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Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted log1p-CPM expression from 224x224 tiles at about 20x, querying the released protein-coding gene panel by symbol, and whole-slide prediction after resolution-aware tiling with histolab.

K-Dense-AI/claude-scientific-skills Agent Skills author: K-Dense-AI MIT 3 files body ≈ 2 282 tokens Open the sourcegithub.com↗ analyzed 13 h ago

Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.

As a process C 51/100 · Has gaps — weak spots: result and completion, when it triggers, inputs and preconditions

GeneratorSoftware developmentAI and agentstype and topics are labelled automatically from the skill text
Runs in: Claude / Claude Code ChatGPT / Codex Gemini CLI Cursor GitHub Copilot / VS Code Qwen Code Kimi Code CLI Z.ai (GLM) DeepSeek (Deep Code) Mistral Vibe LangChain (deepagents) OpenClaw Goose OpenCode
JSON
Technical rating
C
84/100
safety, quality, tests
Safety 60%
89
Quality 40%
77
Run on models
none yet
Process rating
C
51/100
Has gaps
Result and completion w 14
0
Inputs and preconditions w 11
0
Failures and branches w 10
0
the three weakest of ten parameters · all ten

What is at stake

Medium-severity findings: the skill is probably honest, but read what alarmed the scanner.

Obfuscation medium severity

Below is the worst case for this category. The finding here is medium: the guard saw a sign, not a proof.

If you install

The files contain invisible characters, encoded commands or comments hidden from readers but visible to the model. What you read differs from what the agent sees.

For the author

Remove invisible characters (they usually sneak in through copy-paste) and encoded strings: no catalog will pass them. Instructions for the model must be readable by a human too.

Broad scope medium severity

Below is the worst case for this category. The finding here is medium: the guard saw a sign, not a proof.

If you install

The skill asks for more than the task needs: broad tool access, credential environment variables, binaries. Every extra permission widens the damage from a mistake or a compromise.

For the author

Narrow allowed-tools and the variable list to the minimum; replace binaries with readable sources or scripts.

How to improve

  1. Say in the description WHEN to use the skill ("use when…", example requests): that is the agent's main cue.
For the model run — optional
  • Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
  • A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.

Guard findings · 3

✓ No critical or high findings

Medium and low: 3
  • medium Obfuscation obf-base64-blob references/whole_slide.md:238
    Long base64-looking blob
    - [Upstream WSI example](https://github.com/ratschlab/DeepSpotM/blob/4d77…628/examples/predict_wsi.py)
  • medium Broad scope meta-broad-allowed-tools SKILL.md:1
    Broad tool permissions pre-approved: Bash
    allowed-tools: Read Write Edit Bash
  • low Obfuscation obf-base64-blob references/api.md:143
    Long base64-looking blob (detector / deny-list definition)
    - [Reviewed upstream model source](https://github.com/ratschlab/DeepSpotM/blob/4d77…628/src/deepspotm/model.py)
    detector

Files scanned: 3. Evidence is masked. Grey chips explain why severity was lowered.

Against the Agent Skills spec

  • warning description-no-when description does not say WHEN to use the skill (no "use when")

Process rating: all ten parameters 51/100

  • 0Result and completion. Does not say what the result is
  • 0Inputs and preconditions. Does not say what the process needs to start
  • 0Failures and branches. Linear process with no failure handling
  • 0Progress reporting. Says nothing while it works
  • 20When it triggers. No condition that starts the skill
  • 30Running it twice. 1 mutating operations with no state check
  • 100Tools and files. Tools declared in frontmatter
  • 100Steps. 17 steps
  • 100Consistency. Name and required fields are in place
  • 100Execution cost. Instruction body is 2282 tokens
  • low 13 top-level sections: this looks like several domains in one skill

Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.

Quality signals

  • +5Description has no quoted example phrases that should trigger the skill
  • +4Description does not say when NOT to use the skill (false activations)
  • +3Output format is not stated: the model decides each time
  • +2Single-language instructions
  • +3Description length 300: enough signal without eating the budget
  • +4Structure: 14 headings
  • +3Step-by-step instructions: 17 items
  • +4Has examples (5 code blocks)
  • +4Reference files are cited in the instructions (2 of 2)
  • +1License stated

Quality base 70; lint remarks subtract, signals add up to 100. Result: 77.