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bioimage-analysis

Microscopy image analysis for cell biology. Cell segmentation (Cellpose, watershed), object tracking (trackpy), morphology quantification, colony counting, colocalization analysis, and cytoskeleton characterization. For pathology WSI use pathml; for flow cytometry use flow-cytometry-analysis.

54

Quality

62%

Does it follow best practices?

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SecuritybySnyk

Passed

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tessl review fix ./backend/cli/skills/biology/bioimage-analysis/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

53%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 dense, code-heavy reference with broad, mostly-executable coverage and useful troubleshooting, but it is monolithic: it duplicates its own capability sections as 'workflows', inlines everything rather than pointing to the five bundled scripts that already exist, and embeds no validation checkpoints in the batch pipeline. Restructuring around the existing scripts would fix both the disclosure and conciseness issues at once.

Suggestions

Reference the existing bundled scripts in each capability section (e.g., 'For full implementation see scripts/segment_cells.py') instead of inlining ~400 lines of code — the five scripts are currently completely orphaned.

Remove or merge the 'Typical Workflows' sections that near-duplicate Core Capabilities 2, 3, 5, and 6, keeping each pipeline in one place.

Add an explicit validation checkpoint inside the Batch Processing loop (e.g., visually verify masks on the first image before processing the rest, and check per-image cell counts for anomalies), and make each code snippet self-contained with its own imports.

DimensionReasoningScore

Conciseness

The body is commendably code-first with almost no prose padding or re-explanation of concepts Claude already knows, but roughly a quarter of its ~540 lines are near-duplicates: the four 'Typical Workflows' restate Core Capabilities 2, 3, 5, and 6 almost verbatim (e.g., the colony-counting watershed code appears twice, and Quick Start duplicates the Cellpose segmentation section). It could be tightened significantly by collapsing the redundant workflow sections.

3 / 5

Actionability

Mostly executable, copy-paste-ready code with concrete parameters and covering all advertised capabilities, but several snippets would not run as-is due to missing imports in the snippet itself (e.g., morphology section uses np without importing numpy, colocalization/mitochondria sections use skimage.io and skimage.filters without importing skimage, Batch Processing uses models without importing cellpose, Workflow 2 uses pd without importing pandas).

4 / 5

Workflow Clarity

Sequences are clear and the Troubleshooting section provides problem/solution recovery guidance, but the Batch Processing workflow — the rubric's flagged batch context — is a fire-and-forget loop with no validate-checkpoint embedded; validation appears only as an implicit Best Practice ('Validate segmentation visually... before batch processing') rather than as a step in the workflow itself, which per the rubric's batch-operations cap holds this at 3.

3 / 5

Progressive Disclosure

The bundle provides five scripts (segment_cells.py, count_colonies.py, track_cells.py, analyze_morphology.py, colocalization.py) that the SKILL.md body never mentions or links — orphaned bundle content — while ~400 lines of per-capability code that clearly belongs in reference files are inlined in a monolithic 540-line document. This matches the anchor for content inlined that belongs in separate files with no signaled references.

2 / 5

Total

12

/

20

Passed

Description

71%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 'what' statement with specific, tool-named capabilities and good routing to adjacent skills, but it lacks any explicit 'use when' trigger clause and omits several natural search terms and file extensions. Adding a 'Use when...' sentence with concrete trigger phrases would raise completeness and trigger-term quality to the top anchors.

Suggestions

Add an explicit trigger clause, e.g. 'Use when the user mentions microscopy images, .tif/.tiff files, segmenting cells or nuclei, counting colonies, or tracking objects in time-lapse sequences.'

Include natural synonyms and file extensions users would say (fluorescence, brightfield, time-lapse, .tif, .tiff, plate images) alongside the existing tool keywords.

Optionally add routing for the clinical-imaging domain mentioned in the body (e.g., 'for MRI/CT use clinical-imaging') to further reduce overlap risk.

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions with named tools — 'Cell segmentation (Cellpose, watershed), object tracking (trackpy), morphology quantification, colony counting, colocalization analysis, and cytoskeleton characterization' — comprehensive coverage of the skill's capabilities with no vague filler.

5 / 5

Completeness

The 'what' is clearly and specifically stated, but there is no 'Use when...' clause or equivalent trigger guidance for this skill — the boundary sentences only route users AWAY to pathml and flow-cytometry-analysis, which at best weakly implies the 'when'. Per the rubric guideline, a missing explicit 'when' caps completeness at 3.

3 / 5

Trigger Term Quality

Good natural keyword coverage ('microscopy image analysis', 'cell segmentation', 'colony counting', 'colocalization', 'object tracking') that users would naturally say, but missing common variations and file extensions (.tif/.tiff, 'fluorescence', 'brightfield', 'time-lapse') that the top anchor requires.

4 / 5

Distinctiveness Conflict Risk

Clear niche (microscopy images for cell biology) with explicit disambiguation from the two closest domains ('For pathology WSI use pathml; for flow cytometry use flow-cytometry-analysis'), but residual overlap risk with other imaging skills (e.g., clinical imaging) that are not routed away, keeping it below the minimal-conflict anchor.

4 / 5

Total

16

/

20

Passed

Validation

81%

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

Validation — 13 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

skill_md_line_count

SKILL.md is long (548 lines); consider splitting into references/ and linking

Warning

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

13

/

16

Passed

Repository
synthetic-sciences/openscience
Reviewed

Table of Contents

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