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Implement quality check of segmentations before quantification. #73

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shanrhoads opened this issue Mar 20, 2024 · 0 comments
Open

Implement quality check of segmentations before quantification. #73

shanrhoads opened this issue Mar 20, 2024 · 0 comments

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@shanrhoads
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A common error in the quantification occurs to the presence of more than one nuclei object in a cell (likely an error during segmentation process). The initial quantification takes a long time and this error only appears in the subsequent summary function, so significant processing time is lost if this segmentation mishap is present in a dataset, especially a large one.

To do: Create a quality check function that runs through the basic requirements/expectations for each segmentation types. Consider adding things like, number of objects for cell/nuc (should be 1), some basic intensity inside vs outside of segmented area and cell, etc.

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