Repositories list

• OMERO-scripts

  Public

  BIOP/OMERO-scripts’s past year of commit activity
  Series of script to make use of OMERO

  pythongroovyfiji+ 5

  pythongroovyfijiscriptsomeropyqt6ezomeroomero-scripts

  Groovy

  •

  GNU General Public License v3.0

  •2•3•0•0•Updated Mar 17, 2026Mar 17, 2026

• ijp-imagetoatlas

  Public

  BIOP/ijp-imagetoatlas’s past year of commit activity
  ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)

  Java

  •

  MIT License

  •9•56•25•0•Updated Mar 13, 2026Mar 13, 2026

• ijp-atlas

  Public

  BIOP/ijp-atlas’s past year of commit activity
  Repository containins Atlases and Atlas Structure for ABBA plugin

  Java

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Mar 13, 2026Mar 13, 2026

• bigdataviewer-biop-tools

  Public
  Another repo for bdv tools.

  Java

  •2•6•24•1•Updated Mar 13, 2026Mar 13, 2026

• qupath-biop-catalog

  Public
  The catalog containing QuPath extensions maintained by the BIOP team

  Groovy

  •

  Apache License 2.0

  •0•6•0•0•Updated Mar 13, 2026Mar 13, 2026

• qupath-extension-abba

  Public
  QuPath extension for Aligning Big Brains and Atlases

  Java

  •

  MIT License

  •2•7•5•0•Updated Mar 13, 2026Mar 13, 2026

• qupath-extension-warpy

  Public
  ImgLib2 RealTransform brought to QuPath

  Java

  •

  Apache License 2.0

  •7•29•7•0•Updated Mar 12, 2026Mar 12, 2026

• qupath-extension-spotiflow

  Public

  BIOP/qupath-extension-spotiflow’s past year of commit activity
  An extension that wraps a Spotiflow environment such that WSI can be analyzed using Spotiflow through QuPath.

  Java

  •

  Apache License 2.0

  •1•4•1•0•Updated Mar 12, 2026Mar 12, 2026

• bigdataviewer-image-loaders

  Public

  BIOP/bigdataviewer-image-loaders’s past year of commit activity
  Java

  •

  GNU General Public License v3.0

  •0•5•11•0•Updated Mar 11, 2026Mar 11, 2026

• .github

  Public
  Organisation README

  0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

• bigdataviewer-playground-display

  Public
  Display additions for bigdataviewer using bigdataviewer-playground

  Java

  •0•2•0•0•Updated Mar 11, 2026Mar 11, 2026

• ijp-kheops

  Public
  Java

  •

  GNU General Public License v2.0

  •2•21•18•0•Updated Mar 11, 2026Mar 11, 2026

• biop-operetta-tools

  Public
  Scripts and tools to use for the PerkinElmer Operetta System

  Groovy

  •2•1•0•0•Updated Mar 9, 2026Mar 9, 2026

• qupath-extension-biop

  Public
  A QuPath extension with tools made at the BIOP

  qupath

  qupath

  Groovy

  •

  Apache License 2.0

  •3•1•0•0•Updated Mar 3, 2026Mar 3, 2026

• qupath

  Public
  QuPath - Bioimage analysis & digital pathology

  Java

  •

  GNU General Public License v3.0

  •336•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• intellij-workshop

  Public
  Java

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• git-workshop

  Public
  ImageJ Macro

  •0•0•0•0•Updated Feb 16, 2026Feb 16, 2026

• qupath-extension-cellpose

  Public
  an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.

  qupathcellposeomnipose

  qupathcellposeomnipose

  Jupyter Notebook

  •

  Apache License 2.0

  •16•89•5•0•Updated Feb 5, 2026Feb 5, 2026

• ijp-operetta-importer

  Public
  PerkinElmer Operetta Importer using BioFormats!

  HTML

  •

  GNU General Public License v3.0

  •4•10•9•0•Updated Feb 4, 2026Feb 4, 2026

• bigdataviewer-spimdata-extras

  Public
  Extra settings that can be stored in spimdata file format

  Java

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jan 13, 2026Jan 13, 2026

• bigdataviewer-selector

  Public
  Source Selection mode for BigDataViewer

  Java

  •0•1•2•0•Updated Jan 13, 2026Jan 13, 2026

• ijp-jacop-b

  Public
  Jacop by F. Cordelières revamped by the BIOP

  Java

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Jan 8, 2026Jan 8, 2026

• ijl-utilities-wrappers

  Public
  Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)

  Java

  •

  MIT License

  •9•40•4•0•Updated Dec 17, 2025Dec 17, 2025

• quick-start-czi-reader

  Public
  A bio-formats image reader for CZI that starts faster

  Java

  •0•4•7•0•Updated Dec 15, 2025Dec 15, 2025

• ijp-template-ij2

  Public
  Template for ImageJ2 command for the PT-BIOP.

  Java

  •0•0•1•0•Updated Dec 2, 2025Dec 2, 2025

• napari-cotcotcot

  Public
  A napari plugin to use CoTracker3

  Python

  •

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

  •0•4•3•1•Updated Dec 1, 2025Dec 1, 2025

• abba_python

  Public
  ABBA, controlled from python

  Python

  •

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

  •5•19•10•2•Updated Nov 24, 2025Nov 24, 2025

• lightsheet-brain-workflows

  Public
  Java

  •

  MIT License

  •0•1•5•0•Updated Nov 5, 2025Nov 5, 2025

• abba-documentation

  Public
  Documentation for ABBA - Aligning Big Brains & Atlases

  2•1•5•0•Updated Nov 4, 2025Nov 4, 2025

• BIOP-desktop

  Public
  JavaScript

  •

  Apache License 2.0

  •3•14•7•0•Updated Oct 24, 2025Oct 24, 2025