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    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.
      imageconversionfile-formatdaskconcatenationomezarrngffbioimageome-zarr
      Python
      •
      MIT License
      •1•11•5•0•Updated Aug 6, 2025Aug 6, 2025

    • bioio-ome-tiff

      Public
      A BioIO reader plugin for reading Tiff files in the OME format.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • bioio-tifffile

      Public
      A BioIO reader plugin for reading TIFFs using Tifffile
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • FAIR101-Workshop-on-data-deposition-into-BioImage-Archive

      Public
      Creative Commons Attribution 4.0 International
      •0•2•0•0•Updated Jun 12, 2025Jun 12, 2025

    • ngff_workshop

      Public
      Training website for the OME-Zarr format and the tooling around it.
      trainingimagetutorialomezarrngffbioimageome-zarr
      HTML
      •
      MIT License
      •0•2•0•0•Updated Apr 6, 2025Apr 6, 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.
      workflowimagenextflowconversionfile-formatome-tiffomezarrbioimageome-zarr
      Python
      •
      MIT License
      •4•23•14•0•Updated Mar 14, 2025Mar 14, 2025

    • bfflow

      Public
      Converts image to OME-TIFF format.
      Nextflow
      •
      MIT License
      •1•0•1•3•Updated Dec 6, 2024Dec 6, 2024

    • zarr_parallel_processing

      Public
      Scratch repo for the OME-NGFF hackathon
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • ome_zarr_pyramid

      Public
      Python
      •
      MIT License
      •0•5•0•0•Updated Oct 7, 2024Oct 7, 2024

    • convert_and_concatenate

      Public
      Python
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • centriole_tracking_preprocess

      Public
      Python
      •0•0•0•0•Updated Sep 22, 2024Sep 22, 2024

    • ngff

      Public
      Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
      Bikeshed
      •
      Other
      •48•0•0•0•Updated Jan 24, 2024Jan 24, 2024

    • Data

      Public
      Example data that can be used to test tools.
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Jan 9, 2024Jan 9, 2024

    • ZarrSeg

      Public
      Command line tool to segment local and remote OME-Zarr data
      Python
      •
      MIT License
      •0•2•0•0•Updated Dec 21, 2023Dec 21, 2023

    • image_processing

      Public
      A repo with several common tools for 3D image processing
      Python
      •
      MIT License
      •1•2•0•0•Updated Dec 20, 2023Dec 20, 2023

    • galaxy-image-analysis

      Public
      Galaxy tools for image analysis
      Python
      •
      MIT License
      •18•0•0•0•Updated Nov 22, 2023Nov 22, 2023

    • Next-Generation-File-Format-Features

      Public
      This repository is a proposal for addin generalistic feature specs in the context of the next generation bioimage analysis workflows hackathon 2023
      2•0•0•0•Updated Nov 9, 2023Nov 9, 2023

    • OME_Zarr_Tools

      Public
      Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023
      cloud-computingbioimage-analysisngffbioimageome-zarrimage-file-formats
      Shell
      •0•3•0•0•Updated Nov 2, 2023Nov 2, 2023

    • Galaxy-OME-Zarr

      Public
      Integration of certain OME-Zarr tools in Galaxy.
      1•0•1•0•Updated Nov 2, 2023Nov 2, 2023

    • 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
      •0•0•0•0•Updated Jul 5, 2023Jul 5, 2023

    • PythonImageConverters

      Public
      A module that runs the image data converters bfconvert and bioformats2raw from python using the subprocess module..
      Python
      •0•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • Rclone-BIA

      Public
      Scripts to facilitate exchange of data between local filesystems and BioImage Archive
      0•0•0•0•Updated Feb 21, 2023Feb 21, 2023