Repositories list

• 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

• ijp-imagetoatlas

  Public
  ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)

  Java

  •

  MIT License

  •9•56•25•0•Updated Dec 15, 2025Dec 15, 2025

• bigdataviewer-image-loaders

  Public
  Java

  •

  GNU General Public License v3.0

  •0•5•9•0•Updated Dec 15, 2025Dec 15, 2025

• bigdataviewer-biop-tools

  Public
  Another repo for bdv tools.

  Java

  •2•5•28•1•Updated Dec 15, 2025Dec 15, 2025

• ijp-operetta-importer

  Public
  PerkinElmer Operetta Importer using BioFormats!

  HTML

  •

  GNU General Public License v3.0

  •4•10•10•0•Updated Dec 15, 2025Dec 15, 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

• OMERO-scripts

  Public
  Series of script to make use of OMERO

  pythongroovyfiji+ 5scriptsomeropyqt6ezomeroomero-scripts

  Groovy

  •

  GNU General Public License v3.0

  •2•3•0•0•Updated Dec 12, 2025Dec 12, 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•2•1•Updated Dec 1, 2025Dec 1, 2025

• qupath-biop-catalog

  Public
  The catalog containing QuPath extensions maintained by the BIOP team

  Groovy

  •

  Apache License 2.0

  •0•5•0•0•Updated Nov 30, 2025Nov 30, 2025

• qupath-extension-cellpose

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

  qupathcellposeomnipose

  Jupyter Notebook

  •

  Apache License 2.0

  •15•84•7•0•Updated Nov 30, 2025Nov 30, 2025

• abba_python

  Public
  ABBA, controlled from python

  Python

  •

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

  •4•17•10•1•Updated Nov 24, 2025Nov 24, 2025

• qupath-extension-spotiflow

  Public
  An extension that wraps a Spotiflow environment such that WSI can be analyzed using Spotiflow through QuPath.

  Java

  •

  Apache License 2.0

  •1•4•0•0•Updated Nov 5, 2025Nov 5, 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•3•0•Updated Nov 4, 2025Nov 4, 2025

• qupath-extension-biop

  Public
  A QuPath extension with tools made at the BIOP

  qupath

  Groovy

  •

  Apache License 2.0

  •3•1•0•0•Updated Nov 3, 2025Nov 3, 2025

• BIOP-desktop

  Public
  JavaScript

  •

  Apache License 2.0

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

• ijp-kheops

  Public
  Java

  •

  GNU General Public License v2.0

  •2•20•18•0•Updated Oct 17, 2025Oct 17, 2025

• qupath-extension-warpy

  Public
  ImgLib2 RealTransform brought to QuPath

  Java

  •

  Apache License 2.0

  •7•28•8•0•Updated Oct 1, 2025Oct 1, 2025

• abba-installer

  Public
  Repository backing the creation of standalone installers for ABBA

  Python

  •

  Other

  •0•2•15•0•Updated Sep 16, 2025Sep 16, 2025

• ArgoLight_analysis_tool

  Public
  Code to control the quality of images taken with our microscopes

  javafijiomero+ 2fiji-pluginmetrology

  Java

  •

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

  •1•2•1•0•Updated Sep 1, 2025Sep 1, 2025

• ijp-atlas

  Public
  Repository containins Atlases and Atlas Structure for ABBA plugin

  Java

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Aug 27, 2025Aug 27, 2025

• qupath-extension-abba

  Public
  QuPath extension for Aligning Big Brains and Atlases

  Java

  •

  MIT License

  •2•7•5•0•Updated Aug 12, 2025Aug 12, 2025

• qupath-scripts

  Public archive
  This repository contains Scripts we found useful when using QuPath

  Groovy

  •

  GNU General Public License v3.0

  •3•7•0•0•Updated Aug 12, 2025Aug 12, 2025

• qupath-extension-biop-omero

  Public
  QuPath extension to work with images through OMERO's Java API (raw)

  javaomeroqupath

  Java

  •

  GNU General Public License v3.0

  •11•5•6•0•Updated Aug 11, 2025Aug 11, 2025

• biop-bash-scripts

  Public
  Bash scripts to simplify your life (let's hope so!)

  Shell

  •9•11•11•0•Updated Jul 21, 2025Jul 21, 2025

• qupath

  Public
  QuPath - Bioimage analysis & digital pathology

  Java

  •

  GNU General Public License v3.0

  •321•0•0•0•Updated Jun 30, 2025Jun 30, 2025

• biop-operetta-tools

  Public
  Scripts and tools to use for the PerkinElmer Operetta System

  Groovy

  •2•1•0•0•Updated Jun 25, 2025Jun 25, 2025

• ijab-biop-channel-tools

  Public
  Tools to ease propagation of channel settings (B&C, LUT) to many images Includes super montage options See https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/imagej_tools/ijab-biop_channel_tools/

  ImageJ Macro

  •0•3•0•0•Updated Jun 25, 2025Jun 25, 2025

• biop-gitlab-admin

  Public
  Our tools to use GitLab at EPFL to manage user Image Analysis projects

  Groovy

  •0•1•3•0•Updated Jun 18, 2025Jun 18, 2025