diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a568e300..1d74212b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -16,7 +16,7 @@ repos:
- id: requirements-txt-fixer
- id: trailing-whitespace
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.5.6
+ rev: v0.6.3
hooks:
- id: ruff
- repo: https://github.com/psf/black
diff --git a/README.md b/README.md
index ed896b0b..449a7245 100644
--- a/README.md
+++ b/README.md
@@ -23,20 +23,23 @@ The brainglobe atlas API (brainglobe-atlasapi) provides a common interface for p
A number of atlases are in development, but those available currently are:
-- [Allen Mouse Brain Atlas](https://doi.org/10.1016/j.cell.2020.04.007) 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/10.1038/s41592-023-02034-3) 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)
-- [Blind Mexican Cavefish Brain Atlas](https://doi.org/10.7554/eLife.80777) at 2 micron resolution
-- [BlueBrain Barrel Cortex Atlas](https://doi.org/10.1162/imag_a_00209) at 10 and 25 micron resolution
+| Atlas Name | Resolution | Ages | Reference Images
+| --- | --- | --- | --- |
+| [Allen Mouse Brain Atlas](https://doi.org/10.1016/j.cell.2020.04.007) | 10, 25, 50, and 100 micron | P56 | STPT
+| [Allen Human Brain Atlas](https://www.brain-map.org) | 500 micron | Adult | MRI
+| [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de) | 1 micron | 6-dpf | FISH
+| [Enhanced and Unified Mouse Brain Atlas](https://kimlab.io/brain-map/atlas/) | 10, 25, 50, and 100 micron | P56 | STPT
+| [Smoothed version of the Kim et al. mouse reference atlas](https://doi.org/10.1016/j.celrep.2014.12.014) | 10, 25, 50 and 100 micron | P56 | STPT
+| [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8) | 20 micron | 8 to 10 weeks post natal | LSFM
+| [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008) | 20 x 10 x 10 micron | Adult | Nissl
+| [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625) | 4 micron | 15-16 weeks post natal | LSFM
+| [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1038/s41592-023-02034-3) | 39 micron | P80 | MRI
+| [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) | 16, 16.75, and 25 micron | E13, E15, E18, P4, P14, P28 & P56 | Nissl
+| [Princeton Mouse Brain Atlas](https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links) | 20 micron | >P56 (older animals included) | LSFM
+| [Kim Lab Developmental CCF](https://data.mendeley.com/datasets/2svx788ddf/1) | 10 micron | P56 | STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2)
+| [Blind Mexican Cavefish Brain Atlas](https://doi.org/10.7554/eLife.80777) | 2 micron | 1 year | IHC
+| [BlueBrain Barrel Cortex Atlas](https://doi.org/10.1162/imag_a_00209) | 10 and 25 micron | P56 | STPT
+| [UNAM Axolotl Brain Atlas](https://doi.org/10.1038/s41598-021-89357-3) | 40 micron | ~ 3 months post hatching | MRI
## Installation
diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/axolotl_atlas.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/axolotl_atlas.py
index 198ad7b3..1c390f9e 100644
--- a/brainglobe_atlasapi/atlas_generation/atlas_scripts/axolotl_atlas.py
+++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/axolotl_atlas.py
@@ -10,6 +10,9 @@
import pooch
from brainglobe_utils.IO.image import load_nii
from rich.progress import track
+from skimage.filters.rank import modal
+from skimage.measure import label, regionprops
+from skimage.morphology import ball
from brainglobe_atlasapi import utils
from brainglobe_atlasapi.atlas_generation.mesh_utils import (
@@ -24,11 +27,10 @@
def create_atlas(working_dir, resolution):
ATLAS_NAME = "unam_axolotl"
SPECIES = "Ambystoma mexicanum"
- ATLAS_LINK = "https://www.nature.com/articles/s41598-021-89357-3"
