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    56 repositories

    • cellvoyager-types

      Public
      Trial project implementing Pydantic models for CellVoyager CV7000/CV8000 metadata
      microscopyhigh-content-screeningcellvoyager
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Feb 1, 2025Feb 1, 2025

    • 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•2•1•Updated Feb 1, 2025Feb 1, 2025

    • 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
      •6•10•16•2•Updated Feb 1, 2025Feb 1, 2025

    • pytorch-rdc-net

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • bioio

      Public
      Image reading, metadata management, and image writing for Microscopy images in Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • ipa-project-template

      Public
      Copier template for image processing & analysis projects.
      Jinja
      •
      MIT License
      •3•5•5•0•Updated Jan 28, 2025Jan 28, 2025

    • napari-save-transformed

      Public
      Save image layers with their transformation applied
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•2•1•Updated Jan 27, 2025Jan 27, 2025

    • bioio-bioformats

      Public
      A BioIO reader plugin for reading bioformats formatted images.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 23, 2025Jan 23, 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
      •5.1k•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • ome-zarr-models-py

      Public
      A minimal Python package for reading OME-Zarr (meta)data
      Python
      •
      MIT License
      •4•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • faim-wako-searchfirst

      Public
      Python scripts for the SearchFirst option in Wako Software Suite
      high-content-screeningwakoyokogawa
      Python
      •
      MIT License
      •1•1•8•4•Updated Jan 7, 2025Jan 7, 2025

    • example-project

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•1•Updated Jan 7, 2025Jan 7, 2025

    • fmi-trackmate-addons

      Public
      Addons for TrackMate in ImageJ
      Java
      •
      GNU General Public License v3.0
      •2•0•1•0•Updated Dec 14, 2024Dec 14, 2024

    • diy-tools

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

    • ngff

      Public
      Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
      Bikeshed
      •
      Other
      •45•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • napari-psf-analysis

      Public
      A napari plugin to analysis point spread functions.
      psfmicroscopy
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•9•11•0•Updated Oct 28, 2024Oct 28, 2024

    • eicm

      Public archive
      Functions to estimate illumination correction matrices from reference illumination samples.
      microscopyillumination-estimation
      Python
      •
      Other
      •1•1•0•0•Updated Oct 28, 2024Oct 28, 2024

    • mobiedantic

      Public
      Pydantic models for MoBIE projects and datasets
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•5•0•Updated Jul 24, 2024Jul 24, 2024

    • cluster_tools

      Public
      Distributed segmentation for bio-image-analysis
      Python
      •
      MIT License
      •14•0•0•0•Updated Jul 8, 2024Jul 8, 2024

    • prefect-workflows

      Public
      A collection of Prefect workflows.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•6•0•Updated Jul 8, 2024Jul 8, 2024

    • mobie-utils-python

      Public
      Python tools for MoBIE
      Python
      •
      MIT License
      •5•0•0•0•Updated Jul 7, 2024Jul 7, 2024

    • rattler-elastix

      Public
      Conda recipe for elastix
      elastix
      Batchfile
      •0•0•0•0•Updated Jun 28, 2024Jun 28, 2024

    • fmi-knime-update-site

      Public
      KNIME Extensions for Image Processing at the FMI Basel
      Shell
      •3•0•1•0•Updated May 3, 2024May 3, 2024

    • fmi-ij2-plugins

      Public
      A collection of ImageJ2 plugins for use with KNIME
      imagejimage-processingbio-image-analysisknime
      Java
      •
      GNU Lesser General Public License v3.0
      •3•7•3•0•Updated May 2, 2024May 2, 2024

    • pixi-psf

      Public
      Pixi project to run napari-psf-analysis
      pixi-sh
      0•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • napari

      Public
      napari: a fast, interactive, multi-dimensional image viewer for python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •428•0•0•0•Updated Apr 28, 2024Apr 28, 2024

    • faim-fiji

      Public
      Custom Fiji bundle for distribution via conda
      Batchfile
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Apr 10, 2024Apr 10, 2024

    • em-tasks

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 13, 2023Dec 13, 2023

    • mobie-viewer-fiji

      Public
      Java
      •
      BSD 2-Clause "Simplified" License
      •13•0•0•0•Updated Dec 11, 2023Dec 11, 2023

    • prefect-faim-hcs

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•1•Updated Nov 13, 2023Nov 13, 2023