Agent skill

Data Extractor

Extract numerical data from scientific figure images using Claude vision + OpenCV calibration.

Install Data Extractor

skills CLI

$ npx skills add ClawBio/ClawBio --skill data-extractor -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio data-extractor --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/data-extractor .claude/skills/data-extractor && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "data-extractor" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/data-extractor into .claude/skills/data-extractor/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-extractor", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/ClawBio/ClawBio/tree/main/skills/data-extractor

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add ClawBio/ClawBio --skill data-extractor -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio data-extractor --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/data-extractor .agents/skills/data-extractor && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "data-extractor" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/data-extractor into .agents/skills/data-extractor/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-extractor", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill data-extractor -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio data-extractor --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/data-extractor .cursor/skills/data-extractor && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "data-extractor" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/data-extractor into .cursor/skills/data-extractor/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-extractor", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/ClawBio/ClawBio.git --path skills/data-extractor

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add ClawBio/ClawBio --skill data-extractor -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio data-extractor --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/data-extractor .gemini/skills/data-extractor && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "data-extractor" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/data-extractor into .gemini/skills/data-extractor/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-extractor", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install ClawBio/ClawBio data-extractor

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add ClawBio/ClawBio --skill data-extractor -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/data-extractor .github/skills/data-extractor && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "data-extractor" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/data-extractor into .github/skills/data-extractor/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-extractor", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill data-extractor -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio data-extractor --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/data-extractor .opencode/skills/data-extractor && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "data-extractor" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/data-extractor into .opencode/skills/data-extractor/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-extractor", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: data-extractor
GitHub stars: 1.2k
Token cost: ~801 tokens
SKILL.md length: 279 words
Files: 13
Skills in repo: 104
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Extract numerical data from scientific figure images using Claude vision + OpenCV calibration.

Works in 4 steps: Panel Detection — Identify sub-panels in… → Pre-Analysis — Identify axes, scale… → CV Calibration + Extraction — OpenCV… → …
Tasks that involve Data visualization
SKILL.md covers When to Use This Skill, Capabilities, Usage and Input Formats, plus 1 more section
Runs Python and JavaScript scripts from its folder; calls python; needs ANTHROPIC_API_KEY

What it does

Data Extractor is an agent skill from ClawBio/ClawBio. Extract numerical data from scientific figure images using Claude vision + OpenCV calibration. Supports 26+ plot types including bar charts, scatter plots, forest plots, Kaplan-Meier curves, box plots, and more.

Its SKILL.md is about 800 tokens, which your agent loads only when the skill is triggered. The skill folder holds 15 other files (for example `data_extractor.py`, `data_extractor_api.py` and `data_extractor_core/__init__.py`).

It sits in Research & Science, covering Data visualization and Performance reviews. It works with OpenCV. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

Tasks that involve Data visualization
Tasks that involve Performance reviews

Example prompts

“/data-extractor”

Requirements

Python 3
Node.js
A credential in ANTHROPIC_API_KEY

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

Panel Detection — Identify sub-panels in multi-panel figures (Claude vision)
Pre-Analysis — Identify axes, scale (linear/log), legend entries, error bars (Claude tool calling)
CV Calibration + Extraction — OpenCV detects markers/bars at pixel level, Claude extracts numerical data with calibration context
Validation — Heuristic checks for axis range, series count, error bar polarity

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python and JavaScript), which the agent can run.
Shell commands in SKILL.md call:
- python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names these keys or tokens, usually read from environment variables:
- ANTHROPIC_API_KEY
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Data Extractor loads about 801 tokens when it runs. Until then it costs about 57 tokens; SKILL.md has 279 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~57
When it runs · the whole SKILL.md, loaded when a task matches: ~801

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 279 words, ~801 tokens.

Download SKILL.mdSave it as .claude/skills/data-extractor/SKILL.md (or your agent's skills folder). This skill also uses 12 other files; get the full folder from GitHub.

name: data-extractor
description: Extract numerical data from scientific figure images using Claude vision + OpenCV calibration. Supports 26+ plot types including bar charts, scatter plots, forest plots, Kaplan-Meier curves, box plots, and more.
license: MIT
metadata.version: 0.1.0

📊 Data Extractor

You are the Data Extractor, a ClawBio skill for digitizing scientific figures. Your role is to extract numerical data from plot images for meta-analyses and systematic reviews.

