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    99 repositories

    • imcf.github.io

      Public
      IMCF github pages
      HTML
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • imcf-fiji-update-site

      Public
      ☕ 🔬 🚚 🌍 Managing the "UniBas-IMCF" update site for Fiji.
      JavaScript
      •1•0•3•1•Updated Oct 30, 2025Oct 30, 2025

    • auto-tx

      Public
      AutoTx - an intelligent background file transfer service for Windows.
      windowsservicedotnetdata-transferemail-notificationspoolingtransfer-service
      C#
      •
      GNU General Public License v3.0
      •1•28•11•0•Updated Oct 29, 2025Oct 29, 2025

    • vizgen-postprocessing

      Public
      Python
      •
      Apache License 2.0
      •7•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
      •16•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
      •2•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • vpt-plugin-cellpose2

      Public
      Python
      •
      Apache License 2.0
      •1•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
      •59•0•0•0•Updated Aug 22, 2025Aug 22, 2025

    • imcf-fiji-scripts

      Public
      🔧 📝 ☕ 🔬 Scripts for Fiji provided by the Imaging Core Facility, Biozentrum, University of Basel
      imagejfijiimage-processingimageprocessingfacility
      Python
      •
      GNU General Public License v3.0
      •3•4•0•1•Updated Aug 19, 2025Aug 19, 2025

    • napari-bioio-reader

      Public
      A simple napari plugin to use Bioio as a reader
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•2•0•Updated Jul 4, 2025Jul 4, 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. 👽 😵
      pythonpowershellpoetrycitrixcvad
      Python
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated May 9, 2025May 9, 2025

    • imcf-fiji-mocks

      Public
      Python mocks 🧌 providing dummy imports e.g. for testing the IMCF Fiji Python packages.
      Python
      •2•1•0•1•Updated May 6, 2025May 6, 2025

    • python-imcflibs

      Public
      🐍 ☕ 🔩 🔧 🪛 A collection of commonly used Python helper functions.
      Python
      •
      GNU General Public License v3.0
      •3•1•6•12•Updated May 6, 2025May 6, 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
      •17•0•0•0•Updated Feb 18, 2025Feb 18, 2025

    • scijava-scripts

      Public
      Shell scripts for scientific projects written in Java
      Shell
      •
      The Unlicense
      •16•0•0•0•Updated Feb 12, 2025Feb 12, 2025

    • file-size-age-metrics

      Public
      Prometheus exporter providing size 📐 and age ⏱ metrics 🧮 about files.
      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
      •141•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • imcf-fiji-toolbars

      Public
      ☕ 🔬 🔣 Fiji Action Bars provided by the IMCF.
      imagejfijiimage-processingimageprocessing
      ImageJ Macro
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • bootstrap-bp-hugo-startpage

      Public
      Bootstrap based Hugo startpage theme which provides out of the box best practices.
      HTML
      •
      MIT License
      •38•0•0•0•Updated Jan 15, 2025Jan 15, 2025

    • omero-scripts

      Public
      Extracted OmeroPy/scripts directory for local modifications.
      Python
      •32•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • python-micrometa

      Public
      ☕ 🐍 🔬 Package for processing metadata from various light-microscopy related data formats.
      imagej2python27jythonjython-library
      Python
      •0•1•0•0•Updated Nov 19, 2024Nov 19, 2024

    • jython-scijava-logging

      Public
      🐍☕📑 Jython package for using SciJava's LogService for logging.
      imagej2scijavaloggingjythonjython-library
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

    • hrm

      Public
      The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.
      PHP
      •
      Other
      •9•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • rlm-prometheus

      Public
      Prometheus exporter providing metrics from a Reprise License Manager (RLM) instance.
      pythonprometheusrepriseimarisrlmlicense-metrics
      HTML
      •
      GNU General Public License v3.0
      •2•8•1•0•Updated Sep 20, 2024Sep 20, 2024

    • omero-py

      Public
      Python project containing Ice remoting code for OMERO
      Python
      •
      GNU General Public License v2.0
      •35•0•0•0•Updated Jun 25, 2024Jun 25, 2024

    • omero-documentation

      Public
      Sphinx-based documentation for the Open Microscopy Environment
      Shell
      •
      BSD 2-Clause "Simplified" License
      •51•0•0•0•Updated Jun 25, 2024Jun 25, 2024