Understanding Pathology Explorer's Analysis Capabilities

Pathology Explorer exposes slide-level histomics features derived from TCGA H&E slides.

This page documents the feature families and naming conventions.

Cell quantification and distribution

For each supported cell_type (for example: lymphocytes, neutrophils, plasmocytes, fibroblasts, eosinophils, cancer cells), the model provides:

• count_{cell_type}: Total number of detected cells in the slide.

• global_density_{cell_type}: Cell density per unit tissue area.

The exact cell_type tokens are returned by the List available cell types tool.

Nuclear morphology metrics

For each cell_type, the model provides:

• mean_area_{cell_type}: Mean nuclear area.

• mean_circularity_{cell_type}: Mean nuclear circularity.

• mean_perimeter_{cell_type}: Mean nuclear perimeter.

Spatial organization and tissue architecture

Pathology Explorer also measures how cells are distributed across tissue regions.

Regional density analysis

For three region types (tumor, tumor core, and stroma in tumor core), the model provides:

• density_{cell_type}_in_{region}: Cell density for a given cell type in a given region.

Regional area measurements

For each region, the model provides:

• area_{region}: Region area within the slide.

Cell–cell interaction analysis

For selected pairs of cell types, the model provides:

• average_co_occurrence_{cell_type}_{cell_type2}_rad_20.0um

This feature answers:

How many cell_type2 nuclei are found, on average, within 20 µm of each cell_type nucleus?

Interpretation:

• 0 means no local co-occurrence at 20 µm.

• Larger values mean denser local neighborhoods of cell_type2 around cell_type.

Tumor-infiltrating lymphocyte assessment

The model also computes:

• tils_diffusivity: a metric that quantifies how diffusely TILs are distributed in the slide.

Supported TCGA cohorts

Histomics features are available for 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