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    120 repositories

    • 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
      •0•0•0•0•Updated Aug 11, 2026Aug 11, 2026

    • pyppms

      Public
      📑 🕙 🐍 A Python package to communicate with Stratocore's PUMAPI.
      pythonweb-apibooking-system
      pythonweb-apibooking-systemppmspumapiresearch-facility
      Python
      •4•6•1•1•Updated Aug 10, 2026Aug 10, 2026

    • imcf-fiji-update-site

      Public
      ☕ 🔬 🚚 🌍 Managing the "UniBas-IMCF" update site for Fiji.
      Shell
      •2•0•4•1•Updated Aug 7, 2026Aug 7, 2026

    • imcf.github.io

      Public
      IMCF github pages
      HTML
      •0•0•0•0•Updated Aug 7, 2026Aug 7, 2026

    • patchworks

      Public
      Tiled processing of arbitrarily large images — any image, any function.
      Python
      •
      GNU General Public License v3.0
      •0•18•1•0•Updated Aug 5, 2026Aug 5, 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
      •0•4•0•0•Updated Jul 31, 2026Jul 31, 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
      •51•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • spot-fiction

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 29, 2026Jul 29, 2026

    • psytricks

      Public
      PowerShell-Python-Citrix vodoo. :alien: :dizzy_face:
      pythonpowershellpoetry
      pythonpowershellpoetrycitrixcvad
      Python
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Jul 21, 2026Jul 21, 2026

    • napari-chunked-regionprops

      Public
      Napari measure widget — dask-image regionprops for huge labelled images
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 21, 2026Jul 21, 2026

    • auto-tx

      Public
      🚚 AutoTx 🪄 - a smart background file transfer service for Windows.
      windowsservicedotnet
      windowsservicedotnetdata-transferemail-notificationspoolingtransfer-service
      C#
      •
      GNU General Public License v3.0
      •2•31•11•1•Updated Jul 8, 2026Jul 8, 2026

    • python-imcflibs

      Public
      🐍 ☕ 🔩 🔧 🪛 A collection of commonly used Python helper functions.
      Python
      •
      GNU General Public License v3.0
      •3•1•9•0•Updated Jun 25, 2026Jun 25, 2026

    • imcf-fiji-scripts

      Public
      🔧 📝 ☕ 🔬 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 Jun 24, 2026Jun 24, 2026

    • TrackMate

      Public
      TrackMate is your buddy for your everyday tracking.
      Java
      •
      GNU General Public License v3.0
      •87•0•0•0•Updated Jun 18, 2026Jun 18, 2026

    • TrackMate-Cellpose

      Public
      Tentative Cellpose integration in TrackMate.
      Java
      •
      GNU Affero General Public License v3.0
      •5•0•0•0•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
      •1•0•0•0•Updated Jun 18, 2026Jun 18, 2026

    • cellstitch-cuda

      Public
      Accelerated CellStitch for 3D labeling of anisotropic image stacks
      Python
      •
      Other
      •5•0•0•0•Updated May 22, 2026May 22, 2026

    • cellpose-appose

      Public
      Fiji plugin to use Cellpose with Appose
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated May 18, 2026May 18, 2026

    • pixi-pack-action-python

      Public
      🧚💛🐍 "pixi-pack" action using "pixi-build-python"
      pythonpackagingconda
      pythonpackagingcondapixigh-actions
      0•1•0•0•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
      •459•0•0•0•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
      •9•0•0•0•Updated Apr 20, 2026Apr 20, 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

    • 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

    • 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
      •12•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
      •645•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
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