Repositories list

• ijp-operetta-importer

  Public
  PerkinElmer Operetta Importer using BioFormats!

  HTML

  •

  GNU General Public License v3.0

  •3•9•10•0•Updated Sep 1, 2025Sep 1, 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

• bigdataviewer-biop-tools

  Public
  Another repo for bdv tools.

  Java

  •2•5•28•1•Updated Aug 29, 2025Aug 29, 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 Aug 28, 2025Aug 28, 2025

• BIOP-desktop

  Public
  JavaScript

  •

  Apache License 2.0

  •2•12•6•0•Updated Aug 28, 2025Aug 28, 2025

• ijp-imagetoatlas

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

  Java

  •9•52•41•0•Updated Aug 27, 2025Aug 27, 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-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•3•1•0•Updated Aug 26, 2025Aug 26, 2025

• abba-documentation

  Public
  Documentation for ABBA - Aligning Big Brains & Atlases

  2•1•2•0•Updated Aug 21, 2025Aug 21, 2025

• qupath-biop-catalog

  Public
  The catalog containing QuPath extensions maintained by the BIOP team

  Groovy

  •

  Apache License 2.0

  •0•1•1•0•Updated Aug 21, 2025Aug 21, 2025

• bigdataviewer-image-loaders

  Public
  Java

  •

  GNU General Public License v3.0

  •0•5•8•0•Updated Aug 20, 2025Aug 20, 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 Aug 20, 2025Aug 20, 2025

• qupath-extension-abba

  Public
  QuPath extension for Aligning Big Brains and Atlases

  Java

  •

  MIT License

  •2•6•5•0•Updated Aug 12, 2025Aug 12, 2025

• qupath-extension-warpy

  Public
  ImgLib2 RealTransform brought to QuPath

  Java

  •

  Apache License 2.0

  •7•26•7•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-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

  •14•77•6•0•Updated Aug 12, 2025Aug 12, 2025

• abba_python

  Public
  ABBA, controlled from python

  Python

  •

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

  •4•15•12•1•Updated Aug 11, 2025Aug 11, 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

• lightsheet-brain-workflows

  Public
  Java

  •

  MIT License

  •0•1•5•0•Updated Jul 31, 2025Jul 31, 2025

• ijp-kheops

  Public
  Java

  •

  GNU General Public License v2.0

  •2•20•17•0•Updated Jul 31, 2025Jul 31, 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

  •311•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

• ijl-utilities-wrappers

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

  Java

  •

  MIT License

  •7•37•5•0•Updated May 26, 2025May 26, 2025

• quick-start-czi-reader

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

  Java

  •0•5•7•0•Updated May 5, 2025May 5, 2025

• gist-query

  Public
  Query Gists by the BIOP and add them into a table format compatible with C4Science

  Jupyter Notebook

  •0•3•0•0•Updated Mar 27, 2025Mar 27, 2025

• abba-installer

  Public
  Repository backing the creation of standalone installers for ABBA

  Python

  •

  Other

  •0•2•15•0•Updated Mar 3, 2025Mar 3, 2025

• bigdataviewer-selector

  Public
  Source Selection mode for BigDataViewer

  Java

  •0•1•2•0•Updated Jan 31, 2025Jan 31, 2025