What imaging formats does PathML support?

PathML supports over 160 proprietary and open formats, including Aperio SVS, Hamamatsu NDPI, Leica SCN, Zeiss ZVI, DICOM, and OME-TIFF.

Can I use this for CODEX or multiplexed imaging?

Yes, PathML includes specialized classes and workflows for processing multiparametric data from platforms like CODEX, Vectra, and MERFISH.

Are there pre-built machine learning models included?

Yes, PathML integrates architectures like HoVer-Net for nucleus segmentation and HACTNet for hierarchical cell-type classification.

How does PathML handle large whole-slide images?

It uses efficient tile-based processing and integrates with HDF5 storage to manage large-scale pathology datasets without overloading memory.

PathML

Name: PathML
Author: youyinnn

byyouyinnn

0•

数据科学与机器学习

Facilitates advanced computational pathology workflows by providing specialized tools for whole-slide image analysis, tissue segmentation, and spatial machine learning.

PathML is a comprehensive toolkit designed for the end-to-end processing of whole-slide pathology images, bridging the gap between raw imaging data and deep learning analysis. It supports over 160 slide formats and offers specialized capabilities for preprocessing H&E slides, constructing tissue-level graphs, and analyzing multiparametric imaging like CODEX and multiplex immunofluorescence. This skill is essential for researchers and developers building AI models for nucleus segmentation, marker quantification, or spatial proteomics, providing a unified interface for handling complex pathology datasets and large-scale HDF5 storage.

主要功能

01Nucleus segmentation and classification using pre-built models like HoVer-Net

02Modular preprocessing pipelines for stain normalization and tissue detection

030 GitHub stars

04Specialized workflows for CODEX and multiparametric imaging analysis

05Spatial graph construction for cellular and tissue-level relationship analysis

06Support for 160+ whole-slide image formats including SVS, NDPI, and OME-TIFF

使用场景

01Managing and processing large-scale pathology datasets with optimized HDF5 storage

02Building deep learning models for automated nucleus detection and segmentation in H&E slides

03Quantifying marker expression and spatial relationships in multiplexed immunofluorescence data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add youyinnn/skills-collection pathml

For use in Claude.ai and ChatGPT