Extended features description for Pathology Explorer

The model powering Pathology Explorer offers a range of capabilities to analyze histopathological slides. Below is an extended description of the slide-level histomics features provided by the model.

Count and density features

For each cell type (lymphocytes, neutrophils, plasmocytes, fibroblasts, eosinophils, cancer cell), the model provides:

• count_{cell_type}: The total number of cells of the specified type detected in the slide.

• global_density_{cell_type}: The density of the specified cell type per unit area of the tissue.

Morphological features of the nucleus

For each cell type, the model provides:

• mean_area_{cell_type}: The average area of the nuclei of the specified cell type in the slides.

• mean_circularity_{cell_type}: The average circularity of the nuclei of the specified cell type in the slides.

• mean_perimeter_{cell_type}: The average perimeter of the nuclei of the specified cell type in the slides.

Spatial organization features

For three types of regions (tumor, tumor core and stroma in tumor core), the model provides for each cell type:

• density_{cell_type}_in_{region}: The density of the specified cell type within the specified region.

For each region, the model also provides:

• area_{region}: The area of the specified region in the slide.

In addition, for a selection of biologically relevant cell-cell interactions, the model provides:

• average_co_occurrence_{cell_type}_{cell_type2}_rad_20.0um: The average co-occurrence of the two specified cell types nuclei within a radius of 20 micrometers. This slide-level histomic answers the question: "How many cells of type cell_type2 are found, on average, within 20.0 microns of every cell of type cell_type"? It provides a compact measure of cell-cell colocalisation on a whole-slide image:

  • a value of 0 indicates that no cell_type cell lies in the specified neighbourhood of any cell_type2 cell;

  • larger values denote an increasingly dense local presence of cell_type2 around cell_type.

The model also computes the tils_diffusivity, a metrics for quantifying the tumor-infiltrating lymphocytes diffusivity for the slide.

Available cohorts

The histomics are available on the following TCGA cohorts:

• TCGA_ACC

• TCGA_BLCA

• TCGA_BRCA

• TCGA_CESC

• TCGA_CHOL

• TCGA_COAD

• TCGA_DLBC

• TCGA_ESCA

• TCGA_HNSC

• TCGA_KICH

• TCGA_KIRC

• TCGA_KIRP

• TCGA_LIHC

• TCGA_LUAD

• TCGA_LUSC

• TCGA_MESO

• TCGA_OV

• TCGA_PAAD

• TCGA_PRAD

• TCGA_READ

• TCGA_SARC

• TCGA_STAD

• TCGA_THCA

• TCGA_THYM

• TCGA_UCEC

• TCGA_UCS