make-figures

Files (137)

• SKILL.md
• data_plot.md · references/critic_rubrics/
• flow_diagram.md · references/critic_rubrics/
• design_principles.md · references/
• README.md · references/exemplar_diagrams/
• README.md · references/exemplar_diagrams/consort/
• template_input.yaml · references/exemplar_diagrams/consort/
• template_output.pdf · references/exemplar_diagrams/consort/
• template_output.png · references/exemplar_diagrams/consort/
• template_output_600.png · references/exemplar_diagrams/consort/
• other_02_why.md · references/exemplar_diagrams/other/
• README.md · references/exemplar_diagrams/pipeline/
• pipeline_01_why.md · references/exemplar_diagrams/pipeline/
• pipeline_03_why.md · references/exemplar_diagrams/pipeline/
• pipeline_04_why.md · references/exemplar_diagrams/pipeline/
• pipeline_05_why.md · references/exemplar_diagrams/pipeline/
• pipeline_06_why.md · references/exemplar_diagrams/pipeline/
• pipeline_07_why.md · references/exemplar_diagrams/pipeline/
• pipeline_08_why.md · references/exemplar_diagrams/pipeline/
• pipeline_09_why.md · references/exemplar_diagrams/pipeline/
• pipeline_10_why.md · references/exemplar_diagrams/pipeline/
• README.md · references/exemplar_diagrams/prisma/
• template_input.yaml · references/exemplar_diagrams/prisma/
• template_output.pdf · references/exemplar_diagrams/prisma/
• template_output.png · references/exemplar_diagrams/prisma/
• template_output_600.png · references/exemplar_diagrams/prisma/
• README.md · references/exemplar_diagrams/stard/
• template_input.yaml · references/exemplar_diagrams/stard/
• template_output.pdf · references/exemplar_diagrams/stard/
• template_output.png · references/exemplar_diagrams/stard/
• template_output_600.png · references/exemplar_diagrams/stard/
• template_input.yaml · references/exemplar_diagrams/strobe/
• template_input_pptx.yaml · references/exemplar_diagrams/strobe/
• template_output.pdf · references/exemplar_diagrams/strobe/
• template_output.png · references/exemplar_diagrams/strobe/
• template_output.pptx · references/exemplar_diagrams/strobe/
• template_output_600.png · references/exemplar_diagrams/strobe/
• README.md · references/exemplar_plots/
• ai_assistance_effect.md · references/exemplar_plots/
• bland_altman.md · references/exemplar_plots/
• calibration_plot.md · references/exemplar_plots/
• clinical_timeline.md · references/exemplar_plots/
• confusion_matrix.md · references/exemplar_plots/
• cumulative_incidence.md · references/exemplar_plots/
• decision_curve.md · references/exemplar_plots/
• external_validation_comparison.md · references/exemplar_plots/
• forest_plot.md · references/exemplar_plots/
• funnel_plot.md · references/exemplar_plots/
• imaging_panel.md · references/exemplar_plots/
• km_curve.md · references/exemplar_plots/
• manhattan_plot.md · references/exemplar_plots/
• model_comparison_leaderboard.md · references/exemplar_plots/
• mrmc_roc.md · references/exemplar_plots/
• roc_pr.md · references/exemplar_plots/
• segmentation_failure_panel.md · references/exemplar_plots/
• shap_beeswarm.md · references/exemplar_plots/
• spider_plot.md · references/exemplar_plots/
• swimmer_plot.md · references/exemplar_plots/
• waterfall_plot.md · references/exemplar_plots/
• figure_manifest.md · references/
• …and 77 more

SKILL.md (first lines)

# Make-Figures Skill

## Data Privacy Check

Before reading any data file, check whether it might contain Protected Health Information (PHI):

1. If `*_deidentified.*` files exist in the working directory, use those preferentially.
2. If only raw CSV/Excel files exist (no `*_deidentified.*` counterpart), ask the user, in their
   language, whether the data contains patient identifiers (names, national ID / RRN, contact
   details, etc.) and, if so, to de-identify it first with the `/deidentify` skill.
3. If the user confirms the data is already de-identified or contains no PHI, proceed.

## Reference Files

- **Figure specifications**: `${CLAUDE_SKILL_DIR}/references/figure_specs.md` — read it before
  generating any figure (journal dimensions, DPI, file formats, palettes, font sizes, panel
  layouts, caption format).
- **Figure style**: `${CLAUDE_SKILL_DIR}/../analyze-stats/references/style/figure_style.mplstyle`

