Understanding Pathology Explorer's Analysis Capabilities

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

It is built on Owkin's pan-cancer H&E cell detection model, trained on more than 100,000 annotated nuclei across 6 indications and 13 cell types. Compared with standard histomics, which focuses on cell densities, Pathology Explorer adds nuclear morphology, spatial interaction scores, finer region-specific densities, and improved detection of rare immune and stromal cell types.

This page documents the feature families and naming conventions.

How Pathology Explorer compares with standard histomics

Feature	Standard histomics	Pathology Explorer
Cell counts and global densities	Yes	Yes
Region-specific densities	Tumor only	Tumor, tumor core, stroma in tumor core
Region areas	No	Yes
Nuclear morphology per cell type	Not by default	Area, circularity, perimeter
TIL diffusivity	Not by default	Yes
Cell–cell co-occurrence	No	9 cell-type pairs, 20 µm radius
Tertiary lymphoid structure (TLS) score	Yes	No

The two are complementary. The TLS score is only available from histomics data in K-Pro (see Analysis methods), not from Pathology Explorer.

Cell quantification and distribution

Pathology Explorer supports six cell types: cancer cells, lymphocytes, neutrophils, plasmocytes, fibroblasts, and eosinophils. For each cell_type, 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 model was designed to improve detection of understudied cell types, including across different tissue types and staining conditions:

• Neutrophils: tumor-associated neutrophils are increasingly linked to immunosuppression in the tumor microenvironment.
• Plasmocytes (plasma cells): key effectors of humoral anti-tumor immunity.
• Eosinophils: emerging roles in anti-tumor responses.
• Fibroblasts: central to cancer-associated stromal remodeling.

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.

These metrics quantify changes in nuclear shape associated with malignancy or immune activation.

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.

Densities are available for all six cell types in every region. This lets you compare immune infiltration in the tumor core with infiltration in the surrounding stroma.

Regional area measurements

For each region, the model provides:

• area_{region}: Region area within the slide (area_tumor, area_tumor_core, area_stroma_in_tumor_core).

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.

Available cell-type pairs

cell_type	cell_type2
cancer_cell	lymphocytes
cancer_cell	neutrophils
cancer_cell	plasmocytes
cancer_cell	fibroblasts
lymphocytes	lymphocytes
neutrophils	neutrophils
plasmocytes	lymphocytes
plasmocytes	plasmocytes
plasmocytes	eosinophils

Tumor-infiltrating lymphocyte assessment

The model also computes:

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

It adds spatial context that TIL density alone does not capture: two slides with the same TIL density can have very different TIL distributions.

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