greyscale images have channel color grey 808080

[will-moore]

There are several examples of images that have rendering settings info generated, possibly by Bio-Formats (I could be wrong) where the images are "greyscale" but the single channel has also been given a colour of grey "color": "808080".

This can be seen in a number of images in IDR, e.g. https://idr.openmicroscopy.org/webclient/img_detail/15159990/?dataset=18501
although it is not usually obvious as the single-channel images are also greyscale by default.

It is more noticeable in OME-Zarr images. E.g.
https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD1520/88bddf0e-84c1-4502-9c5c-5fc96c26a06a/3709c79d-38d1-40fc-84d5-ead5684ddd8a.ome.zarr/0

Vizarr reads the omero rendering settings but doesn't take into account the greyscale flag.

This was also an issue in OMERO.figure for a while. Reading images from OMERO with grey channels (before it was updated to read the greyscale flag).

Is there an reason for setting the channel color to grey instead of white?

[melissalinkert]

This color does not come from Bio-Formats. showinf -nopix -omexml 'B2-Strobl2014A-DS0001TP(TS)DR0004CH0001PL(ZM).TIF' can confirm that a Color is not set on Channel at all.

I would expect this specific grey color is coming from:

https://github.com/ome/omero-blitz/blob/master/src/main/java/ome/formats/model/ChannelProcessor.java#L114
https://github.com/ome/omero-blitz/blob/master/src/main/java/ome/formats/model/ColorsFactory.java#L373

As far as I know, this has been the behavior for single-channel images with no color assigned by Bio-Formats for a very long time.

[sbesson]

Seconding @melissalinkert's explanation, the code history reveals this behaviour was introduced in ome/openmicroscopy#3140 and relased in OMERO 5.1.0.

[will-moore]

Ah, OK. So the OME-Zarr image above must have come from OMERO originally.
I'll open a fix for vizarr, but can we also change grey default to white?
I can't think of any time when it's better to have the colour as grey instead of white?
cc @jburel

[jburel]

I cannot remember the reason for selecting grey instead of white but we will need to check with existing image like DICOM

[will-moore]

@jburel What do you need to check? Anything I can help with?