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flowio

Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, NumPy event extraction, multi-dataset files, table export, and FCS 3.1 creation; use FlowKit for compensation, cytometry transforms, gating, or FlowJo workspaces.

Quality

94%

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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.

Excellent procedural content: executable, validated workflows covering read, multi-dataset, write, and inspection paths, with a clean one-level-deep reference bundle and a hard-earned catalog of FlowIO 1.4.0 gotchas. The only room for improvement is tightening a few verbose caution passages and the citation boilerplate.

Suggestions

Condense the write_fcs spill/spillover caution paragraphs into a short checklist, keeping the detector-name-vs-PnN matching rule and the validation requirement; the current four-paragraph treatment spends tokens on peripheral detail.

Trim the citation section's procedural prose (fetching, version handling) to the essential instruction and citation, or move the extended citation protocol into a reference file alongside sources.md.

Mention the ".fcs" file extension once in the quick-start examples' context (or in the frontmatter description) so users who name files by extension trigger the skill naturally.

DimensionReasoningScore

Conciseness

The body is dense with FlowIO-specific semantics Claude cannot know (TEXT key "$"-stripping, PnR range masks, the read_multiple_data_sets handle-closing bug), with no generic concept explanations. Not 5: minor trims are possible — the multi-paragraph write_fcs/spill caution and the lengthy citation boilerplate could be tightened; not 3: there is no padding or over-explanation of known concepts.

4 / 5

Actionability

Everything is executable: uv install/version commands, validated quick starts for read, multi-dataset, and create paths, copy-paste inspector CLI invocations with flags, and round-trip assertions ("np.testing.assert_allclose"). Not 4: the code is complete and covers all common cases with built-in validation.

5 / 5

Workflow Clarity

The six-step Operating Workflow sequences inspect-before-load, explicit preprocessing semantics, strict-parsing, privacy, and "Validate writes by reopening them"; code embeds shape checks ("raise ValueError" on $TOT/$PAR mismatch) and round-trip verification, and the Non-Negotiable Checks section acts as a checklist. Not 4: explicit validation checkpoints and feedback loops are present for the destructive write/overwrite path.

5 / 5

Progressive Disclosure

The body is a genuine overview: "Read only the reference needed for the current task" followed by five one-level-deep, per-topic reference files (all verified to exist) and a bundled scripts/inspect_fcs.py, with reference files containing no nested references. Not 4: references are well-signaled with topic labels and content is appropriately split.

5 / 5

Total

19

/

20

Passed

Description

92%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 model description: concrete, third-person, comprehensive capability list with an explicit "Use for…" trigger clause and clear routing that separates FlowIO from the FlowKit analysis package. The only weakness is a couple of missing natural trigger terms (notably the ".fcs" extension).

DimensionReasoningScore

Specificity

Concrete actions cover the full read/inspect/write surface: "Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files", "low-level FCS metadata and channel inspection, NumPy event extraction, multi-dataset files, table export, and FCS 3.1 creation" — comprehensive with no vague filler. Not 4: no meaningful coverage gaps remain.

5 / 5

Completeness

Explicitly answers both: what ("Reads, inspects, and writes… files with FlowIO" plus enumerated capabilities) and when ("Use for low-level FCS metadata and channel inspection, NumPy event extraction… FCS 3.1 creation"). Not 4: the when-clause is explicit and enumerated, and it adds negative routing ("use FlowKit for compensation…").

5 / 5

Trigger Term Quality

Strong natural vocabulary ("FCS files", "Flow Cytometry Standard", "gating", "compensation", "FlowJo workspaces", "FlowKit") including domain synonyms users would actually say. Not 5: the ".fcs" file extension and phrases like "flow cytometry data" are missing, matching anchor 4's "a few natural terms missing" rather than the file-extension-inclusive anchor 5.

4 / 5

Distinctiveness Conflict Risk

Clear niche (low-level FCS file I/O with FlowIO) with distinct triggers and an explicit boundary against the closest overlapping skill ("use FlowKit for compensation, cytometry transforms, gating, or FlowJo workspaces"). Not 4: the main overlap risk is actively disambiguated, leaving minimal conflict risk.

5 / 5

Total

19

/

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/flowio/SKILL.md

Reviewed

Table of Contents

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