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14. curateThumbnails: This module programmatically generates cropped regions of tissue showing cells drawn at random from each cluster identified by the clustering module. Image contrast settings defined in the setContrast are applied to images prior to thumbnail curation. A single white pixel corresponding to the nuclear centroid of the reference cell is shown in each image as a fiducial reference. Optionally, images can be saved with segmentation outlines superimposed by toggling the segOutlines parameter in config.yml. The number and size of thumbnail examples can also be specified using the numThumbnails and squareWindowDimension parameters in config.yml. Image galleries per cluster are saved in <output_dir>/clustering/thumbnails/.

YAML configurations (config.yml)

ParameterDefaultDescription
numThumbnails10(int) Number of examples per cluster to be curated.
topMarkersThumbnails“channels”(str) Normalization axis (“channels” or “clusters”) used to define highest expressed markers per cluster.
squareWindowDimension35(int) Number of pixels from the centroid of the reference cell in x and y dimensions.
segOutlinesFalse(bool) Whether to overlay cell segmentation outlines on thumbnail images.