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    110 repositories

    • imcf-fiji-update-site

      Public
      ☕ 🔬 🚚 🌍 Managing the "UniBas-IMCF" update site for Fiji.
      Shell
      •1•0•3•1•Updated Apr 23, 2026Apr 23, 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
      •462•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • cellstitch-cuda

      Public
      Accelerated CellStitch for 3D labeling of anisotropic image stacks
      Python
      •
      Other
      •5•0•0•0•Updated Apr 21, 2026Apr 21, 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 Apr 20, 2026Apr 20, 2026

    • python-imcflibs

      Public
      🐍 ☕ 🔩 🔧 🪛 A collection of commonly used Python helper functions.
      Python
      •
      GNU General Public License v3.0
      •3•1•10•2•Updated Apr 17, 2026Apr 17, 2026

    • imcf-fiji-mocks

      Public
      Python mocks 🧌 providing dummy imports e.g. for testing the IMCF Fiji Python packages.
      Python
      •3•1•0•0•Updated Apr 8, 2026Apr 8, 2026

    • omero-figure

      Public
      An OMERO.web app for creating Figures from images in OMERO
      JavaScript
      •
      GNU Affero General Public License v3.0
      •38•0•0•0•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
      •0•0•1•0•Updated Mar 30, 2026Mar 30, 2026

    • auto-tx

      Public
      AutoTx - an intelligent background file transfer service for Windows.
      windowsservicedotnet
      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
      imagejfijiimage-processingimageprocessingfacility
      Python
      •
      GNU General Public License v3.0
      •4•4•0•1•Updated Mar 25, 2026Mar 25, 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
      •609•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
      imagej2python27jythonjython-library
      Python
      •0•1•0•0•Updated Jan 22, 2026Jan 22, 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
      •49•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • auto-subtitle

      Public
      Automatically generate and overlay subtitles for any video.
      Python
      •
      MIT License
      •361•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
      •192•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • vizgen-postprocessing

      Public
      Python
      •
      Apache License 2.0
      •9•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
      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
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