4. areaFilter: cell segmentation errors can be a significant source of noise in image-derived, single-cell data. In this module, users assign lower and upper bounds on cell segmentation area (pixel count) to remove severely under- and over-segmented cells. Cell segmentation area is a standard component of MCMICRO feature table output and is calculated using skimage.measure.regionprops(). This module functions similar to the intensityFilter module in that it allows users to assign lower and upper thresholds on interactive histogram widgets of per-cell data. Gaussian mixture modeling (GMM) assist in identifying default cutoffs that can be manually refined. Once thresholds have been adjusted for a given sample, users can visualize selected cells in their corresponding image by clicking the Plot Points button. Segmentation outlines are provided in the layer list at the left of the Napari viewer as a reference for evaluating segmentation quality. Data points falling between lower and upper sliders are carried forward into downstream analysis. Users will move to the next sample in the series by clicking the Apply Gates and Move to Next Sample button beneath the histogram. Users may jump between tissues in the series by entering the name of a given sample in the Sample Name field of the Arbitrary Sample Selection widget at the right of the Napari viewer to adjust thresholds of previously analyzed tissues. To re-define thresholds, remove the metadata associated with the target sample(s) from cylinter_report.yml located in the CyLinter output directory specified in cylinter_config.yml and re-run the areaFilter module with cylinter --module areaFilter cylinter_config.yml.

YAML configurations