/sci-figure

name: sci-figure
description: Extracts figures and sub-figures from academic PDF papers. Supports Fig/Figure, Scheme, Chart, Supplementary Figure, Extended Data Figure (Nature), and Chinese equivalents (图/方案/示意图/附图/补充图). Sub-figure label recognition supports (a)/(A)/a)/(i)/(1)/a. formats. High-quality PNG output at configurable DPI. Use when user asks to "extract figure", "截取文献图片", "提取子图", "get figure from paper", "Scheme", "方案图", "补充图", "Supplementary Figure", or "Extended Data".
author: Shuo Zhao         
license: AGPL-3.0-or-later
copyright: © 2026 Shuo Zhao. All rights reserved.
triggers:
  - 提取图片
  - 截取文献图片
  - 提取子图
  - 提取附图
  - 补充图
  - 方案图
  - 示意图
  - 图片提取
  - extract figure
  - extract subfigure
  - get figure from paper
  - Supplementary Figure
  - Extended Data
  - Scheme
  - figure extraction

Sci-Figure — Scientific Figure Extractor

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

> **License note**: sci-figure is licensed under **AGPL-3.0-or-later** because it links [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/), which is AGPL-licensed.

Installation

Install the package from the skill directory before first use:

cd ${SKILL_DIR}
pip install -e .

This registers the `sh-sci-fig` CLI command. Requires Tesseract OCR:

• Windows: `winget install UB-Mannheim.TesseractOCR`
• Linux: `apt install tesseract-ocr`
• macOS: `brew install tesseract`

Preferences (EXTEND.md)

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

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

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

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

Usage

sh-sci-fig <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/jpg) | png | | `--strategy` | | Extraction strategy: hybrid/native/cv | hybrid | | `--ocr` | | OCR engine: tesseract/easyocr/none | tesseract | | `--render-page` | | Render full page with annotations | false | | `--annotate` | | Draw bounding boxes on rendered page | false | | `--bbox` | | Manual bbox override (x0,y0,x1,y1 in px) | None | | `--no-trim` | | Disable whitespace trimming | false | | `--debug` | | Enable debug logging | false | | `--quiet` | `-q` | Suppress info messages | false |

Examples

# Extract Figure 2, sub-figure c
sh-sci-fig paper.pdf -f 2 -s c

# Extract entire Figure 3
sh-sci-fig paper.pdf -f 3

# List all available figures in a PDF
sh-sci-fig paper.pdf --list

# Extract all figures
sh-sci-fig paper.pdf --all

# Custom output directory and DPI
sh-sci-fig paper.pdf -f 2 -s c -o ./output/ -d 300

# Use EasyOCR for sub-figure label detection
sh-sci-fig paper.pdf --all --ocr easyocr

# CV-only strategy (skip native extraction)
sh-sci-fig paper.pdf --all --strategy cv

# Render page with annotated bounding boxes (debugging)
sh-sci-fig paper.pdf -f 1 --render-page --annotate

# Manual bbox extraction (multimodal correction)
sh-sci-fig paper.pdf -f 1 --bbox 100,200,800,1200

**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 (caption detection) | | PyMuPDF (fitz) | Native image extraction + high-quality page rendering | | opencv-python | CV region detection, connected-component analysis, content validation | | Pillow | Final cropping, format conversion | | pytesseract | OCR for sub-figure label recognition (default) | | easyocr | Alternative OCR engine (optional, `pip install sci-figure[ocr]`) | | numpy | Image array operations |

Extraction Engines (v2)

| Engine | Priority | Best For | |--------|----------|----------| | Native (PyMuPDF) | 1st | Raster images embedded in PDF | | CV (connected-component) | 2nd | Vector graphics, colored plots | | Caption-anchored | 3rd | Fallback when above engines fail |

The `hybrid` strategy (default) tries all three in order and validates results.

Detected Figure Fields

Each figure returned by `FigureExtractor.detect_all()` is a dict with these keys:

| Field | Type | Description | |-------|------|-------------| | `number` | int | Figure number | | `page` | int | Page index (0-based) | | `bbox_pdf` | tuple | Crop region in PDF points (x0, y0, x1, y1) | | `bbox_px` | tuple | Crop region in pixels (x0, y0, x1, y1) | | `caption_text` | str | Full caption text | | `figure_type` | str | One of: `figure`, `scheme`, `chart`, `supplementary`, `extended_data` | | `sublabels` | list[str] | Sub-figure labels, e.g. `["a","b","c"]` | | `image` | ndarray | Cropped figure image (numpy array) | | `engine_used` | str | Engine that produced the crop: `native`, `cv`, or `fallback` |

`list_figures()` returns the same dicts without the `image` field.

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**: