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pathml

Use PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and QC pipelines, manage h5path data, quantify multiplex images, construct spatial graphs, and plan bounded model inference.

68

Quality

82%

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SecuritybySnyk

Passed

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SKILL.md
Quality
Evals
Security

Quality

Content

86%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A well-structured, highly actionable skill body with executable examples, explicit safety/version baselines, and clean progressive disclosure to verified reference files; only marginally verbose in the boilerplate sections.

DimensionReasoningScore

Conciseness

Dense and mostly assumes competence (API gotchas, version pins, security notes each earn their place), with minor padding in the citing/licensing boilerplate that could be tightened.

4 / 5

Actionability

Provides copy-paste-ready executable code (HESlide pipeline, islice tiling loop with an assertion) and concrete shell commands (uv pip install, apt-get, bundled CLIs) covering the common cases.

5 / 5

Workflow Clarity

An explicit 8-step Research workflow plus a minimal workflow with a pilot-then-full-run checkpoint and an assertion; most checkpoints are present, though the 8 steps read more as advisory guidance than hard validate→fix→retry loops.

4 / 5

Progressive Disclosure

Clear overview in SKILL.md with well-signaled, one-level-deep references to six existing reference files (each annotated with its scope) and a scripts directory; all referenced paths exist and navigation is easy.

5 / 5

Total

18

/

20

Passed

Description

78%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A specific, comprehensive description with concrete actions and a clear niche, weakened only by an imperative voice and a purpose-style 'when' clause rather than explicit user-trigger phrasing.

Suggestions

Rewrite in third person (e.g. 'Loads and tiles slides, builds preprocessing and QC pipelines...') to match the rubric's voice expectation.

Add an explicit 'Use when the user mentions whole-slide images, WSI, staining, multiplex IF, or computational pathology' trigger clause.

Include common synonyms/extensions like 'WSI', '.svs', '.ndpi', or 'stain normalization' to broaden trigger coverage.

DimensionReasoningScore

Specificity

Lists multiple concrete actions ('load and tile slides, build preprocessing and QC pipelines, manage h5path data, quantify multiplex images, construct spatial graphs, and plan bounded model inference') matching the score-5 anchor, but reduced by one for the imperative 'Use PathML' voice rather than third person.

4 / 5

Completeness

Answers both what (the enumerated actions) and when ('for local, research-only computational pathology workflows'), but the when is a purpose/scope clause rather than an explicit user-trigger phrase like 'Use when the user mentions slides'.

4 / 5

Trigger Term Quality

Strong natural domain keywords ('computational pathology', 'slides', 'preprocessing', 'QC', 'h5path', 'multiplex images', 'spatial graphs', 'model inference') that a pathology researcher would say, though common variations like 'WSI', 'whole slide images', 'stain', or '.svs' are absent.

4 / 5

Distinctiveness Conflict Risk

Computational pathology with PathML is a clear, narrow niche with distinct triggers and minimal overlap risk with other skills.

5 / 5

Total

17

/

20

Passed

Validation

100%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
K-Dense-AI/scientific-agent-skills
Reviewed

Table of Contents

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