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guiwitz / napari-steinpose

A plugin to process Imaging Mass Cytometry data with cellpose and steinbock
https://guiwitz.github.io/napari-steinpose
BSD 3-Clause "New" or "Revised" License
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export intensities, regionprops and neighbors folders #4

Open sokratiag opened 9 months ago

sokratiag commented 9 months ago

HI,

thanks for the great tool. I am trying to run cell segmentation on IMC data (using CP) but the 'intensities','reionprops' and 'neighbors' folders are not being exported to the output folder as expected (even though the corresponding fields in the export tab are selected). Any ideas why this is might happening?

Thanks!

guiwitz commented 9 months ago

Hi @sokratiag, if you want to export these measurements directly when segmenting, you need to tick the box "Run Steinbock post-processing" in the Segmentation tab. If you want to extract measurements after segmentation, you need to click on "Run Steinbock postproc" in the Export tab. Did you do any of those? Just ticking the fields in the Export tab is not sufficient. In case something is not clear you can find the procedure here: https://guiwitz.github.io/napari-steinpose/Standard_use.html#post-processing