> For the complete documentation index, see [llms.txt](https://docs.owkin.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.owkin.com/connect-and-integrate/pathology-explorer-mcp-ai-powered-tissue-analysis/understanding-pathology-explorers-analysis-capabilities.md).

# 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 <a href="#cell-quantification-and-distribution" id="cell-quantification-and-distribution"></a>

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.

{% hint style="info" %}
The exact `cell_type` tokens are returned by the **List available cell types** tool.
{% endhint %}

### Nuclear morphology metrics <a href="#nuclear-morphology-metrics" id="nuclear-morphology-metrics"></a>

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 <a href="#spatial-organization-and-tissue-architecture" id="spatial-organization-and-tissue-architecture"></a>

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

#### Regional density analysis <a href="#regional-density-analysis" id="regional-density-analysis"></a>

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 <a href="#regional-area-measurements" id="regional-area-measurements"></a>

For each region, the model provides:

* `area_{region}`: Region area within the slide.

#### Cell–cell interaction analysis <a href="#cell-cell-interaction-analysis" id="cell-cell-interaction-analysis"></a>

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 <a href="#tumor-infiltrating-lymphocyte-assessment" id="tumor-infiltrating-lymphocyte-assessment"></a>

The model also computes:

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

### Supported TCGA cohorts <a href="#supported-tcga-cohorts" id="supported-tcga-cohorts"></a>

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


---

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