+ ATLAS_LINK = "https://zenodo.org/records/4595016"
CITATION = (
"Lazcano, I. et al. 2021, https://doi.org/10.1038/s41598-021-89357-3"
)
- ATLAS_FILE_URL = "https://zenodo.org/records/4595016"
ORIENTATION = "lpi"
ROOT_ID = 999
ATLAS_PACKAGER = "Saima Abdus, David Perez-Suarez, Alessandro Felder"
@@ -57,7 +59,7 @@ def create_atlas(working_dir, resolution):
}
for filename, hash in list_files.items():
pooch.retrieve(
- url=f"{ATLAS_FILE_URL}/files/{filename}",
+ url=f"{ATLAS_LINK}/files/{filename}",
known_hash=hash,
path=atlas_path,
progressbar=True,
@@ -76,6 +78,21 @@ def create_atlas(working_dir, resolution):
reference_image = (reference_image - dmin) * dscale
reference_image = reference_image.astype(np.uint16)
+ # mask: put 1 where there is an annotation
+ annotation_mask = np.zeros(annotation_image.shape)
+ annotation_mask[annotation_image > 0] = 1
+
+ # find the connected regions in the mask
+ labeled_image = label(annotation_mask)
+ regions = regionprops(labeled_image)
+
+ # find the pixels belonging to the largest region
+ largest_region = max(regions, key=lambda region: region.area)
+ largest_mask = labeled_image == largest_region.label
+
+ # keep only annotations in the largest connected region
+ annotation_image = annotation_image * largest_mask
+
hierarchy = []
# create dictionaries # create dictionary from data read from the CSV file
@@ -165,13 +182,19 @@ def create_structure_id_path(main_structure):
node.data = Region(is_label)
# Mesh creation parameters
- closing_n_iters = 5
- decimate_fraction = 0.1
+ closing_n_iters = 10
+ decimate_fraction = 0.6
smooth = True
meshes_dir_path = working_dir / "meshes"
meshes_dir_path.mkdir(exist_ok=True)
+ # pass a smoothed version of the annotations for meshing
+ smoothed_annotations = annotation_image.copy()
+ smoothed_annotations = modal(
+ smoothed_annotations.astype(np.uint8), ball(5)
+ )
+
# Measure duration of mesh creation
start = time.time()
@@ -188,7 +211,7 @@ def create_structure_id_path(main_structure):
node,
tree,
labels,
- annotation_image,
+ smoothed_annotations,
ROOT_ID,
closing_n_iters,
decimate_fraction,
diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/whs_sd_rat.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/whs_sd_rat.py
index 2f36817a..8cabb19d 100644
--- a/brainglobe_atlasapi/atlas_generation/atlas_scripts/whs_sd_rat.py
+++ b/brainglobe_atlasapi/atlas_generation/atlas_scripts/whs_sd_rat.py
@@ -1,15 +1,16 @@
-__version__ = "0"
+__version__ = "2"
__atlas__ = "whs_sd_rat"
+
import json
import multiprocessing as mp
import time
from pathlib import Path
-import imio
import numpy as np
import pooch
import xmltodict
+from brainglobe_utils.IO.image import load_any
from rich.progress import track
from brainglobe_atlasapi import utils
@@ -201,15 +202,14 @@ 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"
- )
+ CITATION = "Kleven et al 2023, https://doi.org/10.1038/s41592-023-02034-3"
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"
+ REFERENCE_URL = "https://www.nitrc.org/frs/download.php/12263/MBAT_WHS_SD_rat_atlas_v4_pack.zip"
+ ANNOTATION_URL = "https://www.nitrc.org/frs/download.php/13400/MBAT_WHS_SD_rat_atlas_v4.01.zip//?i_agree=1&download_now=1"
ATLAS_PACKAGER = (
- "Ben Kantor, Tel Aviv University, Israel, benkantor@mail.tau.ac.il"
+ "Harry Carey, University of Oslo, Norway, harry.carey@medisin.uio.no"
)
assert len(ORIENTATION) == 3, (
@@ -217,7 +217,7 @@ def create_atlas(working_dir):
)
assert len(RESOLUTION) == 3, "Resolution is not correct, Got " + RESOLUTION
assert (
- ATLAS_FILE_URL
+ REFERENCE_URL
), "No download link provided for atlas in ATLAS_FILE_URL"
# Generated atlas path:
@@ -228,22 +228,30 @@ def create_atlas(working_dir):
