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cellprofiler

Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/channel manifests, headless batch execution, segmentation overlays, and measurement QC for 2D fluorescence assays.

69

Quality

87%

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SecuritybySnyk

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SKILL.md
Quality
Evals
Security

Quality

Content

92%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.

The content is a dense, highly actionable operator guide: executable commands with a concrete manifest example, a clearly sequenced workflow with strong validation and failure handling for batch execution, and clean one-level-deep delegation to real bundle files. Its only weakness is mild over-density — the version-discrepancy discussion and a few overloaded sentences could be tightened or moved to the runtime reference.

DimensionReasoningScore

Conciseness

The body is efficient and assumes competence — no explanations of what CellProfiler or TIFFs are, and nearly every sentence carries non-obvious domain knowledge (LoadData turning '001' into '1', 12-bit-in-uint16 scaling, storage-maximum saturation semantics). It falls short of level 5 only because the 4.2.8 vs PyPI 4.2.8.1 version discussion and some very dense multi-clause sentences (e.g., the run contract paragraph) could be trimmed or delegated to the runtime reference.

4 / 5

Actionability

The guidance is fully executable: copy-paste-ready commands ('python scripts/nuclei_assay.py prepare images.csv load_data.csv', 'run ... --executable cellprofiler', 'summarize results'), a concrete CSV manifest example, exact engine flags (-c -r, --data-file, --done-file), and links to real bundled files (assets/nuclei.cppipe, references/runtime-and-qc.md) that were verified to exist. Specific examples cover the common 2D nuclear-channel assay case.

5 / 5

Workflow Clarity

The 5-step workflow is clearly sequenced with explicit validation checkpoints and feedback loops appropriate to a batch operation: pilot across controls/dim/plate-edge images with overlay inspection, threshold and declumping tuning, pipeline freezing, then batch analysis with QC review (saturation warnings, zero counts, count/area distributions). Failure handling is explicit — success requires exit code zero plus a Complete marker and valid tables, failed runs retain status and error, and the instruction to rerun in a new output folder.

5 / 5

Progressive Disclosure

SKILL.md is a well-organized overview (Workflow / Run the bounded assay / Interpret the outputs / Sources) with bulk detail correctly split one level deep into references/runtime-and-qc.md (container target, verification evidence, review sources — verified no nested reference chains), the starting pipeline in assets/nuclei.cppipe, and the helper in scripts/nuclei_assay.py. All referenced paths exist in the bundle and are clearly signaled.

5 / 5

Total

19

/

20

Passed

Description

75%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 strong, specific description that clearly states what the skill does with concrete capabilities and a distinct niche, but it entirely lacks an explicit 'when to use it' trigger clause and omits common trigger variants and file extensions (.cppipe, TIFF, DAPI) that would help discovery.

Suggestions

Add an explicit trigger clause such as 'Use when the user needs to run or build CellProfiler .cppipe pipelines, count nuclei, or quantify nuclear fluorescence from microscopy TIFFs.'

Include natural trigger synonyms and file extensions users would say: .cppipe, TIFF/.tif, DAPI, high-content imaging/analysis.

Clarify scope boundaries in the trigger (e.g., 2D grayscale nuclear-channel assays) so it fires for the right requests and not for volumetric or multichannel tasks.

DimensionReasoningScore

Specificity

The description lists multiple specific concrete actions with comprehensive coverage: 'Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements' plus 'image/channel manifests, headless batch execution, segmentation overlays, and measurement QC'. It matches the level-5 anchor (multiple specific concrete actions) rather than level 4, which would have minor coverage gaps.

5 / 5

Completeness

The 'what' is clearly and explicitly stated (segmentation, counts, per-object measurements, manifests, overlays, QC), but there is no 'Use when...' clause or equivalent explicit trigger guidance — 'for 2D fluorescence assays' only weakly implies scope, not when to invoke the skill. Per the judging guidelines, a missing 'Use when...' clause caps completeness at 3.

3 / 5

Trigger Term Quality

Natural keywords users would say are present: 'CellProfiler', 'nuclear segmentation', 'cell counts', 'microscopy', 'fluorescence', 'batch execution'. However, common variations and file extensions are missing (.cppipe, .tif/TIFF, DAPI, high-content analysis/screening), so it fits 'good keyword coverage; a few natural terms missing' rather than the comprehensive level-5 anchor.

4 / 5

Distinctiveness Conflict Risk

The description names a specific tool (CellProfiler) and a clear niche (reproducible 2D fluorescence nuclear-segmentation assays with headless batch execution), giving it distinct triggers with minimal conflict risk against generic image-analysis or document 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.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

K-Dense-AI/scientific-agent-skills

Path

skills/cellprofiler/SKILL.md

Reviewed

Table of Contents

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