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    43 repositories

    • VollSeg

      Public
      Segmentation method able to detect membrane/nuclei-labelled cells with low signal-to-noise ratio and dense packing in 2D and 3D. Available via pip package vollseg.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•33•0•0•Updated Nov 25, 2024Nov 25, 2024

    • NapaTrackMater

      Public
      Napari Visualization tool for Trackmate > 6.0 and bTrackmate XML files for 2/3D + time tracks. Available via pip package napatrackmater.
      xml-filestrackmatenaparinapari-visualization
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•16•0•0•Updated Nov 19, 2024Nov 19, 2024

    • KapoorLabs-Lightning

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Nov 19, 2024Nov 19, 2024

    • cookiecutter-kapoorlabs-napari-plugin

      Public
      Cookiecutter template for generating KapoorLabs written Napari plugins.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • vollseg-napari-trackmate

      Public
      Track analysis using TrackMate xml and csv generated tracks using NapaTrackMater as the base library
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • caped-ai-oneat

      Public
      oneat = Osis Network for Event as Action Topologies. Available via pip package oneat
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•0•Updated Sep 8, 2024Sep 8, 2024

    • .github

      Public
      0•0•0•0•Updated Aug 3, 2024Aug 3, 2024

    • caped-ai-tabulour

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 20, 2024Jul 20, 2024

    • trackastra

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•0•0•0•Updated May 30, 2024May 30, 2024

    • vollseg-napari-mtrack

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated May 29, 2024May 29, 2024

    • vollseg-napari

      Public
      Napari plugin for vollseg
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•13•0•0•Updated May 27, 2024May 27, 2024

    • caped-ai-metrics

      Public
      Metrics for instance segmentation and static and action classification. Available via pip package caped-ai-metrics.
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 22, 2024Apr 22, 2024

    • nellie-actin-tubules

      Public
      Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
      Python
      •
      Other
      •4•0•0•0•Updated Apr 18, 2024Apr 18, 2024

    • VNet

      Public
      Visualize activations of any neural network in Napari
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 9, 2023Dec 9, 2023

    • caped-ai-mtrack

      Public
      Ransac based methods for function fitting on Microtubule Kymographs
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 7, 2023Oct 7, 2023

    • quartic-solver

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 6, 2023Oct 6, 2023

    • caped-ai-augmentations

      Public
      Augmentation library built on top of albumentations for augmentation of segmentation and classification catasets. Available via pip package caped-ai-augmentations
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 25, 2023Aug 25, 2023

    • vollseg-napari-btrack

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 2, 2023Jul 2, 2023

    • caped-ai

      Public
      Mother package of oneat and vollseg algorithms. Combining the mix of both to create image analysis workflows.
      Python
      •1•0•0•0•Updated Jul 1, 2023Jul 1, 2023

    • cookiecutter-template

      Public
      Cookiecutter for pypi packages
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 15, 2023May 15, 2023

    • segment-anything

      Public
      The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.
      Jupyter Notebook
      •
      Apache License 2.0
      •5.7k•0•0•0•Updated Apr 7, 2023Apr 7, 2023

    • Server-Setup-Scripts

      Public
      The SSS of setting up things on remote linux servers, AWS servers
      Shell
      •0•0•0•0•Updated Mar 19, 2023Mar 19, 2023

    • caped-ai-cellpose3D

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Feb 25, 2023Feb 25, 2023

    • caped-ai-sentinal

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 4, 2023Feb 4, 2023

    • vollseg-napari-metrics

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 4, 2023Feb 4, 2023

    • tabulour

      Public
      A table data viewer for Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•0•0•0•Updated Jan 23, 2023Jan 23, 2023

    • cellpose

      Public
      a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •402•0•0•0•Updated Jan 22, 2023Jan 22, 2023

    • napari-hub-collections

      Public
      collections of plugins for the napari hub
      Python
      •
      MIT License
      •7•0•0•0•Updated Jan 13, 2023Jan 13, 2023

    • caped-ai-visualizations

      Public
      Visualization library for bounding boxes, activation maps of vollseg segmentation and oneat classification networks. Available via pip package caped-ai-visualizations.
      Python
      •0•0•0•0•Updated Dec 20, 2022Dec 20, 2022

    • caped-ai-skeletonize

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 30, 2022Nov 30, 2022