Colorectal Pathology

What it does

Colorectal Pathology reads the H&E slides of colorectal polypectomy specimens, biopsies and cancer resections, the highest-volume specimens in GI pathology. For a polyp, histology sets the colonoscopy surveillance interval; for a cancer, universal MSI or mismatch-repair testing is the guideline standard.

For polyps the run classifies tubular, tubulovillous and villous adenoma, sessile serrated lesion and hyperplastic polyp, and grades dysplasia. For carcinoma it returns the MSI-high/dMMR probability from H&E and a nine-class tissue map (tumour, stroma, lymphocytes, necrosis and debris, normal mucosa, muscle, adipose tissue, mucus, background) with the tumour–stroma ratio.

Intended use

Decision support: a second look at the serrated-versus-hyperplastic distinction and at dysplasia grade, and an MSI probability that puts likely MSI-high cancers first in the queue for MMR immunohistochemistry or MSI PCR. Tangentially sectioned polyps and small biopsies are the hard cases.

Who it is for

GI and general surgical pathologists, residents, and screening programmes with large polyp volumes. Developers use the run for structured polyp data in a LIS or for optical-versus-histological diagnosis audits.

Accepted input

• Polyps and biopsies: one or more H&E whole-slide images per specimen; several polyps can be uploaded as separate parts of one case.
• Resections: H&E slides of the tumour, for the MSI probability and the tissue map.
• Formats: DICOM VL Whole Slide Microscopy Image or vendor slide files (Aperio SVS, Hamamatsu NDPI, 3DHISTECH MRXS, Philips iSyntax, Leica SCN, Ventana BIF, Zeiss CZI, OME-TIFF).

Requirements

Requirement	Why
H&E stain	All three sections read H&E morphology
Pixel spacing in µm/px	Tissue-class areas and tumour–stroma ratio are measured in mm²
Part label per polyp	Histology is reported per polyp, matching the colonoscopy site

Optional context

Polyp site, endoscopic findings or the clinical question can be passed in clinical_context.

The result

Section	Content
Polyp histology	Tubular, tubulovillous or villous adenoma, sessile serrated lesion or hyperplastic polyp, with dysplasia grade
MSI prediction	MSI-high/dMMR probability from H&E for carcinoma
Tissue map	Nine-class tissue segmentation with class areas and the tumour–stroma ratio
Draft report	Opt-in (options.report): an English narrative that interprets the result for the reader (findings, impression, limitations); every number is checked against the findings

Standards

• Classification: WHO Classification of Digestive System Tumours, 5th edition; Revised Vienna classification of GI epithelial neoplasia.
• Biomarker: ESMO 2019 recommendations on MSI and dMMR testing.
• Reporting: CAP colon and rectum cancer protocol.
• DICOM: tissue map as Label Map Segmentation and measurements in SR TID 1500; FHIR R4 DiagnosticReport and IHE PaLM APSR for LIS export.

Works with

The polyp-histology result pairs with the polyp characterisation of the Colonoscopy model (endo/colonoscopy), to compare the optical diagnosis from the recorded colonoscopy with the final histology.