Sci-Figure — Scientific Figure Extractor

Precisely extract figures and sub-figures from academic PDF papers.

Script Directory

Scripts in scripts/ subdirectory. Replace ${SKILL_DIR} with this SKILL.md's directory path.

Script	Purpose
scripts/extract_figure.py	Main CLI for figure extraction

Preferences (EXTEND.md)

Use Bash to check EXTEND.md existence (priority order):

# Check project-level first
test -f .baoyu-skills/Sh_Sci_Fig/EXTEND.md && echo "project"

# Then user-level (cross-platform: $HOME works on macOS/Linux/WSL)
test -f "$HOME/.baoyu-skills/Sh_Sci_Fig/EXTEND.md" && echo "user"

EXTEND.md Supports: Default DPI | Default output format | Tesseract path

Usage

python ${SKILL_DIR}/scripts/extract_figure.py <input.pdf> [options]

Options

Option	Short	Description	Default
<input>		PDF file path	Required
--figure	-f	Figure number (1, 2, 3...)	Required (except --list/--all)
--subfigure	-s	Sub-figure label (a, b, c...)	None (returns whole figure)
--output	-o	Output directory	Current directory
--dpi	-d	Output resolution	600
--list	-l	List all available figure numbers	false
--all		Extract all figures	false
--format		Output format	png

Examples

# Extract Figure 2, sub-figure c
python ${SKILL_DIR}/scripts/extract_figure.py paper.pdf -f 2 -s c

# Extract entire Figure 3
python ${SKILL_DIR}/scripts/extract_figure.py paper.pdf -f 3

# List all available figures in a PDF
python ${SKILL_DIR}/scripts/extract_figure.py paper.pdf --list

# Extract all figures
python ${SKILL_DIR}/scripts/extract_figure.py paper.pdf --all

# Custom output directory and DPI
python ${SKILL_DIR}/scripts/extract_figure.py paper.pdf -f 2 -s c -o ./output/ -d 300

Output:

Extracted: figure_2c.png (1920x1080, 600 DPI)

Error Handling

Scenario	Behavior
Figure number not found	Error + list all available figure numbers
OCR recognition failed	Return entire figure region
Sub-figure split failed	Return entire figure region
No sub-figure labels found	Return entire figure region

Tech Stack

Library	Role
pdfplumber	Text + coordinate extraction (locate "Figure X" labels)
PyMuPDF (fitz)	PDF → high-quality image rendering (600 DPI)
opencv-python	Boundary detection, contour analysis
Pillow	Final cropping, format conversion
pytesseract	OCR for sub-figure label recognition

Detected Figure Fields

Field	Type	Description
number	int	Figure number
page	int	Page index (0-based)
bbox	tuple	Crop region in pixels
bbox_pdf	tuple	Crop region in PDF points
caption	str	Caption text (truncated to 200 chars)
caption_full	str	Full caption text (no truncation)
caption_bbox_pdf	tuple	Caption bounding box in PDF points
sublabels	list[str]	Sub-figure labels, e.g. ["a","b","c"]
sublabel_details	list[dict]	Labels with detected format, e.g. {"label":"a","format":"(a)"}
figure_type	str	One of: figure, scheme, chart, supplementary, extended_data
is_supplementary	bool	True for supplementary and extended_data types
image	ndarray	Cropped figure image (numpy array)

Extension Support

Custom configurations via EXTEND.md. See Preferences section for paths and supported options.

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© License & Copyright

Aut_Sci_Write — Autonomous Scientific Writer

• Author: Shuo Zhao
• License: MIT License
• Copyright: © 2026 Shuo Zhao. All rights reserved.
• Original Work: This is an original work created by the author. No reproduction, redistribution, or commercial use without explicit permission. Permission is hereby granted, free of charge, to any person obtaining a copy of this software... (See the LICENSE file in the root directory for the full MIT terms.)

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This skill is part of the Aut_Sci_Write suite. For full license terms, see the LICENSE file in the project root.