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CellProfiler / CellProfiler-plugins

Community-contributed and experimental CellProfiler modules.
http://plugins.cellprofiler.org/
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Add "Remove Edge Masks" functionality to RunCellpose plugin #168

Closed jenna-tomkinson closed 1 year ago

jenna-tomkinson commented 1 year ago

As I was working with the RunCellpose plugin in CellProfiler, I noticed that there was a function missing that is normally available in the IdentifyPrimaryObjects and IdentifySecondaryObjects modules, which is to remove the objects that have pixels touching the edge of the image.

Cellpose 2.0 does have this functionality, called remove_edge_masks, within their documentation. It would be nice to have this ability within the module to remove the cells on the edge when wanting to proceed with further analysis like feature extraction.

lauracmurphy commented 1 year ago

There’s an option in the FilterObjects module where you can filter using “Image or mask border” that does what you need.