % (this_layer, this_id))\n", - "\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "These IDs are indeed present in the annotation volume:" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "1565" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# For example, we find over a thousand voxels associated with primary visual cortex layer 6\n", - "# in the annotation volume\n", - "(bg_atlas.annotation==778).sum()" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "So lets use `get_structure_mask` to return a mask volume that retains only `VISp`." - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [], - "source": [ - "mask_VISp = bg_atlas.get_structure_mask('VISp')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", - "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", - " axs[i].imshow(mask_VISp.max(i), cmap=\"gray\")\n", - " axs[i].set_title(f\"{plane.capitalize()} view\")\n", - " axs[i].set_ylabel(labels[0])\n", - " axs[i].set_xlabel(labels[1])\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The `root` node encompases the whole brain and we can use this to provide a background image for the above area." - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [], - "source": [ - "mask_root = bg_atlas.get_structure_mask('root')\n", - "\n", - "# The mask images have pixel values equal to the ID of the parent area, so we change these for\n", - "# plotting purposes. \n", - "mask_root[mask_root>0]=5\n", - "mask_VISp[mask_VISp>0]=2\n", - "mask_VISp_root = mask_VISp + mask_root" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "space = bg_atlas.space\n", - "\n", - "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", - "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", - " axs[i].imshow(mask_VISp_root.max(i), cmap=\"gray\")\n", - " axs[i].set_title(f\"{plane.capitalize()} view\")\n", - " axs[i].set_ylabel(labels[0])\n", - " axs[i].set_xlabel(labels[1])\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 1.3 Regions meshes" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "If we need to access the structure meshes, we can either query for the file (e.g., if we need to load the file through some library like `vedo`):" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "PosixPath('/home/rob/.brainglobe/allen_mouse_100um_v1.2/meshes/567.obj')" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "bg_atlas.meshfile_from_structure(\"CH\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Or directly obtain the mesh, as a mesh object of the `meshio` library:" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "\n", - " Number of points: 56703\n", - " Number of cells:\n", - " triangle: 112948\n", - " Point data: obj:vn\n", - " Cell data: obj:group_ids" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "bg_atlas.mesh_from_structure(\"CH\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## 2 Query the `BrainGlobeAtlas`" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 2.0 Query for structures:" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "A very convenient feature of the `BrainGlobeAtlas` API is the simplicity of querying for the identity of the structure or the hemisphere at a given location, either from stack indexes or space coordinates, and even cutting the hierarchy at some higher level:" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "By index: CP\n", - "By coordinates: CP\n", - "Higher hierarchy level: CH\n" - ] - } - ], - "source": [ - "# Ask for identity of some indexes in the stack:\n", - "print(\"By index:\", bg_atlas.structure_from_coords((50, 40, 30), \n", - " as_acronym=True))\n", - "\n", - "# Now give coordinates in microns\n", - "print(\"By coordinates:\", bg_atlas.structure_from_coords((5000, 4000, 3000), \n", - " as_acronym=True, \n", - " microns=True))\n", - "\n", - "# Now cut hierarchy at some level\n", - "print(\"Higher hierarchy level:\", bg_atlas.structure_from_coords((5000, 4000, 3000), \n", - " as_acronym=True, \n", - " microns=True, \n", - " hierarchy_lev=2))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 2.1 Query for hemispheres" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "A very similar method can be used for hemispheres. 0 correspond to outside the brain, a,d 1 and 2 to left and right hemispheres - but we can just ask for the side name instead of the number:" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "By index: 2\n", - "By coordinates: 2\n", - "By : 2\n" - ] - } - ], - "source": [ - "# Ask for identity of some indexes in the stack:\n", - "print(\"By index:\", bg_atlas.hemisphere_from_coords((50, 40, 30)))\n", - "\n", - "# Now give coordinates in microns\n", - "print(\"By coordinates:\", bg_atlas.hemisphere_from_coords((5000, 4000, 3000), microns=True))\n", - "\n", - "# Now print side string\n", - "print(\"By :\", bg_atlas.hemisphere_from_coords((5000, 4000, 3000), microns=True))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.8.10" - } - }, - "nbformat": 4, - "nbformat_minor": 4 + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Introduction to the `BrainGlobeAtlas` class" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 0. Creating a `BrainGlobeAtlas` object and list availabe options" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "To instantiate a `BrainGlobeAtlas` object, we need to instantiate it with the atlas name. The first time we use it, a version of this atlas files will be downloaded from the [remote GIN repository](http://gin.g-node.org/brainglobe/atlases) and stored on your local machine (by default, in .../Users/username/.brainglobe):" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "allen mouse atlas (res. 100um)\n", + "From: http://www.brain-map.org (Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007 )\n" + ] + } + ], + "source": [ + "import numpy as np\n", + "from brainglobe_atlasapi import BrainGlobeAtlas\n", + "from pprint import pprint\n", + "\n", + "bg_atlas = BrainGlobeAtlas(\"allen_mouse_100um\", check_latest=False)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "To know what atlases are available through BrainGlobe, we can use the `show_atlases` function (we need to be online):" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
                                                                                  \n",
+                            "                                                                                  \n",
