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15. curateThumbnails: this module is fully automated. It programmatically generates image patchs of cells drawn at random from each cluster identified in the clustering module and each cell type defined in the gating module for visual review. The number of examples shown per cluster is adjusted using the numThumbnails parameter in cylinter_config.yml. The size of the image window areound the reference cells is controlled by the squareWindowDimension parameter in the same configuration file. A white pixel corresponding to the nuclear centroid of the example cell is shown in each image as a reference. Images can be saved with or without segmentation outlines superimposed by toggling the segOutlines parameter in configuration file. To facilitate interpretation, only the three most highly expressed protein markers are shown per cluster (based on channel z-scores. Image contrast settings defined in the setContrast module are applied to improve image appearance. Image galleries for each cluster and gate-based cell type class are saved to the thumbnails directory in the clustering subdirectory of the main CyLinter output directory. This path is thumbnails/2d/frequency_stats in the case of 2D clusterings and thumbnails/3d/frequency_stats in the case of 3D clusterings.

YAML configurations

numThumbnails25(int) Number of example cells per cluster to be curated.
windowSize30(int) Number of pixels from the centroid of the reference cell in x and y dimensions.
segOutlinesTrue(bool) Whether to overlay cell segmentation outlines on thumbnail images.