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__
+
)
atlas_files_dir = atlas_files_dir / "MBAT_WHS_SD_rat_atlas_v4_pack/Data"
+ annotation_files_dir = download_atlas_files(
+ download_dir_path, ANNOTATION_URL, ATLAS_NAME + "_annotation"
+ )
+ annotation_files_dir = (
+ annotation_files_dir / "MBAT_WHS_SD_rat_atlas_v4.01/Data"
+ )
+
# Parse structure metadata
structures = parse_structures(
- atlas_files_dir / "WHS_SD_rat_atlas_v4_labels.ilf"
+ annotation_files_dir / "WHS_SD_rat_atlas_v4.01_labels.ilf"
)
# Load files
- annotation_stack = imio.load_any(
- atlas_files_dir / "WHS_SD_rat_atlas_v4.nii.gz", as_numpy=True
+ annotation_stack = load_any(
+ annotation_files_dir / "WHS_SD_rat_atlas_v4.01.nii.gz", as_numpy=True
).astype(np.int64)
- reference_stack = imio.load_any(
+ reference_stack = load_any(
atlas_files_dir / "WHS_SD_rat_T2star_v1.01.nii.gz", as_numpy=True
)
diff --git a/brainglobe_atlasapi/bg_atlas.py b/brainglobe_atlasapi/bg_atlas.py
index 13c14917..5aafdb22 100644
--- a/brainglobe_atlasapi/bg_atlas.py
+++ b/brainglobe_atlasapi/bg_atlas.py
@@ -8,7 +8,11 @@
from rich.console import Console
from brainglobe_atlasapi import config, core, descriptors, utils
-from brainglobe_atlasapi.utils import _rich_atlas_metadata
+from brainglobe_atlasapi.utils import (
+ _rich_atlas_metadata,
+ check_gin_status,
+ check_internet_connection,
+)
COMPRESSED_FILENAME = "atlas.tar.gz"
@@ -80,13 +84,13 @@ def __init__(
# Look for this atlas in local brainglobe folder:
if self.local_full_name is None:
if self.remote_version is None:
- raise ValueError(f"{atlas_name} is not a valid atlas name!")
+ check_internet_connection(raise_error=True)
+ check_gin_status(raise_error=True)
- rprint(
- f"[magenta2]brainglobe_atlasapi: {self.atlas_name} "
- "not found locally. Downloading...[magenta2]"
- )
- self.download_extract_file()
+ # If internet and GIN are up, then the atlas name was invalid
+ raise ValueError(f"{atlas_name} is not a valid atlas name!")
+ else:
+ self.download_extract_file()
# Instantiate after eventual download:
super().__init__(self.brainglobe_dir / self.local_full_name)
@@ -113,11 +117,11 @@ def remote_version(self):
"""
remote_url = self._remote_url_base.format("last_versions.conf")
- # Grasp remote version if a connection is available:
try:
+ # Grasp remote version
versions_conf = utils.conf_from_url(remote_url)
except requests.ConnectionError:
- return
+ return None
try:
return _version_tuple_from_str(
@@ -161,7 +165,8 @@ def remote_url(self):
def download_extract_file(self):
"""Download and extract atlas from remote url."""
- utils.check_internet_connection()
+ check_internet_connection()
+ check_gin_status()
# Get path to folder where data will be saved
destination_path = self.interm_download_dir / COMPRESSED_FILENAME
diff --git a/brainglobe_atlasapi/list_atlases.py b/brainglobe_atlasapi/list_atlases.py
index 5924d7d5..9a5da303 100644
--- a/brainglobe_atlasapi/list_atlases.py
+++ b/brainglobe_atlasapi/list_atlases.py
@@ -51,12 +51,20 @@ def get_local_atlas_version(atlas_name):
def get_all_atlases_lastversions():
- """Read from URL all available last versions"""
- available_atlases = utils.conf_from_url(
- descriptors.remote_url_base.format("last_versions.conf")
- )
- available_atlases = dict(available_atlases["atlases"])
- return available_atlases
+ """Read from URL or local cache all available last versions"""
+ cache_path = config.get_brainglobe_dir() / "last_versions.conf"
+
+ if utils.check_internet_connection(
+ raise_error=False
+ ) and utils.check_gin_status(raise_error=False):
+ available_atlases = utils.conf_from_url(
+ descriptors.remote_url_base.format("last_versions.conf")
+ )
+ else:
+ print("Cannot fetch latest atlas versions from the server.")
