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akoyabio / phenoptrReports

Create analysis reports from inForm data.
https://akoyabio.github.io/phenoptrReports
zlib License
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Don't require tissue segmentation #4

Closed AB-Kent closed 4 years ago

AB-Kent commented 5 years ago

Not everyone has a tissue segmentation step.

AB-Kent commented 5 years ago

One solution might be to add a Tissue Category column with value "All" to the consolidated data if there is no existing Tissue Category.

AB-Kent commented 5 years ago

The cell density calculations won't work without tissue segmentation; that puts the tissue category areas into the cell seg summary and that is what pR uses to calculate density. However, in that case the overall density is reported in  the summary file so it is directly available there.

I think the other functions will work OK with Tissue Category "All" in the cell seg data.