Data & ReproMedical Imaging & PathologyK-Dense-AI/claude-scientific-skillsData & Reproduction

PathML

Maintainer K-Dense Inc. · Last updated April 1, 2026

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.

Claude CodeOpenClawNanoClawAnalysisReproductionpathmlimagingpackagemedical imaging & digital pathology

Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pathml

Maintainer: K-Dense Inc.
License: GPL-2.0 license
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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.
uv pip install pathml[all].

Source Doc

Excerpt From SKILL.md

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.

Use cases

Loading and processing whole-slide images (WSI) in various proprietary formats.
Preprocessing H&E stained tissue images with stain normali.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Related skills

Back to directory

Data & ReproMedical Imaging & Pathology

OMERO Integration

OMERO is an open-source platform for managing, visuali.

Claude CodeOpenClawAnalysis

K-Dense-AI/claude-scientific-skillsView

Data & ReproMedical Imaging & Pathology

pptx

| Task | Guide | |------|-------| | Read/analyze content | `python -m markitdown presentation.pptx` | | Edit or create from template | Read…

Claude CodeOpenClawAnalysis

K-Dense-AI/claude-scientific-skillsView

Data & ReproProtein Structure & Design

Adaptyv

Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein sequences via API or…

Claude CodeOpenClawAnalysis

K-Dense-AI/claude-scientific-skillsView

Data & ReproStatistics & Data Analysis

aeon

Aeon is a scikit-learn compatible Python toolkit for time series machine learning. It provides state-of-the-art algorithms for classificatio…

Claude CodeOpenClawAnalysis

K-Dense-AI/claude-scientific-skillsView