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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 20 2

  2. ome_zarr_pyramid ome_zarr_pyramid Public

    Python 6

  3. 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

  4. ZarrSeg ZarrSeg Public

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

    Python 2

  5. image_processing image_processing Public

    Forked from bugraoezdemir/image_processing

    A repo with several common tools for 3D image processing

    Python 2

  6. Rclone-BIA Rclone-BIA Public

    Scripts to facilitate exchange of data between local filesystems and BioImage Archive

    1

Repositories

Showing 10 of 17 repositories
  • bfflow Public

    Converts image to OME-TIFF format.

    Euro-BioImaging/bfflow’s past year of commit activity
    Nextflow 0 MIT 1 0 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
  • 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 20 MIT 2 13 0 Updated Nov 3, 2024
  • ome_zarr_pyramid Public
    Euro-BioImaging/ome_zarr_pyramid’s past year of commit activity
    Python 6 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
  • centriole_tracking_preprocess Public
    Euro-BioImaging/centriole_tracking_preprocess’s past year of commit activity
    Python 0 0 0 0 Updated Sep 22, 2024
  • ngff Public Forked from ome/ngff

    Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

    Euro-BioImaging/ngff’s past year of commit activity
    Bikeshed 0 42 0 0 Updated Jan 24, 2024
  • Data Public

    Example data that can be used to test tools.

    Euro-BioImaging/Data’s past year of commit activity
    0 CC0-1.0 0 0 0 Updated Jan 9, 2024
  • ZarrSeg Public

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

    Euro-BioImaging/ZarrSeg’s past year of commit activity
    Python 2 MIT 0 0 0 Updated Dec 21, 2023
  • image_processing Public Forked from bugraoezdemir/image_processing

    A repo with several common tools for 3D image processing

    Euro-BioImaging/image_processing’s past year of commit activity
    Python 2 MIT 1 0 0 Updated Dec 20, 2023
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