Repositories list

• python-imcflibs

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

  Python

  •

  GNU General Public License v3.0

  •3•1•8•3•Updated Mar 25, 2026Mar 25, 2026

• imcf-fiji-update-site

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

  Shell

  •1•0•3•1•Updated Mar 25, 2026Mar 25, 2026

• auto-tx

  Public
  AutoTx - an intelligent background file transfer service for Windows.

  windowsservicedotnet+ 4

  windowsservicedotnetdata-transferemail-notificationspoolingtransfer-service

  C#

  •

  GNU General Public License v3.0

  •1•28•12•0•Updated Mar 25, 2026Mar 25, 2026

• imcf-fiji-scripts

  Public
  :wrench: :memo: :coffee: :microscope: 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

  •4•4•0•1•Updated Mar 25, 2026Mar 25, 2026

• ijl-utilities-wrappers

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

  Java

  •

  MIT License

  •9•0•0•0•Updated Mar 11, 2026Mar 11, 2026

• napari-bioio-reader

  Public
  A simple napari plugin to use Bioio as a reader

  Python

  •

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

  •2•5•1•0•Updated Mar 9, 2026Mar 9, 2026

• imcf.github.io

  Public
  IMCF github pages

  HTML

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

• imarisconverter-wine

  Public
  Imaris File Converter for wine on Linux

  1•0•0•0•Updated Feb 20, 2026Feb 20, 2026

• wine

  Public
  C

  •

  Other

  •1.3k•0•0•0•Updated Feb 20, 2026Feb 20, 2026

• RESPAN

  Public
  Robust, accurate, and unbiased quantification of neurons and dendritic spines.

  Python

  •

  GNU General Public License v3.0

  •8•0•0•0•Updated Feb 18, 2026Feb 18, 2026

• cellpose

  Public
  a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

  Python

  •

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

  •597•0•0•0•Updated Feb 9, 2026Feb 9, 2026

• python-micrometa

  Public
  :coffee: :snake: :microscope: Package for processing metadata from various light-microscopy related data formats.

  imagej2python27jython+ 1

  imagej2python27jythonjython-library

  Python

  •0•1•0•0•Updated Jan 22, 2026Jan 22, 2026

• imcf-fiji-mocks

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

  Python

  •2•1•0•0•Updated Jan 16, 2026Jan 16, 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

  •46•0•0•0•Updated Dec 15, 2025Dec 15, 2025

• auto-subtitle

  Public
  Automatically generate and overlay subtitles for any video.

  Python

  •

  MIT License

  •359•0•0•0•Updated Nov 27, 2025Nov 27, 2025

• auto-subs

  Public
  Instantly generate AI-powered subtitles on your device. Works standalone or connects to DaVinci Resolve.

  TypeScript

  •

  MIT License

  •175•0•0•0•Updated Nov 20, 2025Nov 20, 2025

• vizgen-postprocessing

  Public
  Python

  •

  Apache License 2.0

  •8•0•0•0•Updated Oct 27, 2025Oct 27, 2025

• mesoSPIM-control

  Public
  Image acquisition software for mesoSPIM light-sheet microscopes.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •17•0•0•0•Updated Oct 23, 2025Oct 23, 2025

• vpt-core

  Public
  Core components of the Vizgen Post-processing Tool

  Python

  •

  Apache License 2.0

  •4•0•0•0•Updated Oct 22, 2025Oct 22, 2025

• vpt-plugin-cellpose2

  Public
  Python

  •

  Apache License 2.0

  •3•0•0•0•Updated Oct 21, 2025Oct 21, 2025

• vpt-segmentation-packing

  Public
  Python

  •0•0•0•0•Updated Oct 21, 2025Oct 21, 2025

• ClearMap

  Public
  ClearMap 2 with WobblyStitcher, TubeMap and CellMap

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •60•0•0•0•Updated Aug 22, 2025Aug 22, 2025

• SwissBIAS.github.io

  Public
  Website for the SwissBIAS network: Swiss BioImage Analysts's network

  JavaScript

  •26•0•0•0•Updated Jun 23, 2025Jun 23, 2025

• omero-prometheus-tools

  Public
  Utilities for monitoring OMERO with Prometheus

  Python

  •11•0•0•0•Updated Jun 6, 2025Jun 6, 2025

• psytricks

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

  pythonpowershellpoetry+ 2

  pythonpowershellpoetrycitrixcvad

  Python

  •

  GNU General Public License v3.0

  •0•0•1•0•Updated May 9, 2025May 9, 2025

• napari-psf-analysis

  Public
  A napari plugin to analysis point spread functions.

  Python

  •

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

  •5•0•0•0•Updated Mar 28, 2025Mar 28, 2025

• omero-cli-transfer

  Public
  An OMERO CLI plugin for creating transfer packets between OMERO servers.

  Python

  •

  GNU General Public License v2.0

  •18•0•0•0•Updated Feb 18, 2025Feb 18, 2025

• scijava-scripts

  Public
  Shell scripts for scientific projects written in Java

  Shell

  •

  The Unlicense

  •15•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• file-size-age-metrics

  Public
  Prometheus exporter providing size 📐 and age ⏱ metrics 🧮 about files.

  pythonmetricsprometheus-exporter+ 1

  pythonmetricsprometheus-exporterprometheus-metrics

  Python

  •

  GNU General Public License v3.0

  •0•0•1•0•Updated Feb 7, 2025Feb 7, 2025

• ZeroCostDL4Mic

  Public
  ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy

  Jupyter Notebook

  •

  MIT License

  •142•0•0•0•Updated Feb 3, 2025Feb 3, 2025