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    • bfflow

      Public
      Converts image to OME-TIFF format.
      Nextflow
      MIT License
      1003Updated Dec 6, 2024Dec 6, 2024
    • Scratch repo for the OME-NGFF hackathon
      Python
      GNU General Public License v3.0
      1000Updated Nov 21, 2024Nov 21, 2024
    • 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
      MIT License
      219130Updated Nov 3, 2024Nov 3, 2024
    • Python
      MIT License
      0600Updated Oct 7, 2024Oct 7, 2024
    • Python
      0000Updated Oct 1, 2024Oct 1, 2024
    • Python
      0000Updated Sep 22, 2024Sep 22, 2024
    • ngff

      Public
      Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
      Bikeshed
      Other
      41000Updated Jan 24, 2024Jan 24, 2024
    • Data

      Public
      Example data that can be used to test tools.
      Creative Commons Zero v1.0 Universal
      0000Updated Jan 9, 2024Jan 9, 2024
    • ZarrSeg

      Public
      Command line tool to segment local and remote OME-Zarr data
      Python
      MIT License
      0200Updated Dec 21, 2023Dec 21, 2023
    • A repo with several common tools for 3D image processing
      Python
      MIT License
      1200Updated Dec 20, 2023Dec 20, 2023
    • Galaxy tools for image analysis
      Python
      MIT License
      17100Updated Nov 22, 2023Nov 22, 2023
    • This repository is a proposal for addin generalistic feature specs in the context of the next generation bioimage analysis workflows hackathon 2023
      2100Updated Nov 9, 2023Nov 9, 2023
    • Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023
      Shell
      0300Updated Nov 2, 2023Nov 2, 2023
    • Integration of certain OME-Zarr tools in Galaxy.
      1110Updated Nov 2, 2023Nov 2, 2023
    • 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
      0100Updated Jul 5, 2023Jul 5, 2023
    • A module that runs the image data converters bfconvert and bioformats2raw from python using the subprocess module..
      Python
      0100Updated Jun 12, 2023Jun 12, 2023
    • Scripts to facilitate exchange of data between local filesystems and BioImage Archive
      0100Updated Feb 21, 2023Feb 21, 2023