+ available_atlases = utils.conf_from_file(cache_path)
+
+ return dict(available_atlases["atlases"])
def get_atlases_lastversions():
diff --git a/brainglobe_atlasapi/utils.py b/brainglobe_atlasapi/utils.py
index 591ab491..2ef6d0dc 100644
--- a/brainglobe_atlasapi/utils.py
+++ b/brainglobe_atlasapi/utils.py
@@ -2,6 +2,7 @@
import json
import logging
import re
+from pathlib import Path
from typing import Callable, Optional
import requests
@@ -19,6 +20,8 @@
from rich.table import Table
from rich.text import Text
+from brainglobe_atlasapi import config
+
logging.getLogger("urllib3").setLevel(logging.WARNING)
@@ -119,15 +122,41 @@ def check_internet_connection(
try:
_ = requests.get(url, timeout=timeout)
+
return True
- except requests.ConnectionError:
+ except requests.ConnectionError as e:
if not raise_error:
print("No internet connection available.")
else:
raise ConnectionError(
"No internet connection, try again when you are "
"connected to the internet."
- )
+ ) from e
+
+ return False
+
+
+def check_gin_status(timeout=5, raise_error=True):
+ """Check that the GIN server is up.
+
+ timeout : int
+ timeout to wait for [in seconds] (Default value = 5).
+ raise_error : bool
+ if false, warning but no error.
+ """
+ url = "https://gin.g-node.org/"
+
+ try:
+ _ = requests.get(url, timeout=timeout)
+
+ return True
+ except requests.ConnectionError as e:
+ error_message = "GIN server is down."
+ if not raise_error:
+ print(error_message)
+ else:
+ raise ConnectionError(error_message) from e
+
return False
@@ -163,9 +192,9 @@ def retrieve_over_http(
)
CHUNK_SIZE = 4096
- response = requests.get(url, stream=True)
try:
+ response = requests.get(url, stream=True)
with progress:
tot = int(response.headers.get("content-length", 0))
@@ -188,9 +217,7 @@ def retrieve_over_http(
fout.write(chunk)
adv = len(chunk)
completed += adv
- progress.update(
- task_id, completed=min(completed, tot), refresh=True
- )
+ progress.update(task_id, completed=min(completed, tot))
if fn_update:
# update handler with completed and total bytes
@@ -263,8 +290,8 @@ def get_download_size(url: str) -> int:
raise IndexError("Improperly formatted URL")
-def conf_from_url(url):
- """Read conf file from an URL.
+def conf_from_url(url) -> configparser.ConfigParser:
+ """Read conf file from an URL. And cache a copy in the brainglobe dir.
Parameters
----------
url : str
@@ -276,6 +303,38 @@ def conf_from_url(url):
"""
text = requests.get(url).text
+ config_obj = configparser.ConfigParser()
+ config_obj.read_string(text)
+ cache_path = config.get_brainglobe_dir() / "last_versions.conf"
+
+ if not cache_path.parent.exists():
+ cache_path.parent.mkdir(parents=True, exist_ok=True)
+
+ # Cache the available atlases
+ with open(cache_path, "w") as f_out:
+ config_obj.write(f_out)
+
+ return config_obj
+
+
+def conf_from_file(file_path: Path) -> configparser.ConfigParser:
+ """Read conf file from a local file path.
+ Parameters
+ ----------
+ file_path : Path
+ conf file path (obtained from config.get_brainglobe_dir())
+
+ Returns
+ -------
+ conf object if file available
+
+ """
+ if not file_path.exists():
+ raise FileNotFoundError("Last versions cache file not found.")
