pathml

SKILL.md

PathML

Overview

PathML is a comprehensive Python toolkit for computational pathology workflows, designed to facilitate machine learning and image analysis for whole-slide pathology images. The framework provides modular, composable tools for loading diverse slide formats, preprocessing images, constructing spatial graphs, training deep learning models, and analyzing multiparametric imaging data from technologies like CODEX and multiplex immunofluorescence.

When to Use This Skill

Apply this skill for:

Loading and processing whole-slide images (WSI) in various proprietary formats

Preprocessing H&E stained tissue images with stain normalization

Nucleus detection, segmentation, and classification workflows

Building cell and tissue graphs for spatial analysis

Training or deploying machine learning models (HoVer-Net, HACTNet) on pathology data

Analyzing multiparametric imaging (CODEX, Vectra, MERFISH) for spatial proteomics

Quantifying marker expression from multiplex immunofluorescence

Managing large-scale pathology datasets with HDF5 storage

Tile-based analysis and stitching operations