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NL-BioImaging / biomero-scripts

Scripts for use with BIOMERO
https://nl-bioimaging.github.io/biomero/
GNU General Public License v2.0
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Support ROI output #1

Open TorecLuik opened 5 months ago

TorecLuik commented 5 months ago

Probably people want to upload ROI objects (as results from a workflow) to OMERO, instead of just label images. Or perhaps both.

We note the limitations of OMERO (web) in handling ROIs, but we could add the uploading option as a feature.

Anyone has a workflow that outputs standardized ROI objects? What types of data do we have to handle as ROI objects? Should we extract ROIs from a label image?

More info/thoughts needed

CellularImagingCF commented 5 months ago

Wendt has a OMERO script to postprocess/convert label images into ROIs. Could be good enough for this use-case? https://forum.image.sc/t/omero-script-to-convert-grey-value-label-images-to-omero-rois/93923