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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 13 2

  2. ome_zarr_pyramid ome_zarr_pyramid Public

    Python 4

  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 2

  4. Rclone-BIA Rclone-BIA Public

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

  5. PatternFileGenerator PatternFileGenerator Public

    Tool to generate a pattern file under the name "new.pattern", which can be used by bioformats to concatenate multiple files into a hyperstack.

    Python

  6. Data Data Public

    Example data that can be used to test tools.

Repositories

Showing 10 of 13 repositories
  • 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 13 MIT 2 13 0 Updated Apr 23, 2024
  • ome_zarr_pyramid Public
    Euro-BioImaging/ome_zarr_pyramid’s past year of commit activity
    Python 4 MIT 0 0 0 Updated Mar 8, 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 38 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 0 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 0 MIT 1 0 0 Updated Dec 20, 2023
  • galaxy-image-analysis Public Forked from BMCV/galaxy-image-analysis

    Galaxy tools for image analysis

    Euro-BioImaging/galaxy-image-analysis’s past year of commit activity
    Python 0 MIT 13 0 0 Updated Nov 22, 2023
  • Next-Generation-File-Format-Features Public Forked from Tpoquillon/Next-Generation-File-Format-Features

    This repository is a proposal for addin generalistic feature specs in the context of the next generation bioimage analysis workflows hackathon 2023

    Euro-BioImaging/Next-Generation-File-Format-Features’s past year of commit activity
    0 2 0 0 Updated Nov 9, 2023
  • OME_Zarr_Tools Public

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

    Euro-BioImaging/OME_Zarr_Tools’s past year of commit activity
    Shell 2 0 0 0 Updated Nov 2, 2023
  • Galaxy-OME-Zarr Public

    Integration of certain OME-Zarr tools in Galaxy.

    Euro-BioImaging/Galaxy-OME-Zarr’s past year of commit activity
    0 1 0 0 Updated Nov 2, 2023
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