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hammerlab / cytokit

Microscopy Image Cytometry Toolkit
Apache License 2.0
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Outputting ROI polygon info #25

Closed mkeays closed 4 years ago

mkeays commented 4 years ago

Hi @eric-czech ,

I've been asked whether it's possible to get Cytokit to output polygon information for the segmented ROIs i.e. nuclei and cell boundaries. The project I'm working on is converging on OME-TIFF as the preferred format for image data, and we'd like to be able to put this information into OME-XML, if it's possible to pull it out from Cytokit somehow?

Thanks, Maria

eric-czech commented 4 years ago

Hi @mkeays, the images in $RESULTS_DIR/cytometry/tile contain the label volumes and boundaries for all cells. In other words, the 5D images in there contain the object images for each cell with an integer label as well as (on a different leading dimension) the boundaries of those same objects. The "extract" command just pulls images from there and stacks them up with images from $RESULTS_DIR/processor/tile so you should be able to use them directly. I don't know how to convert to OME-XML off the top of my head, but I imagine it's pretty straightforward from the labeled images.

mkeays commented 4 years ago

Hi @eric-czech , thanks for explaining! I had a feeling the information was already there, I'll look more closely at these images.