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How to draft a method figure from a paper's methods section with Auto Illustrate

Generate an editable draw.io figure and a restyled PNG from a LaTeX methods section in one command.

Short answer: Install the draw.io desktop app so the drawio command is on PATH, and install the Claude Code CLI so claude is on PATH; then npm install -g autoillustrate; autoillustrate doctor. All steps.

  • Top pick
  • Research
  • Intermediate
  • 1 hour
  • From the README
  • Claude Code

Credentials. Coding agents launched by the tool inherit your environment, including OPENAI_API_KEY, so run it on trusted papers and preferably inside a container or VM.

Who it is forA researcher preparing a paper who needs a front-page or method diagram and has the methods text in a .tex file.

The problemDrawing a clear method diagram by hand in draw.io takes hours, and a figure that is not editable is hard to revise after feedback.

The outcomeA run folder with an editable full_figure.drawio, a deterministic full_figure.png, and a restyled full_figure_enhanced.png.

What you need first

  • Node 22 or newer
  • draw.io desktop CLI on PATH as drawio
  • Claude Code CLI (claude) on PATH, since it is the default agent
  • OPENAI_API_KEY set in the shell or a .env file
  • Python 3.10 or newer (the CLI creates its own cached venv on first run)

Steps

  1. Install the draw.io desktop app so the drawio command is on PATH, and install the Claude Code CLI so claude is on PATH. (inferred, check the README)
  2. npm install -g autoillustrate
  3. autoillustrate doctor
  4. autoillustrate examples/ai_scientist_method.tex --prompt "Please make a diagram illustrating the method of our scientific research paper in a single panel. We intend to use it as front-page diagram in our research paper." (replace the path with your own .tex file and edit the prompt to describe your method) (inferred, check the README)
  5. Open the newest folder under runs/ and read the files in its figures/ folder. Use full_figure.drawio for edits and full_figure_enhanced.png for the restyled image.

Prompt for your agent

Using the repo SakanaAI/AutoIllustrate, run autoillustrate on <path to methods .tex file> with a prompt asking for a single-panel front-page method diagram. Confirm that the newest runs/ folder contains figures/full_figure.drawio, figures/full_figure.png and figures/full_figure_enhanced.png, and report that folder path.

Caveat. Matplotlib subplots and placeholder boxes are not directly editable in draw.io, and a default medium run takes about 15 minutes.

Use this in your AI agent

Ask your agent

Using the Deduped MCP, get the setup steps for SakanaAI/AutoIllustrate and "Draft a method figure from a paper's methods section"

Add Deduped to Claude Code once

claude mcp add --transport http deduped https://dedupedai.com/mcp

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