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    69 repositories

    • ome2xarray

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•2•1•Updated Jan 15, 2026Jan 15, 2026

    • faim-ipa

      Public
      A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)
      ome-zarrome-zarr-converter
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•18•20•1•Updated Jan 12, 2026Jan 12, 2026

    • napari-save-transformed

      Public
      Save image layers with their transformation applied
      napari-plugin
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•2•1•Updated Jan 12, 2026Jan 12, 2026

    • robocopy-command-builder

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

    • faim-wako-searchfirst

      Public
      Python scripts for the SearchFirst option in Wako Software Suite
      high-content-screeningwakoyokogawa
      Python
      •
      MIT License
      •1•2•8•3•Updated Jan 6, 2026Jan 6, 2026

    • ipa-project-template

      Public
      Copier template for image processing & analysis projects.
      Jinja
      •
      MIT License
      •3•7•6•1•Updated Jan 5, 2026Jan 5, 2026

    • example-project

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•1•Updated Jan 5, 2026Jan 5, 2026

    • metamorph-mda-parser

      Public
      Light-weight parsing of Metamorph/VisiView Multi Dimensional Acquisition .nd files.
      metadatamicroscopymetamorphvisiview
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•0•Updated Jan 2, 2026Jan 2, 2026

    • cellvoyager-types

      Public
      Pydantic models for CellVoyager CV7000/CV8000 metadata
      microscopyhigh-content-screeningcellvoyager
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•1•1•Updated Jan 2, 2026Jan 2, 2026

    • faim-tablespy

      Public
      Python
      •0•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.7k•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • pixi-psf

      Public
      Pixi project to run napari-psf-analysis
      pixi-sh
      0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • bioio-base-feedstock

      Public
      A conda-smithy repository for bioio-base.
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Dec 5, 2025Dec 5, 2025

    • pixi-assistant

      Public
      Helper CLI to check local system settings to work with pixi projects
      Rust
      •
      MIT License
      •0•1•1•0•Updated Dec 5, 2025Dec 5, 2025

    • bioio-conversion

      Public
      A BioIO conversion tool for going between image formats
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Nov 14, 2025Nov 14, 2025

    • mcoz

      Public
      MoBIE Collections from OME-Zarr datasets
      0•0•0•0•Updated Nov 14, 2025Nov 14, 2025

    • faim-pixi-stubs

      Public
      Simple pixi projects to simplify using common tools for bio-image processing
      image-processingpixibio-image-analysis
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2025Oct 9, 2025

    • napari-explore-points

      Public
      Napari plugin to explore points by feature
      napari-plugin
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•2•0•Updated Sep 25, 2025Sep 25, 2025

    • bioio-lif

      Public
      A BioIO reader plugin for reading LIF (Leica Image File) images.
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 11, 2025Sep 11, 2025

    • fmi-trackmate-addons

      Public
      Addons for TrackMate in ImageJ
      Java
      •
      GNU General Public License v3.0
      •2•0•1•0•Updated Aug 13, 2025Aug 13, 2025

    • image-processing-basics

      Public
      Teaching material for image processing and analysis
      Python
      •
      Apache License 2.0
      •0•7•0•0•Updated May 27, 2025May 27, 2025

    • faim_rdcnet

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 30, 2025Apr 30, 2025

    • pytorch-rdc-net

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • bioio

      Public
      Image reading, metadata management, and image writing for Microscopy images in Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • napari-stitcher

      Public
      A napari plugin for stitching large multi-positioning datasets in 2/3D+t using multiview-stitcher
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • napari-psf-analysis

      Public
      A napari plugin to analysis point spread functions.
      psfmicroscopy
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•12•11•1•Updated Mar 28, 2025Mar 28, 2025

    • pixi-fiji

      Public
      Small demo project for starting a reproducible Fiji instance using pixi (via pyimagej or jgo)
      Python
      •0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

    • bioio-bioformats

      Public
      A BioIO reader plugin for reading bioformats formatted images.
      Python
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • ome-zarr-models-py

      Public
      A minimal Python package for reading OME-Zarr (meta)data
      Python
      •
      MIT License
      •15•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • diy-tools

      Public
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Dec 12, 2024Dec 12, 2024