When to Use This Skill

Route to this skill when the user:

Provides an image file (PNG, JPG, TIFF) containing a scientific figure
Asks to "extract data from a figure", "digitize a plot", "read values from a chart"
Mentions "meta-analysis data extraction" or "figure digitization"
Wants to convert a bar chart, scatter plot, or other figure to CSV/JSON

Capabilities

Supported Plot Types (26)

scatter, bar, line, box, violin, histogram, heatmap, forest, kaplan_meier, dot_strip, stacked_bar, funnel, roc, volcano, waterfall, bland_altman, paired, bubble, area, dose_response, manhattan, correlation_matrix, error_bar, table, other

Pipeline (4 phases)

Panel Detection — Identify sub-panels in multi-panel figures (Claude vision)
Pre-Analysis — Identify axes, scale (linear/log), legend entries, error bars (Claude tool calling)
CV Calibration + Extraction — OpenCV detects markers/bars at pixel level, Claude extracts numerical data with calibration context
Validation — Heuristic checks for axis range, series count, error bar polarity

Output Formats

CSV — One row per data point with series name, x/y values, error bars
JSON — Structured ExtractedData objects with full metadata
Web UI — Interactive table + SVG preview with editable cells

Usage

CLI

bash

python data_extractor.py --image figure.png --output results/
python data_extractor.py --web --port 8765
python data_extractor.py --demo

API (importable)

python

from data_extractor_api import run
result = run(options={"image_path": "figure.png", "output_dir": "results/"})

Web UI

Launch with --web flag. Upload images, draw boxes around plots, extract and edit data interactively.

Input Formats

PNG, JPG, JPEG, TIFF image files
Screenshots from papers, posters, slides
Multi-panel composite figures (auto-detected and split)

Notes

Requires ANTHROPIC_API_KEY environment variable
Uses Claude Sonnet for pre-analysis/detection, Claude Opus for extraction
OpenCV calibration improves accuracy for scatter/bar plots with clear markers
Error bars are reported as ± extent (delta from mean), not absolute positions

Files

SKILL.md and 12 other files in skills/data-extractor of ClawBio/ClawBio.

SKILL.md
data_extractor.py
data_extractor_api.py
data_extractor_core/__init__.py
data_extractor_core/cv_calibration.py
data_extractor_core/digitizer.py
data_extractor_core/models.py
requirements.txt
tests/test_extractor.py
web/app.js
web/index.html
web/server.py
web/styles.css

Open the folder on GitHubat commit 5e045e3

Compare with similar skills

Data Extractor next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Data Extractor compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Data Extractor this skillClawBio/ClawBio	1.2k	—	~801	Automated safety check: Pass	MIT	today
Decision Curve Analysisaipoch/medical-research-skills	2k	—	~2.8k	Automated safety check: Pass	MIT	21 days ago
Nature-Style Scientific FiguresYuan1z0825/nature-skills	46k	—	~2.9k	Automated safety check: Pass	Apache-2.0	yesterday
Engineering Figure Agentheyu-233/engineering-figure-agent	305	—	~1.1k	Automated safety check: Pass	MIT	4 mo ago
Scientific Figure GeneratorDeepshare-Official/CCF-Figure	225	—	~1.8k	Automated safety check: Pass	MIT	3 mo ago
Scanpy Single-Cell Analysisdavila7/claude-code-templates	32k	16 repos	~2.8k	Automated safety check: Pass	MIT	today

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Questions about Data Extractor

What does Data Extractor do?

Extract numerical data from scientific figure images using Claude vision + OpenCV calibration. Data Extractor is an agent skill from ClawBio/ClawBio. Extract numerical data from scientific figure images using Claude vision + OpenCV calibration.

When should I use Data Extractor?

Data Extractor fits situations like: tasks that involve Data visualization; tasks that involve Performance reviews.

How do I install Data Extractor in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill data-extractor -a claude-code`. Or copy the skill folder (skills/data-extractor in ClawBio/ClawBio) into .claude/skills/data-extractor in your project. Claude Code loads it when a task matches its description.

How do I install Data Extractor in Codex?

Run `npx skills add ClawBio/ClawBio --skill data-extractor -a codex`. Or copy the skill folder (skills/data-extractor in ClawBio/ClawBio) into .agents/skills/data-extractor in your project. Codex loads it when a task matches its description.

Can I use Data Extractor in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill data-extractor -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/data-extractor, .gemini/skills/data-extractor, .github/skills/data-extractor and .opencode/skills/data-extractor in your project.

What does Data Extractor need to run?

Going by SKILL.md and its folder, Data Extractor needs Python and JavaScript for the scripts in its folder, the command-line tools its instructions call (python) and credentials named ANTHROPIC_API_KEY. Our summary lists: Python 3; Node.js; A credential in ANTHROPIC_API_KEY.

Does Data Extractor access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Data Extractor safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Data Extractor use?

Data Extractor is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Data Extractor use?

About 801 tokens (SKILL.md is roughly 3.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Data Extractor?

Skills that share tags, products or a category with Data Extractor: Decision Curve Analysis (aipoch/medical-research-skills, 2k stars), Nature-Style Scientific Figures (Yuan1z0825/nature-skills, 46k stars), Engineering Figure Agent (heyu-233/engineering-figure-agent, 305 stars) and Scientific Figure Generator (Deepshare-Official/CCF-Figure, 225 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Data Extractor?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 7, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Data Extractor

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

📊 Data Extractor

When to Use This Skill

Capabilities

Supported Plot Types (26)

Pipeline (4 phases)

Output Formats

Usage

CLI

API (importable)

Web UI

Input Formats

Notes

Files

Compare with similar skills

Similar skills

More from ClawBio/ClawBio

Related

Questions about Data Extractor