Repositories list

• patchworks

  Public
  Tiled processing of arbitrarily large images — any image, any function.

  Python

  •

  GNU General Public License v3.0

  •00 forks in imcf/patchworks•1818 stars in imcf/patchworks•11 issue in imcf/patchworks•11 pull request in imcf/patchworks•Updated Oct 21, 2026Oct 21, 2026

• auto-tx

  Public
  🚚 AutoTx 🪄 - a smart background file transfer service for Windows.

  windowsservicedotnet+ 4

  windowsservicedotnetdata-transferemail-notificationspoolingtransfer-service

  C#

  •

  GNU General Public License v3.0

  •22 forks in imcf/auto-tx•3232 stars in imcf/auto-tx•1212 issues in imcf/auto-tx•11 pull request in imcf/auto-tx•Updated Oct 21, 2026Oct 21, 2026

• python-imcflibs

  Public
  🐍 ☕ 🔩 🔧 🪛 A collection of commonly used Python helper functions.

  Python

  •

  GNU General Public License v3.0

  •44 forks in imcf/python-imcflibs•11 star in imcf/python-imcflibs•1010 issues in imcf/python-imcflibs•33 pull requests in imcf/python-imcflibs•Updated Oct 14, 2026Oct 14, 2026

• imcf-fiji-mocks

  Public
  Python mocks 🧌 providing dummy imports e.g. for testing the IMCF Fiji Python packages.

  Python

  •33 forks in imcf/imcf-fiji-mocks•11 star in imcf/imcf-fiji-mocks•00 issues in imcf/imcf-fiji-mocks•00 pull requests in imcf/imcf-fiji-mocks•Updated Oct 14, 2026Oct 14, 2026

• imcf.github.io

  Public
  IMCF github pages

  HTML

  •00 forks in imcf/imcf.github.io•00 stars in imcf/imcf.github.io•00 issues in imcf/imcf.github.io•00 pull requests in imcf/imcf.github.io•Updated Oct 13, 2026Oct 13, 2026

• instanseg-fiji

  Public
  This repository is a thin wrapper around InstanSeg (https://github.com/instanseg), developed by Goldsborough, T. et al. (2024) for Fiji, making the model runnab…

  Python

  •

  GNU General Public License v3.0

  •00 forks in imcf/instanseg-fiji•88 stars in imcf/instanseg-fiji•00 issues in imcf/instanseg-fiji•00 pull requests in imcf/instanseg-fiji•Updated Oct 12, 2026Oct 12, 2026

• napari-chunked-regionprops

  Public
  Napari measure widget — dask-image regionprops for huge labelled images

  Python

  •

  GNU General Public License v3.0

  •00 forks in imcf/napari-chunked-regionprops•00 stars in imcf/napari-chunked-regionprops•00 issues in imcf/napari-chunked-regionprops•11 pull request in imcf/napari-chunked-regionprops•Updated Oct 8, 2026Oct 8, 2026

• omero-downloader-gui

  Public
  A simple OMERO downloader GUI using Python 🪄📥

  Python

  •

  GNU General Public License v3.0

  •00 forks in imcf/omero-downloader-gui•22 stars in imcf/omero-downloader-gui•22 issues in imcf/omero-downloader-gui•00 pull requests in imcf/omero-downloader-gui•Updated Oct 8, 2026Oct 8, 2026

• mesoSPIM-control

  Public
  Image acquisition software for mesoSPIM light-sheet microscopes.

