Repositories list

• pycellin

  Public
  Graph-based framework to manipulate and analyze cell lineages from cell tracking data

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•2424 stars•66 issues•33 pull requests•Updated Aug 8, 2026Aug 8, 2026

• cellpose-appose

  Public
  Fiji plugin to use Cellpose with Appose

  cellsegmentationnuclei+ 2

  cellsegmentationnucleifiji-plugincellpose

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •22 forks•88 stars•11 issue•00 pull requests•Updated Aug 6, 2026Aug 6, 2026

• DeProj

  Public
  MATLAB

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 21, 2026Jul 21, 2026

• .github

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Jul 17, 2026Jul 17, 2026

• Epicure

  Public
  Napari plugin to ease manual correction of epithelial movie segmentation

  trackingtissueinteractive+ 4

  trackingtissueinteractivesegmentationcorrectionepitheliatissue-analysis

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •11 fork•1313 stars•00 issues•00 pull requests•Updated Jul 17, 2026Jul 17, 2026

• nnInterappose

  Public
  nnInteractive in Fiji for assisted manual annotation

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 1, 2026Jul 1, 2026

• Pasteur-BioImage-Analysis-Course-2026

  Public archive
  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jun 5, 2026Jun 5, 2026

• Icy-Cellpose

  Public
  Java

  •

  GNU Lesser General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 4, 2026Jun 4, 2026

• yolo-appose

  Public
  Fiji plugin for Yolo image detection via Appose

  Java

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 4, 2026Jun 4, 2026

• bigfish-appose

  Public
  Big-fish in Fiji through appose

  Java

  •

  GNU Affero General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• dextrusion-appose

  Public
  Dextrusion as a Fiji plugin thanks to Appose

  Java

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• DeXtrusion

  Public
  Automatic detection of epithelial cell events, in particular cell extrusion

  PureBasic

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• napari-epyseg

  Public
  Plugin to run epyseg within napari

  segmentationepithelianapari-plugin

  segmentationepithelianapari-plugin

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Mar 24, 2026Mar 24, 2026

• BacteriaMethodsCode

  Public
  Notebooks and scripts for Bacteria Methods paper

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 10, 2025Dec 10, 2025

• localZBackProjector

  Public
  Retrieves the height map from 2D denoised projected epithelia image

  tissueprojectionheightmap+ 2

  tissueprojectionheightmapbioimage-analysisepithelia

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 4, 2025Dec 4, 2025

• Pasteur-BioImage-Analysis-Course-2025

  Public
  Teaching materials and outline for the Pasteur Bioimage Analysis vour

  segmentationteaching-materialsbioimage-analysis+ 1

  segmentationteaching-materialsbioimage-analysisspatial-transcriptomics

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •11 fork•1717 stars•00 issues•00 pull requests•Updated Jun 2, 2025Jun 2, 2025

• LocalZProjector

  Public
  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•33 stars•00 issues•00 pull requests•Updated Sep 25, 2023Sep 25, 2023