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PathML
维护者 K-Dense Inc. · 最近更新 2026年4月1日
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 analy.
原始来源
K-Dense-AI/claude-scientific-skills
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pathml
- 维护者
- K-Dense Inc.
- 许可
- GPL-2.0 license
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- PathML是一个comprehensive Python 工具包 ，用于 computational pathology workflows，designed to facilitate 机器学习 、 image analysis ，用于 whole-slide pathology images. 框架 provides modular，composable tools ，用于 loading diverse slide formats，preprocessing images，constructing spatial graphs，training 深度学习 models，、 analyzing multiparametric imaging data ，面向 technologies like CODEX 、 multiplex immunofluorescence。
- uv pip install pathml[all]。
原始文档
SKILL.md 摘录
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
Core Capabilities
PathML provides six major capability areas documented in detail within reference files:
1. Image Loading & Formats
Load whole-slide images from 160+ proprietary formats including Aperio SVS, Hamamatsu NDPI, Leica SCN, Zeiss ZVI, DICOM, and OME-TIFF. PathML automatically handles vendor-specific formats and provides unified interfaces for accessing image pyramids, metadata, and regions of interest.
See: references/image_loading.md for supported formats, loading strategies, and working with different slide types.
适用场景
- Loading 、 processing whole-slide images (WSI) in various proprietary formats。
- Preprocessing H&E stained tissue images ，支持 stain normali。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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