+                            "                                Brainglobe Atlases                                \n",
+                            "╭──────────────────────────────────┬────────────┬───────────────┬────────────────╮\n",
+                            "│ Name                             │ Downloaded │ Local version │ Latest version │\n",
+                            "├──────────────────────────────────┼────────────┼───────────────┼────────────────┤\n",
+                            "│ whs_sd_rat_39um                  │     ✔      │      1.0      │      1.0       │\n",
+                            "│ allen_mouse_25um                 │     ✔      │      1.2      │      1.2       │\n",
+                            "│ allen_mouse_100um                │     ✔      │      1.2      │      1.2       │\n",
+                            "│ allen_mouse_50um                 │     ✔      │      1.2      │      1.2       │\n",
+                            "│ example_mouse_100um              │    ---     │      ---      │      1.2       │\n",
+                            "│ allen_mouse_10um                 │    ---     │      ---      │      1.2       │\n",
+                            "│ mpin_zfish_1um                   │    ---     │      ---      │      1.0       │\n",
+                            "│ allen_human_500um                │    ---     │      ---      │      0.1       │\n",
+                            "│ kim_mouse_10um                   │    ---     │      ---      │      1.0       │\n",
+                            "│ kim_mouse_25um                   │    ---     │      ---      │      1.0       │\n",
+                            "│ kim_mouse_50um                   │    ---     │      ---      │      1.0       │\n",
+                            "│ kim_mouse_100um                  │    ---     │      ---      │      1.0       │\n",
+                            "│ osten_mouse_10um                 │    ---     │      ---      │      1.1       │\n",
+                            "│ osten_mouse_25um                 │    ---     │      ---      │      1.1       │\n",
+                            "│ osten_mouse_50um                 │    ---     │      ---      │      1.1       │\n",
+                            "│ osten_mouse_100um                │    ---     │      ---      │      1.1       │\n",
+                            "│ allen_cord_20um                  │    ---     │      ---      │      1.0       │\n",
+                            "│ azba_zfish_4um                   │    ---     │      ---      │      1.1       │\n",
+                            "│ perens_lsfm_mouse_20um           │    ---     │      ---      │      1.0       │\n",
+                            "│ admba_3d_e11_5_mouse_16um        │    ---     │      ---      │      1.0       │\n",
+                            "│ admba_3d_e13_5_mouse_16um        │    ---     │      ---      │      1.0       │\n",
+                            "│ admba_3d_e15_5_mouse_16um        │    ---     │      ---      │      1.0       │\n",
+                            "│ admba_3d_e18_5_mouse_16um        │    ---     │      ---      │      1.0       │\n",
+                            "│ admba_3d_p4_mouse_16.752um       │    ---     │      ---      │      1.0       │\n",
+                            "│ admba_3d_p14_mouse_16.752um      │    ---     │      ---      │      1.0       │\n",
+                            "│ admba_3d_p28_mouse_16.752um      │    ---     │      ---      │      1.0       │\n",
+                            "│ admba_3d_p56_mouse_25um          │    ---     │      ---      │      1.0       │\n",
+                            "╰──────────────────────────────────┴────────────┴───────────────┴────────────────╯\n",
+                            "
\n" + ], + "text/plain": [ + "\u001b[3m \u001b[0m\n", + "\u001b[3m \u001b[0m\n", + "\u001b[3m Brainglobe Atlases \u001b[0m\n", + "╭──────────────────────────────────┬────────────┬───────────────┬────────────────╮\n", + "│\u001b[1;32m \u001b[0m\u001b[1;32mName \u001b[0m\u001b[1;32m \u001b[0m│\u001b[1;32m \u001b[0m\u001b[1;32mDownloaded\u001b[0m\u001b[1;32m \u001b[0m│\u001b[1;32m \u001b[0m\u001b[1;32mLocal version\u001b[0m\u001b[1;32m \u001b[0m│\u001b[1;32m \u001b[0m\u001b[1;32mLatest version\u001b[0m\u001b[1;32m \u001b[0m│\n", + "├──────────────────────────────────┼────────────┼───────────────┼────────────────┤\n", + "│ \u001b[1mwhs_sd_rat_39um\u001b[0m │ \u001b[32m✔\u001b[0m │ 1.0 │ 1.0 │\n", + "│ \u001b[1mallen_mouse_25um\u001b[0m │ \u001b[32m✔\u001b[0m │ 1.2 │ 1.2 │\n", + "│ \u001b[1mallen_mouse_100um\u001b[0m │ \u001b[32m✔\u001b[0m │ 1.2 │ 1.2 │\n", + "│ \u001b[1mallen_mouse_50um\u001b[0m │ \u001b[32m✔\u001b[0m │ 1.2 │ 1.2 │\n", + "│ \u001b[1mexample_mouse_100um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.2 │\n", + "│ \u001b[1mallen_mouse_10um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.2 │\n", + "│ \u001b[1mmpin_zfish_1um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1mallen_human_500um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 0.1 │\n", + "│ \u001b[1mkim_mouse_10um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1mkim_mouse_25um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1mkim_mouse_50um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1mkim_mouse_100um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1mosten_mouse_10um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", + "│ \u001b[1mosten_mouse_25um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", + "│ \u001b[1mosten_mouse_50um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", + "│ \u001b[1mosten_mouse_100um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", + "│ \u001b[1mallen_cord_20um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1mazba_zfish_4um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.1 │\n", + "│ \u001b[1mperens_lsfm_mouse_20um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1madmba_3d_e11_5_mouse_16um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1madmba_3d_e13_5_mouse_16um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1madmba_3d_e15_5_mouse_16um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1madmba_3d_e18_5_mouse_16um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1madmba_3d_p4_mouse_16.752um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1madmba_3d_p14_mouse_16.752um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1madmba_3d_p28_mouse_16.752um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "│ \u001b[1madmba_3d_p56_mouse_25um\u001b[0m │ \u001b[31m---\u001b[0m │ \u001b[31m---\u001b[0m │ 1.0 │\n", + "╰──────────────────────────────────┴────────────┴───────────────┴────────────────╯\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "from brainglobe_atlasapi import show_atlases\n", + "show_atlases()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Using a `BrainGlobe` atlas" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "A BrainGlobe atlas is a convenient API for interacting with an anatomical atlas. BrainGlobe atlases contain:\n", + " * Metadata\n", + " * The reference anatomical stack used for the registration itself\n", + " * Region annotation stack (the segmented atlas image that occupies the same space as the reference stack)\n", + " * Hemisphere annotation stack which denotes left and right\n", + " * Description of the region hierarchy\n", + " * Meshes for the regions" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 1.0 Metadata" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "All atlases have a standard set of medatata describing their source, species, resolution, etc:" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'name': 'allen_mouse',\n", + " 'citation': 'Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007',\n", + " 'atlas_link': 'http://www.brain-map.org',\n", + " 'species': 'Mus musculus',\n", + " 'symmetric': True,\n", + " 'resolution': [100.0, 100.0, 100.0],\n", + " 'orientation': 'asr',\n", + " 'version': '1.2',\n", + " 'shape': [132, 80, 114],\n", + " 'trasform_to_bg': [[1.0, 0.0, 0.0, 0.0],\n", + " [0.0, 1.0, 0.0, 0.0],\n", + " [0.0, 0.0, 1.0, 0.0],\n", + " [0.0, 0.0, 0.0, 1.0]],\n", + " 'additional_references': []}" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bg_atlas.metadata" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 1.1 Anatomical, annotation and hemispheres stack" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "from matplotlib import pyplot as plt" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Anatomical reference:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "space = bg_atlas.space\n", + "stack = bg_atlas.reference\n", + "\n", + "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", + "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", + " mid_index = stack.shape[i]//2\n", + " axs[i].imshow(np.moveaxis(stack,i,0)[mid_index,:,:], cmap=\"gray\",clim=(0,250))\n", + " axs[i].set_title(f\"{plane.capitalize()} view\")\n", + " axs[i].set_ylabel(labels[0])\n", + " axs[i].set_xlabel(labels[1])" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Annotations stack:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "space = bg_atlas.space\n", + "stack = bg_atlas.annotation\n", + "\n", + "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", + "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", + " mid_index = stack.shape[i]//2\n", + " axs[i].imshow(np.moveaxis(stack,i,0)[mid_index,:,:], cmap=\"gray\",clim=(0,1250))\n", + " axs[i].set_title(f\"{plane.capitalize()} view\")\n", + " axs[i].set_ylabel(labels[0])\n", + " axs[i].set_xlabel(labels[1])\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "space = bg_atlas.space\n", + "stack = bg_atlas.hemispheres\n", + "\n", + "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", + "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", + " axs[i].imshow(stack.max(i), cmap=\"gray\")\n", + " axs[i].set_title(f\"{plane.capitalize()} view\")\n", + " axs[i].set_ylabel(labels[0])\n", + " axs[i].set_xlabel(labels[1])" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 1.2 Regions hierarchy" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The atlas comes with the description of a hierarchy of brain structures. To have an overview:" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "root (997)\n", + "├── VS (73)\n", + "│ ├── AQ (140)\n", + "│ ├── V3 (129)\n", + "│ ├── V4 (145)\n", + "│ │ └── V4r (153)\n", + "│ ├── VL (81)\n", + "│ │ ├── SEZ (98)\n", + "│ │ └── chpl (108)\n", + "│ └── c (164)\n", + "├── fiber tracts (1009)\n", + "│ ├── cbf (960)\n", + "│ │ ├── arb (728)\n", + "│ │ ├── cbc (744)\n", + "│ │ └── cbp (752)\n", + "│ │ ├── icp (1123)\n", + "│ │ │ └── sctd (553)\n", + "│ │ ├── mcp (78)\n", + "│ │ └── scp (326)\n", + "│ │ ├── dscp (812)\n", + "│ │ ├── sctv (866)\n", + "│ │ └── uf (850)\n", + "│ ├── cm (967)\n", + "│ │ ├── IIIn (832)\n", + "│ │ │ ├── mlf (62)\n", + "│ │ │ └── pc (158)\n", + "│ │ ├── IIn (848)\n", + "│ │ │ ├── bsc (916)\n", + "│ │ │ ├── csc (336)\n", + "│ │ │ ├── och (117)\n", + "│ │ │ └── opt (125)\n", + "│ │ ├── IVn (911)\n", + "│ │ ├── In (840)\n", + "│ │ │ ├── aco (900)\n", + "│ │ │ ├── lotg (21)\n", + "│ │ │ │ ├── lot (665)\n", + "│ │ │ │ └── lotd (538)\n", + "│ │ │ └── onl (1016)\n", + "│ │ ├── VIIIn (933)\n", + "│ │ │ ├── cVIIIn (948)\n", + "│ │ │ │ ├── bic (482)\n", + "│ │ │ │ ├── cic (633)\n", + "│ │ │ │ ├── das (506)\n", + "│ │ │ │ ├── ll (658)\n", + "│ │ │ │ └── tb (841)\n", + "│ │ │ └── vVIIIn (413)\n", + "│ │ ├── VIIn (798)\n", + "│ │ │ └── gVIIn (1116)\n", + "│ │ ├── Vn (901)\n", + "│ │ │ ├── moV (93)\n", + "│ │ │ └── sV (229)\n", + "│ │ │ └── sptV (794)\n", + "│ │ ├── Xn (917)\n", + "│ │ │ └── ts (237)\n", + "│ │ ├── drt (792)\n", + "│ │ │ └── cett (932)\n", + "│ │ │ ├── dc (514)\n", + "│ │ │ │ └── cuf (380)\n", + "│ │ │ └── ml (697)\n", + "│ │ └── von (949)\n", + "│ ├── eps (1000)\n", + "│ │ ├── epsc (760)\n", + "│ │ │ └── nst (102)\n", + "│ │ ├── rust (863)\n", + "│ │ │ └── vtd (397)\n", + "│ │ └── tsp (877)\n", + "│ │ ├── dtd (1060)\n", + "│ │ ├── tspc (1043)\n", + "│ │ └── tspd (1051)\n", + "│ ├── lfbs (983)\n", + "│ │ ├── cc (776)\n", + "│ │ │ ├── ccb (484682516)\n", + "│ │ │ ├── ccg (1108)\n", + "│ │ │ ├── ccs (986)\n", + "│ │ │ ├── ee (964)\n", + "│ │ │ ├── fa (956)\n", + "│ │ │ │ └── ec (579)\n", + "│ │ │ └── fp (971)\n", + "│ │ ├── cst (784)\n", + "│ │ │ ├── cpd (924)\n", + "│ │ │ ├── int (6)\n", + "│ │ │ ├── py (190)\n", + "│ │ │ └── pyd (198)\n", + "│ │ └── lfbst (896)\n", + "│ │ ├── ar (484682524)\n", + "│ │ ├── em (1092)\n", + "│ │ └── or (484682520)\n", + "│ ├── mfbs (991)\n", + "│ │ ├── mfbc (768)\n", + "│ │ │ ├── act (908)\n", + "│ │ │ ├── amc (884)\n", + "│ │ │ ├── cing (940)\n", + "│ │ │ ├── fxs (1099)\n", + "│ │ │ │ ├── alv (466)\n", + "│ │ │ │ ├── df (530)\n", + "│ │ │ │ ├── fi (603)\n", + "│ │ │ │ ├── fxpo (737)\n", + "│ │ │ │ │ ├── fx (436)\n", + "│ │ │ │ │ └── mct (428)\n", + "│ │ │ │ └── hc (618)\n", + "│ │ │ │ ├── dhc (443)\n", + "│ │ │ │ └── vhc (449)\n", + "│ │ │ └── st (301)\n", + "│ │ │ └── stc (484682528)\n", + "│ │ └── mfsbshy (824)\n", + "│ │ ├── mfb (54)\n", + "│ │ ├── mfbse (1083)\n", + "│ │ │ ├── fr (595)\n", + "│ │ │ ├── hbc (611)\n", + "│ │ │ └── sm (802)\n", + "│ │ ├── mfbsma (46)\n", + "│ │ │ ├── mp (673)\n", + "│ │ │ ├── mtg (681)\n", + "│ │ │ ├── mtt (690)\n", + "│ │ │ └── pm (753)\n", + "│ │ └── sup (349)\n", + "│ └── scwm (484682512)\n", + "└── grey (8)\n", + " ├── BS (343)\n", + " │ ├── HB (1065)\n", + " │ │ ├── MY (354)\n", + " │ │ │ ├── MY-mot (370)\n", + " │ │ │ │ ├── ACVII (576)\n", + " │ │ │ │ ├── AMB (135)\n", + " │ │ │ │ │ ├── AMBd (939)\n", + " │ │ │ │ │ └── AMBv (143)\n", + " │ │ │ │ ├── DMX (839)\n", + " │ │ │ │ ├── GRN (1048)\n", + " │ │ │ │ ├── ICB (372)\n", + " │ │ │ │ ├── IO (83)\n", + " │ │ │ │ ├── IRN (136)\n", + " │ │ │ │ ├── ISN (106)\n", + " │ │ │ │ ├── LIN (203)\n", + " │ │ │ │ ├── LRN (235)\n", + " │ │ │ │ │ ├── LRNm (955)\n", + " │ │ │ │ │ └── LRNp (963)\n", + " │ │ │ │ ├── MARN (307)\n", + " │ │ │ │ ├── MDRN (395)\n", + " │ │ │ │ │ ├── MDRNd (1098)\n", + " │ │ │ │ │ └── MDRNv (1107)\n", + " │ │ │ │ ├── PARN (852)\n", + " │ │ │ │ ├── PAS (859)\n", + " │ │ │ │ ├── PGRN (938)\n", + " │ │ │ │ │ ├── PGRNd (970)\n", + " │ │ │ │ │ └── PGRNl (978)\n", + " │ │ │ │ ├── PHY (154)\n", + " │ │ │ │ │ ├── NR (177)\n", + " │ │ │ │ │ └── PRP (169)\n", + " │ │ │ │ ├── PPY (1069)\n", + " │ │ │ │ ├── VI (653)\n", + " │ │ │ │ ├── VII (661)\n", + " │ │ │ │ ├── VNC (701)\n", + " │ │ │ │ │ ├── LAV (209)\n", + " │ │ │ │ │ ├── MV (202)\n", + " │ │ │ │ │ ├── SPIV (225)\n", + " │ │ │ │ │ └── SUV (217)\n", + " │ │ │ │ ├── XII (773)\n", + " │ │ │ │ ├── x (765)\n", + " │ │ │ │ └── y (781)\n", + " │ │ │ ├── MY-sat (379)\n", + " │ │ │ │ ├── RM (206)\n", + " │ │ │ │ ├── RO (222)\n", + " │ │ │ │ └── RPA (230)\n", + " │ │ │ └── MY-sen (386)\n", + " │ │ │ ├── AP (207)\n", + " │ │ │ ├── CN (607)\n", + " │ │ │ │ ├── DCO (96)\n", + " │ │ │ │ └── VCO (101)\n", + " │ │ │ ├── DCN (720)\n", + " │ │ │ │ ├── CU (711)\n", + " │ │ │ │ └── GR (1039)\n", + " │ │ │ ├── ECU (903)\n", + " │ │ │ ├── NTB (642)\n", + " │ │ │ ├── NTS (651)\n", + " │ │ │ ├── Pa5 (589508451)\n", + " │ │ │ ├── SPVC (429)\n", + " │ │ │ ├── SPVI (437)\n", + " │ │ │ └── SPVO (445)\n", + " │ │ └── P (771)\n", + " │ │ ├── P-mot (987)\n", + " │ │ │ ├── Acs5 (549009219)\n", + " │ │ │ ├── B (280)\n", + " │ │ │ ├── DTN (880)\n", + " │ │ │ ├── I5 (549009227)\n", + " │ │ │ ├── P5 (549009215)\n", + " │ │ │ ├── PC5 (549009223)\n", + " │ │ │ ├── PCG (898)\n", + " │ │ │ ├── PDTg (599626927)\n", + " │ │ │ ├── PG (931)\n", + " │ │ │ ├── PRNc (1093)\n", + " │ │ │ ├── SG (318)\n", + " │ │ │ ├── SUT (534)\n", + " │ │ │ ├── TRN (574)\n", + " │ │ │ └── V (621)\n", + " │ │ ├── P-sat (1117)\n", + " │ │ │ ├── CS (679)\n", + " │ │ │ ├── LC (147)\n", + " │ │ │ ├── LDT (162)\n", + " │ │ │ ├── NI (604)\n", + " │ │ │ ├── PRNr (146)\n", + " │ │ │ ├── RPO (238)\n", + " │ │ │ ├── SLC (350)\n", + " │ │ │ └── SLD (358)\n", + " │ │ └── P-sen (1132)\n", + " │ │ ├── NLL (612)\n", + " │ │ ├── PB (867)\n", + " │ │ │ └── KF (123)\n", + " │ │ ├── PSV (7)\n", + " │ │ └── SOC (398)\n", + " │ │ ├── POR (122)\n", + " │ │ ├── SOCl (114)\n", + " │ │ └── SOCm (105)\n", + " │ ├── IB (1129)\n", + " │ │ ├── HY (1097)\n", + " │ │ │ ├── LZ (290)\n", + " │ │ │ │ ├── LHA (194)\n", + " │ │ │ │ ├── LPO (226)\n", + " │ │ │ │ ├── PST (356)\n", + " │ │ │ │ ├── PSTN (364)\n", + " │ │ │ │ ├── PeF (576073704)\n", + " │ │ │ │ ├── RCH (173)\n", + " │ │ │ │ ├── STN (470)\n", + " │ │ │ │ ├── TU (614)\n", + " │ │ │ │ └── ZI (797)\n", + " │ │ │ │ └── FF (804)\n", + " │ │ │ ├── ME (10671)\n", + " │ │ │ ├── MEZ (467)\n", + " │ │ │ │ ├── AHN (88)\n", + " │ │ │ │ ├── MBO (331)\n", + " │ │ │ │ │ ├── LM (210)\n", + " │ │ │ │ │ ├── MM (491)\n", + " │ │ │ │ │ │ ├── MMd (606826659)\n", + " │ │ │ │ │ │ ├── MMl (606826647)\n", + " │ │ │ │ │ │ ├── MMm (606826651)\n", + " │ │ │ │ │ │ ├── MMme (732)\n", + " │ │ │ │ │ │ └── MMp (606826655)\n", + " │ │ │ │ │ ├── SUM (525)\n", + " │ │ │ │ │ └── TM (557)\n", + " │ │ │ │ │ ├── TMd (1126)\n", + " │ │ │ │ │ └── TMv (1)\n", + " │ │ │ │ ├── MPN (515)\n", + " │ │ │ │ ├── PH (946)\n", + " │ │ │ │ ├── PMd (980)\n", + " │ │ │ │ ├── PMv (1004)\n", + " │ │ │ │ ├── PVHd (63)\n", + " │ │ │ │ └── VMH (693)\n", + " │ │ │ ├── PVR (141)\n", + " │ │ │ │ ├── ADP (72)\n", + " │ │ │ │ ├── AVP (263)\n", + " │ │ │ │ ├── AVPV (272)\n", + " │ │ │ │ ├── DMH (830)\n", + " │ │ │ │ ├── MEPO (452)\n", + " │ │ │ │ ├── MPO (523)\n", + " │ │ │ │ ├── OV (763)\n", + " │ │ │ │ ├── PD (914)\n", + " │ │ │ │ ├── PS (1109)\n", + " │ │ │ │ ├── PVp (126)\n", + " │ │ │ │ ├── PVpo (133)\n", + " │ │ │ │ ├── SBPV (347)\n", + " │ │ │ │ ├── SCH (286)\n", + " │ │ │ │ ├── SFO (338)\n", + " │ │ │ │ ├── VLPO (689)\n", + " │ │ │ │ └── VMPO (576073699)\n", + " │ │ │ └── PVZ (157)\n", + " │ │ │ ├── ARH (223)\n", + " │ │ │ ├── ASO (332)\n", + " │ │ │ ├── PVH (38)\n", + " │ │ │ ├── PVa (30)\n", + " │ │ │ ├── PVi (118)\n", + " │ │ │ └── SO (390)\n", + " │ │ └── TH (549)\n", + " │ │ ├── DORpm (856)\n", + " │ │ │ ├── ATN (239)\n", + " │ │ │ │ ├── AD (64)\n", + " │ │ │ │ ├── AM (127)\n", + " │ │ │ │ │ ├── AMd (1096)\n", + " │ │ │ │ │ └── AMv (1104)\n", + " │ │ │ │ ├── AV (255)\n", + " │ │ │ │ ├── IAD (1113)\n", + " │ │ │ │ ├── IAM (1120)\n", + " │ │ │ │ └── LD (155)\n", + " │ │ │ ├── EPI (958)\n", + " │ │ │ │ ├── LH (186)\n", + " │ │ │ │ └── MH (483)\n", + " │ │ │ ├── GENv (1014)\n", + " │ │ │ │ ├── IGL (27)\n", + " │ │ │ │ ├── IntG (563807439)\n", + " │ │ │ │ ├── LGv (178)\n", + " │ │ │ │ └── SubG (321)\n", + " │ │ │ ├── ILM (51)\n", + " │ │ │ │ ├── CL (575)\n", + " │ │ │ │ ├── CM (599)\n", + " │ │ │ │ ├── PCN (907)\n", + " │ │ │ │ ├── PF (930)\n", + " │ │ │ │ ├── PIL (560581563)\n", + " │ │ │ │ └── RH (189)\n", + " │ │ │ ├── LAT (138)\n", + " │ │ │ │ ├── Eth (560581551)\n", + " │ │ │ │ ├── LP (218)\n", + " │ │ │ │ ├── PO (1020)\n", + " │ │ │ │ ├── POL (1029)\n", + " │ │ │ │ └── SGN (325)\n", + " │ │ │ ├── MED (444)\n", + " │ │ │ │ ├── IMD (59)\n", + " │ │ │ │ ├── MD (362)\n", + " │ │ │ │ ├── PR (1077)\n", + " │ │ │ │ └── SMT (366)\n", + " │ │ │ ├── MTN (571)\n", + " │ │ │ │ ├── PT (15)\n", + " │ │ │ │ ├── PVT (149)\n", + " │ │ │ │ ├── RE (181)\n", + " │ │ │ │ └── Xi (560581559)\n", + " │ │ │ └── RT (262)\n", + " │ │ └── DORsm (864)\n", + " │ │ ├── GENd (1008)\n", + " │ │ │ ├── LGd (170)\n", + " │ │ │ │ ├── LGd-co (496345668)\n", + " │ │ │ │ ├── LGd-ip (496345672)\n", + " │ │ │ │ └── LGd-sh (496345664)\n", + " │ │ │ └── MG (475)\n", + " │ │ │ ├── MGd (1072)\n", + " │ │ │ ├── MGm (1088)\n", + " │ │ │ └── MGv (1079)\n", + " │ │ ├── PP (1044)\n", + " │ │ ├── SPA (609)\n", + " │ │ ├── SPF (406)\n", + " │ │ │ ├── SPFm (414)\n", + " │ │ │ └── SPFp (422)\n", + " │ │ └── VENT (637)\n", + " │ │ ├── PoT (563807435)\n", + " │ │ ├── VAL (629)\n", + " │ │ ├── VM (685)\n", + " │ │ └── VP (709)\n", + " │ │ ├── VPL (718)\n", + " │ │ ├── VPLpc (725)\n", + " │ │ ├── VPM (733)\n", + " │ │ └── VPMpc (741)\n", + " │ └── MB (313)\n", + " │ ├── MBmot (323)\n", + " │ │ ├── AT (231)\n", + " │ │ ├── CUN (616)\n", + " │ │ ├── DT (75)\n", + " │ │ ├── EW (975)\n", + " │ │ ├── III (35)\n", + " │ │ ├── IV (115)\n", + " │ │ ├── LT (66)\n", + " │ │ ├── MA3 (549009211)\n", + " │ │ ├── MRN (128)\n", + " │ │ ├── MT (58)\n", + " │ │ ├── PAG (795)\n", + " │ │ │ ├── INC (67)\n", + " │ │ │ ├── ND (587)\n", + " │ │ │ ├── PRC (50)\n", + " │ │ │ └── Su3 (614454277)\n", + " │ │ ├── PN (607344830)\n", + " │ │ ├── PRT (1100)\n", + " │ │ │ ├── APN (215)\n", + " │ │ │ ├── MPT (531)\n", + " │ │ │ ├── NOT (628)\n", + " │ │ │ ├── NPC (634)\n", + " │ │ │ ├── OP (706)\n", + " │ │ │ ├── PPT (1061)\n", + " │ │ │ └── RPF (549009203)\n", + " │ │ ├── Pa4 (606826663)\n", + " │ │ ├── RN (214)\n", + " │ │ ├── RR (246)\n", + " │ │ ├── SCm (294)\n", + " │ │ │ ├── SCdg (26)\n", + " │ │ │ ├── SCdw (42)\n", + " │ │ │ ├── SCig (10)\n", + " │ │ │ └── SCiw (17)\n", + " │ │ ├── SNr (381)\n", + " │ │ ├── VTA (749)\n", + " │ │ └── VTN (757)\n", + " │ ├── MBsen (339)\n", + " │ │ ├── IC (4)\n", + " │ │ │ ├── ICc (811)\n", + " │ │ │ ├── ICd (820)\n", + " │ │ │ └── ICe (828)\n", + " │ │ ├── MEV (460)\n", + " │ │ ├── NB (580)\n", + " │ │ ├── PBG (874)\n", + " │ │ ├── SAG (271)\n", + " │ │ ├── SCO (599626923)\n", + " │ │ └── SCs (302)\n", + " │ │ ├── SCop (851)\n", + " │ │ ├── SCsg (842)\n", + " │ │ └── SCzo (834)\n", + " │ └── MBsta (348)\n", + " │ ├── PPN (1052)\n", + " │ ├── RAmb (165)\n", + " │ │ ├── CLI (591)\n", + " │ │ ├── DR (872)\n", + " │ │ ├── IF (12)\n", + " │ │ ├── IPN (100)\n", + " │ │ │ ├── IPA (607344842)\n", + " │ │ │ ├── IPC (607344838)\n", + " │ │ │ ├── IPDL (607344858)\n", + " │ │ │ ├── IPDM (607344854)\n", + " │ │ │ ├── IPI (607344850)\n", + " │ │ │ ├── IPL (607344846)\n", + " │ │ │ ├── IPR (607344834)\n", + " │ │ │ └── IPRL (607344862)\n", + " │ │ └── RL (197)\n", + " │ └── SNc (374)\n", + " ├── CB (512)\n", + " │ ├── CBN (519)\n", + " │ │ ├── DN (846)\n", + " │ │ ├── FN (989)\n", + " │ │ ├── IP (91)\n", + " │ │ └── VeCB (589508455)\n", + " │ └── CBX (528)\n", + " │ ├── HEM (1073)\n", + " │ │ ├── AN (1017)\n", + " │ │ │ ├── ANcr1 (1056)\n", + " │ │ │ └── ANcr2 (1064)\n", + " │ │ ├── COPY (1033)\n", + " │ │ ├── FL (1049)\n", + " │ │ ├── PFL (1041)\n", + " │ │ ├── PRM (1025)\n", + " │ │ └── SIM (1007)\n", + " │ └── VERM (645)\n", + " │ ├── CENT (920)\n", + " │ │ ├── CENT2 (976)\n", + " │ │ └── CENT3 (984)\n", + " │ ├── CUL (928)\n", + " │ │ └── CUL4, 5 (1091)\n", + " │ ├── DEC (936)\n", + " │ ├── FOTU (944)\n", + " │ ├── LING (912)\n", + " │ ├── NOD (968)\n", + " │ ├── PYR (951)\n", + " │ └── UVU (957)\n", + " └── CH (567)\n", + " ├── CNU (623)\n", + " │ ├── PAL (803)\n", + " │ │ ├── PALc (809)\n", + " │ │ │ ├── BAC (287)\n", + " │ │ │ └── BST (351)\n", + " │ │ ├── PALd (818)\n", + " │ │ │ ├── GPe (1022)\n", + " │ │ │ └── GPi (1031)\n", + " │ │ ├── PALm (826)\n", + " │ │ │ ├── MSC (904)\n", + " │ │ │ │ ├── MS (564)\n", + " │ │ │ │ └── NDB (596)\n", + " │ │ │ └── TRS (581)\n", + " │ │ └── PALv (835)\n", + " │ │ ├── MA (298)\n", + " │ │ └── SI (342)\n", + " │ └── STR (477)\n", + " │ ├── LSX (275)\n", + " │ │ ├── LS (242)\n", + " │ │ │ ├── LSc (250)\n", + " │ │ │ ├── LSr (258)\n", + " │ │ │ └── LSv (266)\n", + " │ │ ├── SF (310)\n", + " │ │ └── SH (333)\n", + " │ ├── STRd (485)\n", + " │ │ └── CP (672)\n", + " │ ├── STRv (493)\n", + " │ │ ├── ACB (56)\n", + " │ │ ├── FS (998)\n", + " │ │ └── OT (754)\n", + " │ └── sAMY (278)\n", + " │ ├── AAA (23)\n", + " │ ├── BA (292)\n", + " │ ├── CEA (536)\n", + " │ │ ├── CEAc (544)\n", + " │ │ ├── CEAl (551)\n", + " │ │ └── CEAm (559)\n", + " │ ├── IA (1105)\n", + " │ └── MEA (403)\n", + " └── CTX (688)\n", + " ├── CTXpl (695)\n", + " │ ├── HPF (1089)\n", + " │ │ ├── HIP (1080)\n", + " │ │ │ ├── CA (375)\n", + " │ │ │ │ ├── CA1 (382)\n", + " │ │ │ │ ├── CA2 (423)\n", + " │ │ │ │ └── CA3 (463)\n", + " │ │ │ ├── DG (726)\n", + " │ │ │ │ ├── DG-mo (10703)\n", + " │ │ │ │ ├── DG-po (10704)\n", + " │ │ │ │ └── DG-sg (632)\n", + " │ │ │ ├── FC (982)\n", + " │ │ │ └── IG (19)\n", + " │ │ └── RHP (822)\n", + " │ │ ├── APr (484682508)\n", + " │ │ ├── ENT (909)\n", + " │ │ │ ├── ENTl (918)\n", + " │ │ │ │ ├── ENTl1 (1121)\n", + " │ │ │ │ ├── ENTl2 (20)\n", + " │ │ │ │ ├── ENTl3 (52)\n", + " │ │ │ │ ├── ENTl5 (139)\n", + " │ │ │ │ └── ENTl6a (28)\n", + " │ │ │ └── ENTm (926)\n", + " │ │ │ ├── ENTm1 (526)\n", + " │ │ │ ├── ENTm2 (543)\n", + " │ │ │ ├── ENTm3 (664)\n", + " │ │ │ ├── ENTm5 (727)\n", + " │ │ │ └── ENTm6 (743)\n", + " │ │ ├── HATA (589508447)\n", + " │ │ ├── PAR (843)\n", + " │ │ ├── POST (1037)\n", + " │ │ ├── PRE (1084)\n", + " │ │ ├── ProS (484682470)\n", + " │ │ └── SUB (502)\n", + " │ ├── Isocortex (315)\n", + " │ │ ├── ACA (31)\n", + " │ │ │ ├── ACAd (39)\n", + " │ │ │ │ ├── ACAd1 (935)\n", + " │ │ │ │ ├── ACAd2/3 (211)\n", + " │ │ │ │ ├── ACAd5 (1015)\n", + " │ │ │ │ ├── ACAd6a (919)\n", + " │ │ │ │ └── ACAd6b (927)\n", + " │ │ │ └── ACAv (48)\n", + " │ │ │ ├── ACAv1 (588)\n", + " │ │ │ ├── ACAv2/3 (296)\n", + " │ │ │ ├── ACAv5 (772)\n", + " │ │ │ ├── ACAv6a (810)\n", + " │ │ │ └── ACAv6b (819)\n", + " │ │ ├── AI (95)\n", + " │ │ │ ├── AId (104)\n", + " │ │ │ │ ├── AId1 (996)\n", + " │ │ │ │ ├── AId2/3 (328)\n", + " │ │ │ │ ├── AId5 (1101)\n", + " │ │ │ │ ├── AId6a (783)\n", + " │ │ │ │ └── AId6b (831)\n", + " │ │ │ ├── AIp (111)\n", + " │ │ │ │ ├── AIp1 (120)\n", + " │ │ │ │ ├── AIp2/3 (163)\n", + " │ │ │ │ ├── AIp5 (344)\n", + " │ │ │ │ ├── AIp6a (314)\n", + " │ │ │ │ └── AIp6b (355)\n", + " │ │ │ └── AIv (119)\n", + " │ │ │ ├── AIv1 (704)\n", + " │ │ │ ├── AIv2/3 (694)\n", + " │ │ │ ├── AIv5 (800)\n", + " │ │ │ ├── AIv6a (675)\n", + " │ │ │ └── AIv6b (699)\n", + " │ │ ├── AUD (247)\n", + " │ │ │ ├── AUDd (1011)\n", + " │ │ │ │ ├── AUDd1 (527)\n", + " │ │ │ │ ├── AUDd2/3 (600)\n", + " │ │ │ │ ├── AUDd4 (678)\n", + " │ │ │ │ ├── AUDd5 (252)\n", + " │ │ │ │ ├── AUDd6a (156)\n", + " │ │ │ │ └── AUDd6b (243)\n", + " │ │ │ ├── AUDp (1002)\n", + " │ │ │ │ ├── AUDp1 (735)\n", + " │ │ │ │ ├── AUDp2/3 (251)\n", + " │ │ │ │ ├── AUDp4 (816)\n", + " │ │ │ │ ├── AUDp5 (847)\n", + " │ │ │ │ ├── AUDp6a (954)\n", + " │ │ │ │ └── AUDp6b (1005)\n", + " │ │ │ ├── AUDpo (1027)\n", + " │ │ │ │ ├── AUDpo1 (696)\n", + " │ │ │ │ ├── AUDpo2/3 (643)\n", + " │ │ │ │ ├── AUDpo4 (759)\n", + " │ │ │ │ ├── AUDpo5 (791)\n", + " │ │ │ │ ├── AUDpo6a (249)\n", + " │ │ │ │ └── AUDpo6b (456)\n", + " │ │ │ └── AUDv (1018)\n", + " │ │ │ ├── AUDv1 (959)\n", + " │ │ │ ├── AUDv2/3 (755)\n", + " │ │ │ ├── AUDv4 (990)\n", + " │ │ │ ├── AUDv5 (1023)\n", + " │ │ │ ├── AUDv6a (520)\n", + " │ │ │ └── AUDv6b (598)\n", + " │ │ ├── ECT (895)\n", + " │ │ │ ├── ECT1 (836)\n", + " │ │ │ ├── ECT2/3 (427)\n", + " │ │ │ ├── ECT5 (988)\n", + " │ │ │ ├── ECT6a (977)\n", + " │ │ │ └── ECT6b (1045)\n", + " │ │ ├── FRP (184)\n", + " │ │ │ ├── FRP1 (68)\n", + " │ │ │ ├── FRP2/3 (667)\n", + " │ │ │ ├── FRP5 (526157192)\n", + " │ │ │ ├── FRP6a (526157196)\n", + " │ │ │ └── FRP6b (526322264)\n", + " │ │ ├── GU (1057)\n", + " │ │ │ ├── GU1 (36)\n", + " │ │ │ ├── GU2/3 (180)\n", + " │ │ │ ├── GU4 (148)\n", + " │ │ │ ├── GU5 (187)\n", + " │ │ │ ├── GU6a (638)\n", + " │ │ │ └── GU6b (662)\n", + " │ │ ├── ILA (44)\n", + " │ │ │ ├── ILA1 (707)\n", + " │ │ │ ├── ILA2/3 (556)\n", + " │ │ │ ├── ILA5 (827)\n", + " │ │ │ ├── ILA6a (1054)\n", + " │ │ │ └── ILA6b (1081)\n", + " │ │ ├── MO (500)\n", + " │ │ │ ├── MOp (985)\n", + " │ │ │ │ ├── MOp1 (320)\n", + " │ │ │ │ ├── MOp2/3 (943)\n", + " │ │ │ │ ├── MOp5 (648)\n", + " │ │ │ │ ├── MOp6a (844)\n", + " │ │ │ │ └── MOp6b (882)\n", + " │ │ │ └── MOs (993)\n", + " │ │ │ ├── MOs1 (656)\n", + " │ │ │ ├── MOs2/3 (962)\n", + " │ │ │ ├── MOs5 (767)\n", + " │ │ │ ├── MOs6a (1021)\n", + " │ │ │ └── MOs6b (1085)\n", + " │ │ ├── ORB (714)\n", + " │ │ │ ├── ORBl (723)\n", + " │ │ │ │ ├── ORBl1 (448)\n", + " │ │ │ │ ├── ORBl2/3 (412)\n", + " │ │ │ │ ├── ORBl5 (630)\n", + " │ │ │ │ ├── ORBl6a (440)\n", + " │ │ │ │ └── ORBl6b (488)\n", + " │ │ │ ├── ORBm (731)\n", + " │ │ │ │ ├── ORBm1 (484)\n", + " │ │ │ │ ├── ORBm2/3 (582)\n", + " │ │ │ │ ├── ORBm5 (620)\n", + " │ │ │ │ ├── ORBm6a (910)\n", + " │ │ │ │ └── ORBm6b (527696977)\n", + " │ │ │ └── ORBvl (746)\n", + " │ │ │ ├── ORBvl1 (969)\n", + " │ │ │ ├── ORBvl2/3 (288)\n", + " │ │ │ ├── ORBvl5 (1125)\n", + " │ │ │ ├── ORBvl6a (608)\n", + " │ │ │ └── ORBvl6b (680)\n", + " │ │ ├── PERI (922)\n", + " │ │ │ ├── PERI1 (540)\n", + " │ │ │ ├── PERI2/3 (888)\n", + " │ │ │ ├── PERI5 (692)\n", + " │ │ │ ├── PERI6a (335)\n", + " │ │ │ └── PERI6b (368)\n", + " │ │ ├── PL (972)\n", + " │ │ │ ├── PL1 (171)\n", + " │ │ │ ├── PL2/3 (304)\n", + " │ │ │ ├── PL5 (363)\n", + " │ │ │ ├── PL6a (84)\n", + " │ │ │ └── PL6b (132)\n", + " │ │ ├── PTLp (22)\n", + " │ │ │ ├── VISa (312782546)\n", + " │ │ │ │ ├── VISa1 (312782550)\n", + " │ │ │ │ ├── VISa2/3 (312782554)\n", + " │ │ │ │ ├── VISa4 (312782558)\n", + " │ │ │ │ ├── VISa5 (312782562)\n", + " │ │ │ │ ├── VISa6a (312782566)\n", + " │ │ │ │ └── VISa6b (312782570)\n", + " │ │ │ └── VISrl (417)\n", + " │ │ │ ├── VISrl1 (312782604)\n", + " │ │ │ ├── VISrl2/3 (312782608)\n", + " │ │ │ ├── VISrl4 (312782612)\n", + " │ │ │ ├── VISrl5 (312782616)\n", + " │ │ │ ├── VISrl6a (312782620)\n", + " │ │ │ └── VISrl6b (312782624)\n", + " │ │ ├── RSP (254)\n", + " │ │ │ ├── RSPagl (894)\n", + " │ │ │ │ ├── RSPagl1 (671)\n", + " │ │ │ │ ├── RSPagl2/3 (965)\n", + " │ │ │ │ ├── RSPagl5 (774)\n", + " │ │ │ │ ├── RSPagl6a (906)\n", + " │ │ │ │ └── RSPagl6b (279)\n", + " │ │ │ ├── RSPd (879)\n", + " │ │ │ │ ├── RSPd1 (442)\n", + " │ │ │ │ ├── RSPd2/3 (434)\n", + " │ │ │ │ ├── RSPd4 (545)\n", + " │ │ │ │ ├── RSPd5 (610)\n", + " │ │ │ │ ├── RSPd6a (274)\n", + " │ │ │ │ └── RSPd6b (330)\n", + " │ │ │ └── RSPv (886)\n", + " │ │ │ ├── RSPv1 (542)\n", + " │ │ │ ├── RSPv2/3 (430)\n", + " │ │ │ ├── RSPv5 (687)\n", + " │ │ │ ├── RSPv6a (590)\n", + " │ │ │ └── RSPv6b (622)\n", + " │ │ ├── SS (453)\n", + " │ │ │ ├── SSp (322)\n", + " │ │ │ │ ├── SSp-bfd (329)\n", + " │ │ │ │ │ ├── SSp-bfd1 (981)\n", + " │ │ │ │ │ ├── SSp-bfd2/3 (201)\n", + " │ │ │ │ │ ├── SSp-bfd4 (1047)\n", + " │ │ │ │ │ ├── SSp-bfd5 (1070)\n", + " │ │ │ │ │ ├── SSp-bfd6a (1038)\n", + " │ │ │ │ │ └── SSp-bfd6b (1062)\n", + " │ │ │ │ ├── SSp-ll (337)\n", + " │ │ │ │ │ ├── SSp-ll1 (1030)\n", + " │ │ │ │ │ ├── SSp-ll2/3 (113)\n", + " │ │ │ │ │ ├── SSp-ll4 (1094)\n", + " │ │ │ │ │ ├── SSp-ll5 (1128)\n", + " │ │ │ │ │ ├── SSp-ll6a (478)\n", + " │ │ │ │ │ └── SSp-ll6b (510)\n", + " │ │ │ │ ├── SSp-m (345)\n", + " │ │ │ │ │ ├── SSp-m1 (878)\n", + " │ │ │ │ │ ├── SSp-m2/3 (657)\n", + " │ │ │ │ │ ├── SSp-m4 (950)\n", + " │ │ │ │ │ ├── SSp-m5 (974)\n", + " │ │ │ │ │ ├── SSp-m6a (1102)\n", + " │ │ │ │ │ └── SSp-m6b (2)\n", + " │ │ │ │ ├── SSp-n (353)\n", + " │ │ │ │ │ ├── SSp-n1 (558)\n", + " │ │ │ │ │ ├── SSp-n2/3 (838)\n", + " │ │ │ │ │ ├── SSp-n4 (654)\n", + " │ │ │ │ │ ├── SSp-n5 (702)\n", + " │ │ │ │ │ ├── SSp-n6a (889)\n", + " │ │ │ │ │ └── SSp-n6b (929)\n", + " │ │ │ │ ├── SSp-tr (361)\n", + " │ │ │ │ │ ├── SSp-tr1 (1006)\n", + " │ │ │ │ │ ├── SSp-tr2/3 (670)\n", + " │ │ │ │ │ ├── SSp-tr4 (1086)\n", + " │ │ │ │ │ ├── SSp-tr5 (1111)\n", + " │ │ │ │ │ ├── SSp-tr6a (9)\n", + " │ │ │ │ │ └── SSp-tr6b (461)\n", + " │ │ │ │ ├── SSp-ul (369)\n", + " │ │ │ │ │ ├── SSp-ul1 (450)\n", + " │ │ │ │ │ ├── SSp-ul2/3 (854)\n", + " │ │ │ │ │ ├── SSp-ul4 (577)\n", + " │ │ │ │ │ ├── SSp-ul5 (625)\n", + " │ │ │ │ │ ├── SSp-ul6a (945)\n", + " │ │ │ │ │ └── SSp-ul6b (1026)\n", + " │ │ │ │ └── SSp-un (182305689)\n", + " │ │ │ │ ├── SSp-un1 (182305693)\n", + " │ │ │ │ ├── SSp-un2/3 (182305697)\n", + " │ │ │ │ ├── SSp-un4 (182305701)\n", + " │ │ │ │ ├── SSp-un5 (182305705)\n", + " │ │ │ │ ├── SSp-un6a (182305709)\n", + " │ │ │ │ └── SSp-un6b (182305713)\n", + " │ │ │ └── SSs (378)\n", + " │ │ │ ├── SSs1 (873)\n", + " │ │ │ ├── SSs2/3 (806)\n", + " │ │ │ ├── SSs4 (1035)\n", + " │ │ │ ├── SSs5 (1090)\n", + " │ │ │ ├── SSs6a (862)\n", + " │ │ │ └── SSs6b (893)\n", + " │ │ ├── TEa (541)\n", + " │ │ │ ├── TEa1 (97)\n", + " │ │ │ ├── TEa2/3 (1127)\n", + " │ │ │ ├── TEa4 (234)\n", + " │ │ │ ├── TEa5 (289)\n", + " │ │ │ ├── TEa6a (729)\n", + " │ │ │ └── TEa6b (786)\n", + " │ │ ├── VIS (669)\n", + " │ │ │ ├── VISal (402)\n", + " │ │ │ │ ├── VISal1 (1074)\n", + " │ │ │ │ ├── VISal2/3 (905)\n", + " │ │ │ │ ├── VISal4 (1114)\n", + " │ │ │ │ ├── VISal5 (233)\n", + " │ │ │ │ ├── VISal6a (601)\n", + " │ │ │ │ └── VISal6b (649)\n", + " │ │ │ ├── VISam (394)\n", + " │ │ │ │ ├── VISam1 (281)\n", + " │ │ │ │ ├── VISam2/3 (1066)\n", + " │ │ │ │ ├── VISam4 (401)\n", + " │ │ │ │ ├── VISam5 (433)\n", + " │ │ │ │ ├── VISam6a (1046)\n", + " │ │ │ │ └── VISam6b (441)\n", + " │ │ │ ├── VISl (409)\n", + " │ │ │ │ ├── VISl1 (421)\n", + " │ │ │ │ ├── VISl2/3 (973)\n", + " │ │ │ │ ├── VISl4 (573)\n", + " │ │ │ │ ├── VISl5 (613)\n", + " │ │ │ │ ├── VISl6a (74)\n", + " │ │ │ │ └── VISl6b (121)\n", + " │ │ │ ├── VISli (312782574)\n", + " │ │ │ │ ├── VISli1 (312782578)\n", + " │ │ │ │ ├── VISli2/3 (312782582)\n", + " │ │ │ │ ├── VISli4 (312782586)\n", + " │ │ │ │ ├── VISli5 (312782590)\n", + " │ │ │ │ ├── VISli6a (312782594)\n", + " │ │ │ │ └── VISli6b (312782598)\n", + " │ │ │ ├── VISp (385)\n", + " │ │ │ │ ├── VISp1 (593)\n", + " │ │ │ │ ├── VISp2/3 (821)\n", + " │ │ │ │ ├── VISp4 (721)\n", + " │ │ │ │ ├── VISp5 (778)\n", + " │ │ │ │ ├── VISp6a (33)\n", + " │ │ │ │ └── VISp6b (305)\n", + " │ │ │ ├── VISpl (425)\n", + " │ │ │ │ ├── VISpl1 (750)\n", + " │ │ │ │ ├── VISpl2/3 (269)\n", + " │ │ │ │ ├── VISpl4 (869)\n", + " │ │ │ │ ├── VISpl5 (902)\n", + " │ │ │ │ ├── VISpl6a (377)\n", + " │ │ │ │ └── VISpl6b (393)\n", + " │ │ │ ├── VISpm (533)\n", + " │ │ │ │ ├── VISpm1 (805)\n", + " │ │ │ │ ├── VISpm2/3 (41)\n", + " │ │ │ │ ├── VISpm4 (501)\n", + " │ │ │ │ ├── VISpm5 (565)\n", + " │ │ │ │ ├── VISpm6a (257)\n", + " │ │ │ │ └── VISpm6b (469)\n", + " │ │ │ └── VISpor (312782628)\n", + " │ │ │ ├── VISpor1 (312782632)\n", + " │ │ │ ├── VISpor2/3 (312782636)\n", + " │ │ │ ├── VISpor4 (312782640)\n", + " │ │ │ ├── VISpor5 (312782644)\n", + " │ │ │ ├── VISpor6a (312782648)\n", + " │ │ │ └── VISpor6b (312782652)\n", + " │ │ └── VISC (677)\n", + " │ │ ├── VISC1 (897)\n", + " │ │ ├── VISC2/3 (1106)\n", + " │ │ ├── VISC4 (1010)\n", + " │ │ ├── VISC5 (1058)\n", + " │ │ ├── VISC6a (857)\n", + " │ │ └── VISC6b (849)\n", + " │ └── OLF (698)\n", + " │ ├── AOB (151)\n", + " │ │ ├── AOBgl (188)\n", + " │ │ ├── AOBgr (196)\n", + " │ │ └── AOBmi (204)\n", + " │ ├── AON (159)\n", + " │ ├── COA (631)\n", + " │ │ ├── COAa (639)\n", + " │ │ └── COAp (647)\n", + " │ │ ├── COApl (655)\n", + " │ │ └── COApm (663)\n", + " │ ├── DP (814)\n", + " │ ├── MOB (507)\n", + " │ ├── NLOT (619)\n", + " │ │ ├── NLOT1 (260)\n", + " │ │ ├── NLOT2 (268)\n", + " │ │ └── NLOT3 (1139)\n", + " │ ├── PAA (788)\n", + " │ ├── PIR (961)\n", + " │ ├── TR (566)\n", + " │ └── TT (589)\n", + " │ ├── TTd (597)\n", + " │ └── TTv (605)\n", + " └── CTXsp (703)\n", + " ├── BLA (295)\n", + " │ ├── BLAa (303)\n", + " │ ├── BLAp (311)\n", + " │ └── BLAv (451)\n", + " ├── BMA (319)\n", + " │ ├── BMAa (327)\n", + " │ └── BMAp (334)\n", + " ├── CLA (583)\n", + " ├── EP (942)\n", + " │ ├── EPd (952)\n", + " │ └── EPv (966)\n", + " ├── LA (131)\n", + " └── PA (780)" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bg_atlas.structures" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The structures attribute is a custom dictionary that can be queried by region number or acronym, and contains all the information for a given structure:" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{'acronym': 'root',\n", + " 'id': 997,\n", + " 'mesh': None,\n", + " 'mesh_filename': PosixPath('/home/rob/.brainglobe/allen_mouse_100um_v1.2/meshes/997.obj'),\n", + " 'name': 'root',\n", + " 'rgb_triplet': [255, 255, 255],\n", + " 'structure_id_path': [997]}\n" + ] + } + ], + "source": [ + "pprint(bg_atlas.structures[\"root\"])" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "In particular, the `structure_id_path` key contains a list description of the path in the hierarchy up to a particular region, and can be used for queries on the hierarchy." + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[997, 8, 567]" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bg_atlas.structures[\"CH\"][\"structure_id_path\"]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We can use the `bg_atlas.get_structure_descendants` and `bg_atlas.get_structure_ancestors` methods to explore the hierarchy:" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['VISC1', 'VISC2/3', 'VISC4', 'VISC5', 'VISC6a', 'VISC6b']" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bg_atlas.get_structure_descendants(\"VISC\")" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['root', 'grey', 'CH', 'CTX', 'CTXpl', 'Isocortex', 'VISC']" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bg_atlas.get_structure_ancestors(\"VISC6a\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "---\n", + "**NOTE**: \n", + "the levels of the hierarchy depends on the underlying atlas, so we cannot ensure the goodness and consistency of their hierarchy three.\n", + "---" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "There is an higher level description of the structures hierarchy that is built using the [treelib](https://treelib.readthedocs.io/en/latest/) package, and is available as: " + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bg_atlas.structures.tree" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "For most applications though the methods described above and the list path of each region should be enough to query the hierarchy without additional layers of complication." