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Primarily driven by the discussion at https://forum.image.sc/t/nikon-slide-scanner-brightfield-nd2-files-lacking-rgb-information-after-conversion-to-ome-tif-when-viewed-in-omero/76438
The scenario can be reproduced by using a file similar to
and either running NGFF-Converter 1.1.4 with the
--rgb
flag in the arguments list or directly:The generated OME-TIFF is a RGB image (SizeC=3, 1 channel with SamplePerPixels=3) as expected but its Channel metadata still contains the green color information
When importing such a file into OMERO, all channels are now populated as green by default. This is at odds with the user expectation when passing a
--rgb
flag.dcb6642 expands the RGB conversion tests to covert the scenario above and add channel metadata assertions
2cfbd1e proposes to change the behavior of the converter to remove the Channel.Color metadata when
--rgb
is passed and adjusts the newly introduced unit test accordingly/cc @DavidStirling