Repositories list

• auto-tx

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

  windowsservicedotnet+ 4data-transferemail-notificationspoolingtransfer-service

  C#

  •

  GNU General Public License v3.0

  •1•27•10•0•Updated Jul 16, 2025Jul 16, 2025

• napari-bioio-reader

  Public
  A simple napari plugin to use Bioio as a reader

  Python

  •

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

  •0•0•2•0•Updated Jul 4, 2025Jul 4, 2025

• imcf.github.io

  Public
  IMCF github pages

  HTML

  •0•0•0•0•Updated Jul 1, 2025Jul 1, 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

  •9•0•0•0•Updated Jun 6, 2025Jun 6, 2025

• psytricks

  Public
  PowerShell-Python-Citrix vodoo. 👽 😵

  pythonpowershellpoetry+ 2citrixcvad

  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•0•0•0•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•0•6•8•Updated May 6, 2025May 6, 2025

• imcf-fiji-scripts

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

  image-processingimageprocessingimagej+ 2fijifacility

  Python

  •

  GNU General Public License v3.0

  •3•1•0•1•Updated Apr 15, 2025Apr 15, 2025

• omero-cli-transfer

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

  Python

  •

  GNU General Public License v2.0

  •16•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

• imcf-fiji-update-site

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

  JavaScript

  •1•0•2•1•Updated Feb 11, 2025Feb 11, 2025

• file-size-age-metrics

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

  pythonmetricsprometheus-exporter+ 1prometheus-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

  •139•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• imcf-fiji-toolbars

  Public
  ☕ 🔬 🔣 Fiji Action Bars provided by the IMCF.

  imagejfijiimage-processing+ 1imageprocessing

  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

  •40•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.

  imagej2python27jython+ 1jython-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.

  imagej2scijavalogging+ 2jythonjython-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.

  pythonprometheusreprise+ 3imarisrlmlicense-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

• omero-common

  Public
  Gradle project containing common utilities for OMERO

  Java

  •

  GNU General Public License v2.0

  •11•0•0•0•Updated Jun 25, 2024Jun 25, 2024

• openmicroscopy

  Public
  OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded …

  Java

  •

  GNU General Public License v2.0

  •102•0•0•0•Updated Jun 25, 2024Jun 25, 2024

• Baysor

  Public
  Bayesian Segmentation of Spatial Transcriptomics Data

  Julia

  •

  MIT License

  •34•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• vpt-plugin-cellpose2

  Public
  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Mar 27, 2024Mar 27, 2024

• vizgen-postprocessing

  Public
  Python

  •

  Apache License 2.0

  •7•0•0•0•Updated Mar 27, 2024Mar 27, 2024

• vpt-core

  Public
  Core components of the Vizgen Post-processing Tool

  Python

  •

  Apache License 2.0

  •2•0•0•0•Updated Mar 22, 2024Mar 22, 2024

• vpt-plugin-cellpose

  Public
  Cellpose plugin for the Vizgen Post-processing Tool

  Python

  •

  Apache License 2.0

  •3•0•0•0•Updated Mar 19, 2024Mar 19, 2024