pathml
Category: clinical-and-health · License: MIT · Version: 1.2 · Includes scripts
Tags: computational pathology, whole slide images, digital pathology, medical imaging
When to use it
Covers local, research-only computational pathology with PathML 3.0.5: loading and tiling whole-slide images (OpenSlide, Bio-Formats), preprocessing and QC pipelines run via SlideData.run(), .h5path data management, multiplex image quantification, spatial graph construction (KNN, RAG, HACT), and bounded local ONNX model inference planning. Use when loading or tiling slides, building tissue-mask or stain pipelines, managing .h5path files and patient-level splits, quantifying CODEX or Vectra multiplex images, or building cell and tissue graphs. Not for clinical diagnosis or patient care decisions.Example requests
Ask your agent in plain language, for example:- “How do I tile a .svs slide with PathML and run a tissue mask on it?”
- “I’m on Python 3.11 and ran
pip install pathml[all]for my lab’s CODEX project, and it errored out with a javabridge build failure on Windows. I have a 40-channel qptiff (codex_run3.qptiff) and want to segment nuclei and get per-cell marker means into AnnData. What should I do?” - “I have 120 H&E slides from 60 patients, with two or three slides per patient. I want to build a graph for each slide in which cells are nodes and neighbours within a certain distance are linked, and then train a classifier on it. How should I set this up so my evaluation isn’t leaky?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole clinical-and-health category with /plugin install clinical-and-health@research-agent-skills.