NGFF Tools
OverviewTools and workflows around Next Generation File Formats
Space: Independent Teams
SEEK ID: https://workflowhub.eu/projects/154
Public web page: https://github.com/Euro-BioImaging
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team created: 27th Mar 2023
Related items
Teams: OME, NGFF Tools
Organizations: University of Dundee, Open Microscopy Enronment (OME)
https://orcid.org/0000-0002-1789-1861
Teams: OME, NGFF Tools
Organizations: German BioImaging, Open Microscopy Enronment (OME)
https://orcid.org/0000-0003-4028-811X
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
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Web page: Not specified
BatchConvert
A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr.
The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system NextFlow is used to perform conversion in parallel for batches of images.
The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). Therefore, input and output locations can be specified as local ...
