Digital Pathology

Overview

This skill teaches the agent to generate correct, runnable code for whole-slide image (WSI) pipelines. It covers TIAToolbox CLI and Python API, the H-optimus-0 foundation model, the standard tissue→tiles→features→aggregate→predict pattern, the CAMELYON datasets, and SageMaker deployment patterns for regulated workloads.

Default to TIAToolbox primitives (WSIReader, PatchPredictor, DeepFeatureExtractor) rather than reimplementing slide I/O. Default to H-optimus-0 at 0.5 mpp / 224×224 unless the task specifies otherwise.

Usage

Invoke this skill when the user asks to:

• Inspect, tile, or stain-normalize a WSI (SVS, NDPI, MRXS, pyramidal TIFF).
• Extract features with a pathology foundation model.
• Build a slide-level classifier on CAMELYON or similar cohorts.
• Deploy a WSI model to AWS SageMaker.

Ask for clarification only if the resolution, model, or output artifact is ambiguous. Otherwise apply the defaults in the Resolution Rules section.