mcmicro_io.zip cell and nucleus bitmasks are the same

[keller-mark]

Is this expected?

[keller-mark]

It also could be improved by having more meaningful labels in channels_metadata - it seems like there are good names in table.var.index

"channels_metadata": {
        "channels": [
            {
                "label": 0
            },
            {
                "label": 1
            },
            {
                "label": 2
            },
            {
                "label": 3
            },
            {
                "label": 4
            },
            {
                "label": 5
            },
            {
                "label": 6
            },
            {
                "label": 7
            },
            {
                "label": 8
            },
            {
                "label": 9
            },
            {
                "label": 10
            },
            {
                "label": 11
            }
        ]
    },

[LucaMarconato]

@keller-mark could you please try using this PR, which improved the mcmicro reader: scverse/spatialdata-io#28?

[LucaMarconato]

Actually, this doesn't fix the problem, I will check for a solution.

[LucaMarconato]

Getting back to this. The incoming PR (I'll try to merge it today) scverse/spatialdata-io#28 assigns the channel names to the image (and generalizes the reader to support more complex outputs of the mcmicro pipeline).

Regarding the cell vs nuclei, I examined the code and the files, and realized that problem is already present in the data, and therefore is not due to our reader. I reported this in the mcmicro repository labsyspharm/mcmicro#531.