  Python

  •

  GNU General Public License v3.0

  •2020 forks in imcf/mesoSPIM-control•00 stars in imcf/mesoSPIM-control•00 issues in imcf/mesoSPIM-control•00 pull requests in imcf/mesoSPIM-control•Updated Oct 7, 2026Oct 7, 2026

• sopa

  Public
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

  Python

  •

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

  •5353 forks in imcf/sopa•00 stars in imcf/sopa•00 issues in imcf/sopa•00 pull requests in imcf/sopa•Updated Sep 3, 2026Sep 3, 2026

• vpt-plugin-cellpose2

  Public
  Python

  •

  Apache License 2.0

  •33 forks in imcf/vpt-plugin-cellpose2•00 stars in imcf/vpt-plugin-cellpose2•00 issues in imcf/vpt-plugin-cellpose2•00 pull requests in imcf/vpt-plugin-cellpose2•Updated Aug 28, 2026Aug 28, 2026

• pyppms

  Public
  📑 🕙 🐍 A Python package to communicate with Stratocore's PUMAPI.

  pythonweb-apibooking-system+ 3

  pythonweb-apibooking-systemppmspumapiresearch-facility

  Python

  •33 forks in imcf/pyppms•66 stars in imcf/pyppms•11 issue in imcf/pyppms•11 pull request in imcf/pyppms•Updated Aug 14, 2026Aug 14, 2026

• generate-well-points

  Public
  For a Nikon Ti2 microscope, generate an entire set of imaging coordinates according to a template from a set of reference points.

  Python

  •

  GNU General Public License v2.0

  •00 forks in imcf/generate-well-points•00 stars in imcf/generate-well-points•00 issues in imcf/generate-well-points•00 pull requests in imcf/generate-well-points•Updated Aug 11, 2026Aug 11, 2026

• imcf-fiji-update-site

  Public
  ☕ 🔬 🚚 🌍 Managing the "UniBas-IMCF" update site for Fiji.

  Shell

  •22 forks in imcf/imcf-fiji-update-site•00 stars in imcf/imcf-fiji-update-site•44 issues in imcf/imcf-fiji-update-site•22 pull requests in imcf/imcf-fiji-update-site•Updated Aug 7, 2026Aug 7, 2026

• spot-fiction

  Public
  Python

  •

  GNU General Public License v3.0

  •00 forks in imcf/spot-fiction•00 stars in imcf/spot-fiction•00 issues in imcf/spot-fiction•00 pull requests in imcf/spot-fiction•Updated Jul 29, 2026Jul 29, 2026

• psytricks

  Public
  PowerShell-Python-Citrix vodoo. :alien: :dizzy_face:

  pythonpowershellpoetry+ 2

  pythonpowershellpoetrycitrixcvad

  Python

  •

  GNU General Public License v3.0

  •00 forks in imcf/psytricks•00 stars in imcf/psytricks•11 issue in imcf/psytricks•00 pull requests in imcf/psytricks•Updated Jul 21, 2026Jul 21, 2026

• imcf-fiji-scripts

  Public
  🔧 📝 ☕ 🔬 Scripts for Fiji provided by the Imaging Core Facility, Biozentrum, University of Basel

  imagejfijiimage-processing+ 2

  imagejfijiimage-processingimageprocessingfacility

  Python

  •

  GNU General Public License v3.0

  •44 forks in imcf/imcf-fiji-scripts•44 stars in imcf/imcf-fiji-scripts•00 issues in imcf/imcf-fiji-scripts•22 pull requests in imcf/imcf-fiji-scripts•Updated Jun 24, 2026Jun 24, 2026

• TrackMate

  Public
  TrackMate is your buddy for your everyday tracking.

  Java

  •

  GNU General Public License v3.0

  •8888 forks in imcf/TrackMate•00 stars in imcf/TrackMate•00 issues in imcf/TrackMate•00 pull requests in imcf/TrackMate•Updated Jun 18, 2026Jun 18, 2026

• TrackMate-Cellpose

  Public
  Tentative Cellpose integration in TrackMate.