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 1.3 Region masks" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The `get_structure_mask` method returns a mask volume where all voxels belonging to an area or to the descendants of that area are non zero. All other voxels are zero. We will generate the structure mask for primary visual cortex to see how this works. \n", + "\n", + "Primary visual cortex (`VISp`) has an ID value of `385` but no voxels in the annotation image actually have that value:" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{'acronym': 'VISp',\n", + " 'id': 385,\n", + " 'mesh': None,\n", + " 'mesh_filename': PosixPath('/home/rob/.brainglobe/allen_mouse_100um_v1.2/meshes/385.obj'),\n", + " 'name': 'Primary visual area',\n", + " 'rgb_triplet': [8, 133, 140],\n", + " 'structure_id_path': [997, 8, 567, 688, 695, 315, 669, 385]}\n" + ] + } + ], + "source": [ + "pprint(bg_atlas.structures[\"VISp\"])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# No voxels in the annotation volume are labelled as being VISp\n", + "(bg_atlas.annotation==385).sum()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The reason no VISp voxels exist is because the annotation volume is segmented more finely. In this case `VISp` is divided into cortical layers and it is IDs associated with these layers that are present in the annotation volume." + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['VISp1', 'VISp2/3', 'VISp4', 'VISp5', 'VISp6a', 'VISp6b']" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# The descendants (children) of VISp are cortical layers\n", + "bg_atlas.get_structure_descendants(\"VISp\")" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "VISp1\t593\n", + "VISp2/3\t821\n", + "VISp4\t721\n", + "VISp5\t778\n", + "VISp6a\t33\n", + "VISp6b\t305\n" + ] + } + ], + "source": [ + "# The IDs associated with each layer in primary visual cortex\n", + "layers = bg_atlas.get_structure_descendants(\"VISp\")\n", + "layer_ids = [bg_atlas.structures[this_layer]['id'] for this_layer in layers]\n", + "\n", + "for (this_layer, this_id) in zip(layers, layer_ids):\n", + " print(\"%s\\t%s\" % (this_layer, this_id))\n", + "\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "These IDs are indeed present in the annotation volume:" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1565" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# For example, we find over a thousand voxels associated with primary visual cortex layer 6\n", + "# in the annotation volume\n", + "(bg_atlas.annotation==778).sum()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "So lets use `get_structure_mask` to return a mask volume that retains only `VISp`." + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [], + "source": [ + "mask_VISp = bg_atlas.get_structure_mask('VISp')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", + "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", + " axs[i].imshow(mask_VISp.max(i), cmap=\"gray\")\n", + " axs[i].set_title(f\"{plane.capitalize()} view\")\n", + " axs[i].set_ylabel(labels[0])\n", + " axs[i].set_xlabel(labels[1])\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The `root` node encompases the whole brain and we can use this to provide a background image for the above area." + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [], + "source": [ + "mask_root = bg_atlas.get_structure_mask('root')\n", + "\n", + "# The mask images have pixel values equal to the ID of the parent area, so we change these for\n", + "# plotting purposes. \n", + "mask_root[mask_root>0]=5\n", + "mask_VISp[mask_VISp>0]=2\n", + "mask_VISp_root = mask_VISp + mask_root" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "space = bg_atlas.space\n", + "\n", + "f, axs = plt.subplots(1,3, figsize=(12, 3))\n", + "for i, (plane, labels) in enumerate(zip(space.sections, space.axis_labels)):\n", + " axs[i].imshow(mask_VISp_root.max(i), cmap=\"gray\")\n", + " axs[i].set_title(f\"{plane.capitalize()} view\")\n", + " axs[i].set_ylabel(labels[0])\n", + " axs[i].set_xlabel(labels[1])\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 1.3 Regions meshes" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "If we need to access the structure meshes, we can either query for the file (e.g., if we need to load the file through some library like `vedo`):" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "PosixPath('/home/rob/.brainglobe/allen_mouse_100um_v1.2/meshes/567.obj')" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bg_atlas.meshfile_from_structure(\"CH\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Or directly obtain the mesh, as a mesh object of the `meshio` library:" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "\n", + " Number of points: 56703\n", + " Number of cells:\n", + " triangle: 112948\n", + " Point data: obj:vn\n", + " Cell data: obj:group_ids" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bg_atlas.mesh_from_structure(\"CH\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2 Query the `BrainGlobeAtlas`" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 2.0 Query for structures:" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "A very convenient feature of the `BrainGlobeAtlas` API is the simplicity of querying for the identity of the structure or the hemisphere at a given location, either from stack indexes or space coordinates, and even cutting the hierarchy at some higher level:" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "By index: CP\n", + "By coordinates: CP\n", + "Higher hierarchy level: CH\n" + ] + } + ], + "source": [ + "# Ask for identity of some indexes in the stack:\n", + "print(\"By index:\", bg_atlas.structure_from_coords((50, 40, 30), \n", + " as_acronym=True))\n", + "\n", + "# Now give coordinates in microns\n", + "print(\"By coordinates:\", bg_atlas.structure_from_coords((5000, 4000, 3000), \n", + " as_acronym=True, \n", + " microns=True))\n", + "\n", + "# Now cut hierarchy at some level\n", + "print(\"Higher hierarchy level:\", bg_atlas.structure_from_coords((5000, 4000, 3000), \n", + " as_acronym=True, \n", + " microns=True, \n", + " hierarchy_lev=2))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### 2.1 Query for hemispheres" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "A very similar method can be used for hemispheres. 0 correspond to outside the brain, a,d 1 and 2 to left and right hemispheres - but we can just ask for the side name instead of the number:" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "By index: 2\n", + "By coordinates: 2\n", + "By : 2\n" + ] + } + ], + "source": [ + "# Ask for identity of some indexes in the stack:\n", + "print(\"By index:\", bg_atlas.hemisphere_from_coords((50, 40, 30)))\n", + "\n", + "# Now give coordinates in microns\n", + "print(\"By coordinates:\", bg_atlas.hemisphere_from_coords((5000, 4000, 3000), microns=True))\n", + "\n", + "# Now print side string\n", + "print(\"By :\", bg_atlas.hemisphere_from_coords((5000, 4000, 3000), microns=True))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.10" + } + }, + "nbformat": 4, + "nbformat_minor": 4 }