It’s my first time posting here so please forgive any faux pas. I re-commented on an issue here but I feel very lost and heard this would be a good place to ask.
It’s not clear to me what
SamplesPerPixel in the OMEXML metadata is for - is it per channel or is global? The description from the OMEXML specification is not clear to me: “The number of samples the detector takes to form each pixel value. [units:none]” refers to “pixel” but multiple channels often come together to form a “pixel.”
My example (as in the Github Issue) input is de-interleaved RGB image with three channel: red, green, and blue. But each channel has a
SamplesPerPixel of 3 and I wonder if that is throwing the pipeline off, causing it to drop the other two channels when the --rgb flag is on (see the link for more description).
So I guess my question is what
SamplesPerPixel should be, and if anyone could point me to some “ground truth” ome-tiff RGB files that I coudl compare against - I have not been able to find any. I’m not expecting a “fix” to the pipeline - that was more just a jumping off point for this question since fixing the input data might fix the odd output of the pipeline.