SPRM Outputs

The following are descriptions of SPRM outputs related to their reg expression naming (xxx).

The outputs can be grouped into x types

OME-TIFFs showing pixel level results (remapping of channels) [3 per input image]

• xxx-channel_pca.ome.tiff

• xxx-superpixel.ome.tiff

CSV showing interpolated cell outlines & polygons [2 per input image]

• xxx-cell_shape.csv

• xxx-cell_polygons_spatial.csv

CSVs containing features for each cell [4 per image]

• xxx_texture.csv

• xxx_cell_channel_meanALL.csv

• xxx-cell_adj_list.csv

• xxx-cell_centers.csv

CSVs containing features for each segmentation [12 per image]

• xxx-[segmentation channel]_channel_covar.csv

• xxx-[segmentation channel_channel_mean.csv

• xxx-[segmentation channel]l_channel_total.csv

Master CSV containing clustering results for each cell (row) for each method (column) [1 per input image]

• xxx-cell_cluster.csv

CSVs containing mean values of “markers” for each cluster for each clustering method [5 per input image]

• xxx-clustercells_cellcovariance_legend.csv

• xxx-clustercells_cellmeanALL_legend.csv

• xxx-clustercells_cellmean_legend.csv

• xxx-clustercells_cellshape_legend.csv

• xxx-clustercells_celltotal_legend.csv

PNGs showing coloring by cluster [10 per input image]

• xxx-ClusterByCovarPerCell.png

• xxx-ClusterByMeansAllMasks.png

• xxx-ClusterByMeansPerCell.png

• xxx-ClusterByShape.png

• xxx-ClusterByTotalPerCell.png

• xxx-Superpixels.png

• xxx-Top3ChannelPCA.png

• xxx_nmf_top3.png

• xxx-ClusterBytSNEAllFeatures.png

• xxx-ClusterByUMAP.png

CSV containing the signal to noise ratios of the image per channel [1 per input image]

• xxx-SNR.csv

CSV containing PCA and Silhouette analysis of the image [2 per input image]

• xxx-channelPCA_summary.csv

• xxxclusteringsilhouetteScores.csv

CSV containing the summary file [3 per run]

• summary_otsu.csv

• summary_zscore.csv

• SPRM_Image_Quality_Measures.json