Aim of this PR is to address an issue with phenoptrReport when reporting H-Score values for cells missing mean pixel intensity measurements (#N/A). Measurement can be missing when the corresponding cellular compartment (cytoplasm, membrane) is missing as a result of cell segmentation. Cells mostly affected will be those located in densely packed clusters, where the cell expansion of the cytoplasm failed due to the presence of neighboring cells in close proximity.
The previous version assigns cells lacking a measurement to the 3+ category
The fixed version does not assign cells lacking a measurement to any category
It has to be noted that the results of the fixed version of phenoptrReports may deviate from inForm.
Inform seems to assign cells lacking a measurement to the 0+ category
As part of QC, compare the total number of cells reported in the Cell Counts tab with the corresponding total number of cells in the individual H-Score tabs. A significant reduction of available cells for the H-Score calculation indicates cell segmentation issues. As a workaround, a different, physiologically relevant, compartment may be selected for scoring.
phenoptrReports passes all tests without warnings.
Aim of this PR is to address an issue with
phenoptrReportwhen reporting H-Score values for cells missing mean pixel intensity measurements (#N/A). Measurement can be missing when the corresponding cellular compartment (cytoplasm, membrane) is missing as a result of cell segmentation. Cells mostly affected will be those located in densely packed clusters, where the cell expansion of the cytoplasm failed due to the presence of neighboring cells in close proximity.3+categoryIt has to be noted that the results of the fixed version of
phenoptrReportsmay deviate frominForm.0+categoryAs part of QC, compare the total number of cells reported in the
Cell Countstab with the corresponding total number of cells in the individualH-Scoretabs. A significant reduction of available cells for the H-Score calculation indicates cell segmentation issues. As a workaround, a different, physiologically relevant, compartment may be selected for scoring.phenoptrReportspasses all tests without warnings.