pathml SKILL.md skillA
pathml from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/pathml@git:20260528.ca3bcfdPins git:20260528.ca3bcfd in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/medical-imaging/pathml/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260528.ca3bcfd, committed May 28, 2026
- Size
- 10,951 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Computational pathology toolkit for whole-slide images (WSIs): load slides, extract tiles, stain normalization, nuclear segmentation, feature extraction, and ML training. Supports H&E and multiplex. For end-to-end pipelines from raw WSIs to quantitative outputs.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# pathml ## Overview PathML is a Python toolkit designed for computational pathology workflows on whole-slide images (WSIs). It provides a unified pipeline from raw slide files (SVS, NDPI, MRXS, TIFF) through tile extraction, preprocessing (stain normalization, nuclear segmentation, tissue detection), feature extraction, and machine learning. PathML integrates with popular Python ML and image processing libraries while abstracting the complexity of WSI handling through its `SlideData` and `Pipeline` abstractions. ## When to Use - **Processing whole-slide H&E images**: Tiling a large WSI, normalizing staining variability across slides from different scanners or batches. - **Nuclear segmentation on pathology slides**: Detecting and segmenting nuclei in H&E or DAPI-stained WSIs using built-in segmentation pipelines. - **Building ML training datasets from WSIs**: Extracting tiles with associated labels for training tissue classifiers, tumor detectors, or survival prediction models. - **Multiplex immunofluorescence (mIF) image analysis**: Processing multi-channel IF slides with channel-specific preprocessing and feature extraction. …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/pathml@sha256:92cbef3d599ce61bThe line at the top of this page pins the label git:20260528.ca3bcfd, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_w5xys5tadtb5ryj2)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on May 28, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (10951 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_w5xys5tadtb5ryj2 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/pathml GET https://markdownregistry.com/api/v1/blob/92cbef3d599ce61b495150b13040c9af63bf28d3ffca9a7639948176e5744c3c
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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