+
+ with open(file_path, "r") as file:
+ text = file.read()
+
config = configparser.ConfigParser()
config.read_string(text)
diff --git a/pyproject.toml b/pyproject.toml
index ec0e5083..a240b5ec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -105,6 +105,9 @@ fix = true
[tool.ruff.lint]
select = ["I", "E", "F"]
+[tool.ruff.lint.per-file-ignores]
+"*.ipynb" = ["E501"]
+
[tool.tox]
legacy_tox_ini = """
[tox]
diff --git a/tests/atlasapi/test_list_atlases.py b/tests/atlasapi/test_list_atlases.py
index afa7b581..945357e6 100644
--- a/tests/atlasapi/test_list_atlases.py
+++ b/tests/atlasapi/test_list_atlases.py
@@ -1,4 +1,8 @@
+from unittest import mock
+
+from brainglobe_atlasapi import config
from brainglobe_atlasapi.list_atlases import (
+ get_all_atlases_lastversions,
get_atlases_lastversions,
get_downloaded_atlases,
get_local_atlas_version,
@@ -39,3 +43,71 @@ def test_lastversions():
def test_show_atlases():
# TODO add more valid testing than just look for errors when running:
show_atlases(show_local_path=True)
+
+
+def test_get_all_atlases_lastversions():
+ last_versions = get_all_atlases_lastversions()
+
+ assert "example_mouse_100um" in last_versions
+ assert "osten_mouse_50um" in last_versions
+ assert "allen_mouse_25um" in last_versions
+
+
+def test_get_all_atlases_lastversions_offline():
+ cleanup_cache = False
+ cache_path = config.get_brainglobe_dir() / "last_versions.conf"
+
+ if not cache_path.exists():
+ cache_path.touch()
+ cache_path.write_text(
+ """
+ [atlases]
+ example_mouse_100um = 1.0
+ osten_mouse_50um = 1.0
+ allen_mouse_25um = 1.0
+ """
+ )
+ cleanup_cache = True
+
+ with mock.patch(
+ "brainglobe_atlasapi.utils.check_internet_connection"
+ ) as mock_check_internet_connection:
+ mock_check_internet_connection.return_value = False
+ last_versions = get_all_atlases_lastversions()
+
+ assert "example_mouse_100um" in last_versions
+ assert "osten_mouse_50um" in last_versions
+ assert "allen_mouse_25um" in last_versions
+
+ if cleanup_cache:
+ cache_path.unlink()
+
+
+def test_get_all_atlases_lastversions_gin_down():
+ cleanup_cache = False
+ cache_path = config.get_brainglobe_dir() / "last_versions.conf"
+
+ if not cache_path.exists():
+ cache_path.touch()
+ cache_path.write_text(
+ """
+ [atlases]
+ example_mouse_100um = 1.0
+ osten_mouse_50um = 1.0
+ allen_mouse_25um = 1.0
+ """
+ )
+ cleanup_cache = True
+
+ with mock.patch(
+ "brainglobe_atlasapi.utils.check_gin_status"
+ ) as mock_check_internet_connection:
+ mock_check_internet_connection.return_value = False
+ last_versions = get_all_atlases_lastversions()
+
+ assert "example_mouse_100um" in last_versions
+ assert "osten_mouse_50um" in last_versions
+ assert "allen_mouse_25um" in last_versions
+
+ if cleanup_cache:
+ cache_path.unlink()
diff --git a/tests/atlasapi/test_utils.py b/tests/atlasapi/test_utils.py
index abd6e310..148ead82 100644
--- a/tests/atlasapi/test_utils.py
+++ b/tests/atlasapi/test_utils.py
@@ -81,3 +81,60 @@ def test_get_download_size_HTTPError():
with pytest.raises(HTTPError):
utils.get_download_size(test_url)
+
+
+def test_check_gin_status():
+ # Test with requests.get returning a valid response
+ with mock.patch("requests.get", autospec=True) as mock_request:
+ mock_response = mock.Mock(spec=requests.Response)
+ mock_response.status_code = 200
+ mock_request.return_value = mock_response
+
+ assert utils.check_gin_status()
+
+
+def test_check_gin_status_down():
+ # Test with requests.get returning a 404 response
+ with mock.patch("requests.get", autospec=True) as mock_request:
+ mock_request.side_effect = requests.ConnectionError()
+
+ with pytest.raises(ConnectionError) as e:
+ utils.check_gin_status()
+ assert "GIN server is down" == e.value
+
+
+def test_check_gin_status_down_no_error():
+ # Test with requests.get returning a 404 response
+ with mock.patch("requests.get", autospec=True) as mock_request:
+ mock_request.side_effect = requests.ConnectionError()
+
+ assert not utils.check_gin_status(raise_error=False)
+
+
+def test_conf_from_file(temp_path):
+ conf_path = temp_path / "conf.conf"
+ content = (
+ "[atlases]\n"
+ "example_mouse_100um = 1.2\n"
+ "allen_mouse_10um = 1.2\n"
+ "allen_mouse_25um = 1.2"
+ )
+ conf_path.write_text(content)
+ # Test with a valid file
+ conf = utils.conf_from_file(conf_path)
+
