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@Euro-BioImaging

Euro-BioImaging ERIC

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  1. BatchConvert BatchConvert Public

    A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.

    Python 26 4

  2. EuBI-Bridge EuBI-Bridge Public

    A Python-based tool for parallelized conversion of image datasets from various formats to OME-Zarr, with support for distributed processing and multi-dimensional concatenation.

    Python 18 1

  3. ome_zarr_pyramid ome_zarr_pyramid Public

    Python 7

  4. OME_Zarr_Tools OME_Zarr_Tools Public

    Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023

    Shell 3

  5. ZarrSeg ZarrSeg Public

    Command line tool to segment local and remote OME-Zarr data

    Python 2

  6. image_processing image_processing Public

    Forked from bugraoezdemir/image_processing

    A repo with several common tools for 3D image processing

    Python 2 1

Repositories

Showing 10 of 22 repositories
  • EuBI-Bridge Public

    A Python-based tool for parallelized conversion of image datasets from various formats to OME-Zarr, with support for distributed processing and multi-dimensional concatenation.

    Euro-BioImaging/EuBI-Bridge’s past year of commit activity
    Python 18 MIT 1 11 0 Updated Feb 17, 2026
  • ngff_workshop Public

    Training website for the OME-Zarr format and the tooling around it.

    Euro-BioImaging/ngff_workshop’s past year of commit activity
    HTML 2 MIT 0 0 0 Updated Jan 27, 2026
  • bioio-ome-tiff Public Forked from bioio-devs/bioio-ome-tiff

    A BioIO reader plugin for reading Tiff files in the OME format.

    Euro-BioImaging/bioio-ome-tiff’s past year of commit activity
    Python 0 BSD-3-Clause 2 0 0 Updated Jun 12, 2025
  • bioio-tifffile Public Forked from bioio-devs/bioio-tifffile

    A BioIO reader plugin for reading TIFFs using Tifffile

    Euro-BioImaging/bioio-tifffile’s past year of commit activity
    Python 0 BSD-3-Clause 4 0 0 Updated Jun 12, 2025
  • FAIR101-Workshop-on-data-deposition-into-BioImage-Archive Public
    Euro-BioImaging/FAIR101-Workshop-on-data-deposition-into-BioImage-Archive’s past year of commit activity
    2 CC-BY-4.0 0 0 0 Updated Jun 12, 2025
  • BatchConvert Public

    A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.

    Euro-BioImaging/BatchConvert’s past year of commit activity
    Python 26 MIT 4 14 0 Updated Mar 14, 2025
  • bfflow Public

    Converts image to OME-TIFF format.

    Euro-BioImaging/bfflow’s past year of commit activity
    Nextflow 0 MIT 1 1 3 Updated Dec 6, 2024
  • zarr_parallel_processing Public Forked from fmi-basel/zarr_parallel_processing

    Scratch repo for the OME-NGFF hackathon

    Euro-BioImaging/zarr_parallel_processing’s past year of commit activity
    Python 0 GPL-3.0 1 0 0 Updated Nov 21, 2024
  • ome_zarr_pyramid Public
    Euro-BioImaging/ome_zarr_pyramid’s past year of commit activity
    Python 7 MIT 0 0 0 Updated Oct 7, 2024
  • convert_and_concatenate Public
    Euro-BioImaging/convert_and_concatenate’s past year of commit activity
    Python 0 0 0 0 Updated Oct 1, 2024
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