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    • intellij-workshop

      Public
      Java
      0000Updated Feb 17, 2026Feb 17, 2026
    • ImageJ Macro
      0000Updated Feb 16, 2026Feb 16, 2026
    • qupath-biop-catalog

      Public
      The catalog containing QuPath extensions maintained by the BIOP team
      Groovy
      0500Updated Feb 12, 2026Feb 12, 2026
    • A QuPath extension with tools made at the BIOP
      Groovy
      3100Updated Feb 12, 2026Feb 12, 2026
    • qupath-extension-cellpose

      Public
      an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.
      Jupyter Notebook
      158850Updated Feb 5, 2026Feb 5, 2026
    • bigdataviewer-image-loaders

      Public
      Java
      05110Updated Feb 5, 2026Feb 5, 2026
    • PerkinElmer Operetta Importer using BioFormats!
      HTML
      41090Updated Feb 4, 2026Feb 4, 2026
    • ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)
      Java
      956250Updated Feb 2, 2026Feb 2, 2026
    • qupath-extension-spotiflow

      Public
      An extension that wraps a Spotiflow environment such that WSI can be analyzed using Spotiflow through QuPath.
      Java
      1400Updated Jan 20, 2026Jan 20, 2026
    • Another repo for bdv tools.
      Java
      26241Updated Jan 19, 2026Jan 19, 2026
    • .github

      Public
      Organisation README
      0000Updated Jan 13, 2026Jan 13, 2026
    • ijp-atlas

      Public
      Repository containins Atlases and Atlas Structure for ABBA plugin
      Java
      0030Updated Jan 13, 2026Jan 13, 2026
    • Extra settings that can be stored in spimdata file format
      Java
      1000Updated Jan 13, 2026Jan 13, 2026
    • Source Selection mode for BigDataViewer
      Java
      0120Updated Jan 13, 2026Jan 13, 2026
    • Display additions for bigdataviewer using bigdataviewer-playground
      Java
      0200Updated Jan 13, 2026Jan 13, 2026
    • Java
      220180Updated Jan 13, 2026Jan 13, 2026
    • Jacop by F. Cordelières revamped by the BIOP
      Java
      0200Updated Jan 8, 2026Jan 8, 2026
    • Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)
      Java
      94040Updated Dec 17, 2025Dec 17, 2025
    • A bio-formats image reader for CZI that starts faster
      Java
      0470Updated Dec 15, 2025Dec 15, 2025
    • Series of script to make use of OMERO
      Groovy
      2300Updated Dec 12, 2025Dec 12, 2025
    • Template for ImageJ2 command for the PT-BIOP.
      Java
      0010Updated Dec 2, 2025Dec 2, 2025
    • A napari plugin to use CoTracker3
      Python
      0431Updated Dec 1, 2025Dec 1, 2025
    • ABBA, controlled from python
      Python
      519102Updated Nov 24, 2025Nov 24, 2025
    • Java
      0150Updated Nov 5, 2025Nov 5, 2025
    • Documentation for ABBA - Aligning Big Brains & Atlases
      2150Updated Nov 4, 2025Nov 4, 2025
    • JavaScript
      31470Updated Oct 24, 2025Oct 24, 2025
    • ImgLib2 RealTransform brought to QuPath
      Java
      72980Updated Oct 1, 2025Oct 1, 2025
    • Repository backing the creation of standalone installers for ABBA
      Python
      02150Updated Sep 16, 2025Sep 16, 2025
    • Code to control the quality of images taken with our microscopes
      Java
      1240Updated Sep 1, 2025Sep 1, 2025
    • QuPath extension for Aligning Big Brains and Atlases
      Java
      2750Updated Aug 12, 2025Aug 12, 2025