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hammerlab / cytokit

Microscopy Image Cytometry Toolkit
Apache License 2.0
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cells at tile edges #17

Closed mkeays closed 4 years ago

mkeays commented 4 years ago

Hello,

I am trying to understand more about the Cytokit analysis results now, and was wondering -- since cytometry is done for each tile separately, what happens for the cells that overlap the edges of the tiles, so e.g. half of the cell is in one tile and the other half is in another tile? Are these cells just not counted, or only the part of the cell that contains the nucleus is used, or something else?

Thanks! Maria

eric-czech commented 4 years ago

There is a "[cm|nm]:on_border" flag in the csv/fcs files that indicates whether or not the cell or nucleus (respectively) shares any pixels with the border of the image. Other than that, the images are segmented as-is and even though the U-Net typically does a good job of identifying nuclei on or near boundaries, I would recommend ignoring them.

eric-czech commented 4 years ago

I'll close this out for now, please re-open if you have any more questions on border objects.