Use Pathology Explorer in K-Pro

Pathology Explorer is built into K-Pro. There is nothing to connect or install: ask a question about H&E slides in the chat, and K-Pro calls Pathology Explorer when your question needs it.

What you can do

• Find cohorts and slides: list the available cohorts, then sort slides by any histomics feature, for example the slides with the highest lymphocyte density.
• Look at slides:

  • Slide thumbnails.
  • An interactive whole-slide viewer: pan, zoom, and go fullscreen. Tiles stream as you move, so large slides open in seconds.
  • Tile mosaics with the model's cell predictions overlaid.
• Quantify the tissue: slide-level histomics features (cell counts and densities, nuclear morphology, region-specific densities, cell–cell co-occurrence, TIL diffusivity) and summary statistics for a cohort. See Understanding Pathology Explorer's analysis capabilities for every feature.
• Ask custom questions of the feature tables: when no built-in tool fits your question, K-Pro can query the H&E feature tables directly.
• Run survival analyses: interactive Kaplan-Meier curves with 95% confidence intervals, for overall or progression-free survival, stratified by a histomics feature. Survival times are reported in years.
• Export the data: download histomics features as a Parquet file for your own analyses.

Because Pathology Explorer runs in the same chat as K-Pro's other analyses, you can move from a slide-level finding to a follow-up question without switching tools.

Available cohorts

Cohort	Slides	Notes
26 TCGA cohorts	—	See the full list. Both TCGA_LUAD and TCGA-LUAD work.
IBDColEpi	132	Colon biopsies from patients with inflammatory bowel disease. There is no survival data, so survival analysis is not available for this cohort.

To see what is available to you, ask:

List the available pathology cohorts.

Example prompts

Find a slide and open it

In TCGA_LUAD, find the slide with the highest lymphocyte density and open it in the slide viewer.

Look at the cells

For that slide, show the tiles with the most cancer cells, with the cell predictions.

Run a survival analysis

In TCGA_BLCA, is plasmocyte density associated with overall survival?

Describe a cohort

Give me summary statistics of neutrophil density across TCGA_STAD slides.

Explore inflammation

In IBDColEpi, which slides have the highest neutrophil density? Show their thumbnails.

Export the features

Export the histomics features for TCGA_LUAD as a Parquet file.

You can also use Pathology Explorer outside K-Pro, from Claude. See Use Pathology Explorer in Claude.