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MubasherMohammed
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data-extractor

Extract numerical data from scientific figures using Claude vision and OpenCV.

Updated May 10, 2026
Search Tags:#data extraction#bioinformatics#scientific figures#plot analysis#figure digitization
One-click install
npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill data-extractor-mubashermohammed
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: data-extractor
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/data-extractor
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill data-extractor-mubashermohammed

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires anthropic, opencv-python-headless, numpy, Pillow, pydantic, fastapi, uvicorn, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill automates the extraction of numerical data from scientific figures, enabling efficient data digitization and analysis.

Core Features & Use Cases

  • Figure Data Extraction: Extracts numerical data from various plot types like bar charts, scatter plots, and Kaplan-Meier curves.
  • Plot Type Support: Handles over 26 plot types, including bar charts, scatter plots, forest plots, and Kaplan-Meier curves.
  • Output Formats: Outputs data in CSV, JSON, or through a web UI with interactive tables and SVG previews.

Quick Start

Run the data-extractor skill with the image path and output directory: python data_extractor.py --image figure.png --output results/

Frequently Asked Questions about data-extractor

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I extract numerical data from scientific figures for a meta-analysis?▼

You can extract numerical data from scientific figures by running a Python script that applies Claude vision and OpenCV image analysis. This process digitizes plots like bar charts and Kaplan-Meier curves into CSV or JSON for systematic reviews.

Can I digitize Kaplan-Meier curves and forest plots into CSV?▼

Yes, you can digitize Kaplan-Meier curves and forest plots into CSV. The extraction process supports over 26 scientific plot types and outputs the numerical results in CSV, JSON, or through an interactive web UI.

What plot types are supported for figure digitization in bioinformatics?▼

Figure digitization in bioinformatics supports over 26 plot types, including bar charts, scatter plots, forest plots, and Kaplan-Meier curves. The tool analyzes these scientific figures to extract raw numerical data.

Do I need OpenCV and FastAPI to run the data-extractor script?▼

Yes, you need OpenCV and FastAPI along with anthropic, numpy, Pillow, pydantic, and uvicorn. These dependencies provide the computer vision, web server, and data validation environment required for image analysis.

How do I extract data from a figure image using Python?▼

To extract data from a figure image using Python, run the extraction script with the image path and output directory: `python data_extractor.py --image figure.png --output results/`. This processes the plot and saves the numerical data.

What is the best way to automate figure data extraction for systematic reviews?▼

The best way to automate figure data extraction for systematic reviews is using a Python script that combines Claude vision and OpenCV. This handles various plot types and outputs structured data like JSON or CSV for meta-analysis.

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