  Java

  •

  GNU Affero General Public License v3.0

  •55 forks in imcf/TrackMate-Cellpose•00 stars in imcf/TrackMate-Cellpose•00 issues in imcf/TrackMate-Cellpose•00 pull requests in imcf/TrackMate-Cellpose•Updated Jun 18, 2026Jun 18, 2026

• napari-tmidas

  Public
  Automated batch processing of cell and tissue microscopy image data in Napari

  Python

  •

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

  •11 fork in imcf/napari-tmidas•00 stars in imcf/napari-tmidas•00 issues in imcf/napari-tmidas•00 pull requests in imcf/napari-tmidas•Updated Jun 18, 2026Jun 18, 2026

• cellstitch-cuda

  Public
  Accelerated CellStitch for 3D labeling of anisotropic image stacks

  Python

  •

  Other

  •55 forks in imcf/cellstitch-cuda•00 stars in imcf/cellstitch-cuda•00 issues in imcf/cellstitch-cuda•00 pull requests in imcf/cellstitch-cuda•Updated May 22, 2026May 22, 2026

• cellpose-appose

  Public
  Fiji plugin to use Cellpose with Appose

  Java

  •

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

  •22 forks in imcf/cellpose-appose•00 stars in imcf/cellpose-appose•00 issues in imcf/cellpose-appose•00 pull requests in imcf/cellpose-appose•Updated May 18, 2026May 18, 2026

• pixi-pack-action-python

  Public
  🧚💛🐍 "pixi-pack" action using "pixi-build-python"

  pythonpackagingconda+ 2

  pythonpackagingcondapixigh-actions

  00 forks in imcf/pixi-pack-action-python•11 star in imcf/pixi-pack-action-python•00 issues in imcf/pixi-pack-action-python•00 pull requests in imcf/pixi-pack-action-python•Updated Apr 29, 2026Apr 29, 2026

• ttkbootstrap

  Public
  A modern theming library for Tkinter that adds sleek, responsive styles inspired by Bootstrap. Includes ready-to-use widgets, 20+ themes, and tools for building…

  Python

  •

  MIT License

  •455455 forks in imcf/ttkbootstrap•00 stars in imcf/ttkbootstrap•00 issues in imcf/ttkbootstrap•00 pull requests in imcf/ttkbootstrap•Updated Apr 27, 2026Apr 27, 2026

• ijl-utilities-wrappers

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

  Java

  •

  MIT License

  •99 forks in imcf/ijl-utilities-wrappers•00 stars in imcf/ijl-utilities-wrappers•00 issues in imcf/ijl-utilities-wrappers•00 pull requests in imcf/ijl-utilities-wrappers•Updated Apr 20, 2026Apr 20, 2026

• omero-figure

  Public
  An OMERO.web app for creating Figures from images in OMERO

  JavaScript

  •

  GNU Affero General Public License v3.0

  •3838 forks in imcf/omero-figure•00 stars in imcf/omero-figure•00 issues in imcf/omero-figure•00 pull requests in imcf/omero-figure•Updated Apr 2, 2026Apr 2, 2026

• citrix-collector

  Public
  PowerShell based collector of Citrix metrics for Prometheus (creating a textfile for the windows_exporter).

  PowerShell

  •

  GNU General Public License v3.0

  •00 forks in imcf/citrix-collector•00 stars in imcf/citrix-collector•11 issue in imcf/citrix-collector•00 pull requests in imcf/citrix-collector•Updated Mar 30, 2026Mar 30, 2026

• napari-bioio-reader

  Public
  A simple napari plugin to use Bioio as a reader

  Python

  •

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

  •22 forks in imcf/napari-bioio-reader•66 stars in imcf/napari-bioio-reader•11 issue in imcf/napari-bioio-reader•00 pull requests in imcf/napari-bioio-reader•Updated Mar 9, 2026Mar 9, 2026

• imarisconverter-wine

  Public
  Imaris File Converter for wine on Linux

  11 fork in imcf/imarisconverter-wine•00 stars in imcf/imarisconverter-wine•00 issues in imcf/imarisconverter-wine•00 pull requests in imcf/imarisconverter-wine•Updated Feb 20, 2026Feb 20, 2026

• wine

  Public
  C

  •

  Other

  •1.5k1.5k forks in imcf/wine•00 stars in imcf/wine•00 issues in imcf/wine•00 pull requests in imcf/wine•Updated Feb 20, 2026Feb 20, 2026