+ assert dict(conf["atlases"]) == {
+ "example_mouse_100um": "1.2",
+ "allen_mouse_10um": "1.2",
+ "allen_mouse_25um": "1.2",
+ }
+
+
+def test_conf_from_file_no_file(temp_path):
+ conf_path = temp_path / "conf.conf"
+
+ # Test with a non-existing file
+ with pytest.raises(FileNotFoundError) as e:
+ utils.conf_from_file(conf_path)
+
+ assert "Last versions cache file not found." == str(e)
diff --git a/tutorials/Atlas API usage.ipynb b/tutorials/Atlas API usage.ipynb
index 21bb8a1a..9c942c86 100644
--- a/tutorials/Atlas API usage.ipynb
+++ b/tutorials/Atlas API usage.ipynb
@@ -1,1715 +1,1718 @@
{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# Introduction to the `BrainGlobeAtlas` class"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## 0. Creating a `BrainGlobeAtlas` object and listing available 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 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 Reference, annotation and hemispheres stack"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
- "metadata": {},
- "outputs": [],
- "source": [
- "from matplotlib import pyplot as plt"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Reference stack:"
- ]
- },
- {
- "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": [
- "Annotation 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": "markdown",
- "metadata": {},
- "source": [
- "Hemispheres stack:"
- ]
- },
- {
- "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 a description of the 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 depend on the underlying atlas, so we cannot ensure the goodness and consistency of their hierarchy tree.\n",
- "---"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "There is a 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 sufficient 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 the 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 the IDs associated with these layers are the ones 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 let's 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 encompasses 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 corresponds to outside the brain, and 1 and 2 to left and right hemispheres respectively - but we can just ask for the hemisphere 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))"
- ]
- }
- ],
- "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": "3.12.4"
- }
- },
- "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 listing available 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 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": [
+ "from pprint import pprint\n",
+ "\n",
+ "import numpy as np\n",
+ "\n",
+ "from brainglobe_atlasapi import BrainGlobeAtlas\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",
+ "\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 Reference, annotation and hemispheres stack"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from matplotlib import pyplot as plt"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Reference stack:"
+ ]
+ },
+ {
+ "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": [
+ "Annotation 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": "markdown",
+ "metadata": {},
+ "source": [
+ "Hemispheres stack:"
+ ]
+ },
+ {
+ "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 a description of the 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 depend on the underlying atlas, so we cannot ensure the goodness and consistency of their hierarchy tree.\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "There is a 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 sufficient 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 the 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 the IDs associated with these layers are the ones 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 let's 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 encompasses 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 corresponds to outside the brain, and 1 and 2 to left and right hemispheres respectively - but we can just ask for the hemisphere 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))"
+ ]
+ }
+ ],
+ "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": "3.12.4"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
}