Repositories list

• 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-format+ 8daskconcatenationomezarrngffbioimageome-zarr+ 1

  Python

  •

  MIT License

  •0•3•2•0•Updated Apr 8, 2025Apr 8, 2025

• ngff_workshop

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

  trainingimagetutorial+ 5omezarrngffbioimageome-zarr

  HTML

  •

  MIT License

  •0•1•0•0•Updated Apr 6, 2025Apr 6, 2025

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

  Public
  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Mar 17, 2025Mar 17, 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.

  workflowimagenextflow+ 8conversionfile-formatome-tiffomezarrbioimageome-zarr+ 1

  Python

  •

  MIT License

  •4•21•15•0•Updated Mar 14, 2025Mar 14, 2025

• bfflow

  Public
  Converts image to OME-TIFF format.

  Nextflow

  •

  MIT License

  •1•0•0•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•6•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

  •45•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

  •17•1•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•1•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-analysisngff+ 3bioimageome-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•1•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•1•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•1•0•0•Updated Jun 12, 2023Jun 12, 2023

• Rclone-BIA

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

  0•1•0•0•Updated Feb 21, 2023Feb 21, 2023