---

## Journal AI-Image Policies (CRITICAL — check BEFORE generation)

| Journal family | Policy on AI-generated images | Disclosure required |
|---|---|---|
| **JACC family (incl. JACC: Asia, JACC Imaging, JACC EP, JACC BTS)** | **Prohibited without prior Editor-in-Chief permission** ([JACC pathway, PMC10167500](https://pmc.ncbi.nlm.nih.gov/articles/PMC10167500/)) | Cover-letter pre-submission inquiry + ICMJE-style declaration |
| NEJM | AI image generation prohibited | N/A |
| Radiology / Radiology AI | Allowed with disclosure | Manuscript disclosure block |
| Springer Nature (Nature Portfolio, BMC, Springer journals) | Allowed only when the visual is derived from **independently verifiable** data, source material, methods or code; AI visuals without verifiable inputs are "opaque" and not permitted. Charts from datasets and author-reviewed code-generated figures are the policy's own allowed examples ([AI in manuscript preparation](https://www.springernature.com/gp/policies/editorial-policies/ai-manuscript-preparation)) | Declare model and purpose; disclose non-generative image edits in the caption |
| Elsevier journals (publisher policy) | Explanatory images (flow charts, schematics) allowed. Data visualizations only when directly derived from the underlying data by reproducible methods. **Primary research images, including radiology scans and patient images, must not be created or altered with AI.** AI images produced as part of the research methods are permitted. Graphical abstracts: dedicated illustration tools, not general-purpose generative AI ([Generative AI policies for journals](https://www.elsevier.com/about/policies-and-standards/generative-ai-policies-for-journals)) | Caption + AI disclosure statement (explanatory); Methods (data visualizations, research-method use) |
| Lancet family | Disclosure required, generation discouraged | Manuscript disclosure |
| Default (target unknown) | Treat as prohibited until confirmed | N/A |

Publisher pages set the floor; a journal's own guide can be stricter (JACC is an Elsevier journal). Check the target journal's guide as well as its publisher's.

**Hard rule**: For JACC, NEJM, or any "unknown" target journal, **never** use Gemini / DALL-E / Midjourney / Stable Diffusion / Nano Banana to create images that will appear in figures, Central Illustrations, or graphical abstracts. AI text-editing of the manuscript prose remains acceptable subject to standard disclosure.

### Default workflow when AI images are not allowed

1. **SMART Servier Medical Art** — https://smart.servier.com/, CC BY 4.0, free, 3,000+ vector medical icons (anatomy, organs, ethnicity-specific human figures, drugs, devices). Commercial / journal use allowed. **Required attribution** (1 line in figure legend OR methods):
   > Anatomical icons modified from SMART Servier Medical Art (CC BY 4.0).
2. **NIAID BioArt** (https://bioart.niaid.nih.gov) — public domain (US Govt), microbiology / immunology / lab-tech focus.
3. **BioRender** (https://www.biorender.com) — institutional license usually required; use the exported "Publication-ready" PNG/TIFF and cite per BioRender publication policy.
4. For "diseased" variants not directly available (e.g., calcified vessel from a clean vessel): reuse the healthy asset and overlay disease markers via matplotlib `scatter` / `Circle` / `PathPatch`. Keeps the entire pipeline non-AI and reproducible.

Even when AI images are allowed, experienced reviewers recognise AI-generated illustrations (small decorative icons that add no information, overly uniform layouts, generic clip-art style). For high-impact submissions, prefer Servier / BioArt / BioRender + matplotlib overlays over AI.

### Asset directory convention

```
manuscript/figures/_assets_servier/      # CC BY 4.0 source PNGs
manuscript/figures/_assets_servier/CITATION.md   # source URL + download date per asset
manuscript/figures/_assets_data/         # data-driven raster (R / matplotlib heat maps, KM, etc.)
manuscript/figures/_legacy/              # archived prior versions
```

Composition scripts should load only from `_assets_servier/` and `_assets_data/`. If a script imports from `_assets_ai/`, treat it as a policy violation for JACC/NEJM/unknown targets.

### AI Image Generation (Optional)

AI illustration is a supplementary option: every figure and visual abstract can be completed without an API key. If `GEMINI_API_KEY` is set, `generate_image.py` can generate illustrations (procedural schematics, anatomical illustrations), subject to the policy table and hard rule above:

```bash
python ${CLAUDE_SKILL_DIR}/scripts/generate_image.py \
  "Clean medical illustration of a CT-guided lung biopsy procedure, \
   flat vector style, white background, no text" \
  --output output.png --aspect 16:9
```

If `GEMINI_API_KEY` is not set, use `${CLAUDE_SKILL_DIR}/references/medical_illustration_sources.md`.

---

## Visual Abstract / Graphical Abstract

European Radiology made graphical abstracts mandatory for all Original Articles from first revision
(Jan 2025); other journals encourage or accept them (status list in `template_guide.md`). Check the
target journal profile (`write-paper/references/journal_profiles/`) for its visual abstract
requirements before starting.

### Workflow

1. **Check journal template.** Look for an official PPTX template in
   `${CLAUDE_SKILL_DIR}/references/visual_abstract_templates/{journal}.pptx`.
   If no journal-specific template exists, use `medsci_default.pptx`.
2. **Extract content from the manuscript:**
   - **Title:** Full article title
   - **Hypothesis/Question:** Derived from Key Point 1 or study objective (max 1 sentence)
   - **Methodology:** Brief flowchart or ≤3 bullets, <6 words each
   - **Visual element:** Study's own figure (ROC curve, flow diagram, representative image)
   - **Badges:** Patient cohort (N=...) | Modality/organ | Single/Multi-center
   - **Main finding:** Derived from Key Point 3 (<20 words)
   - **Citation:** Journal (year) Authors; DOI
3. **Select visual element** (priority order):
   1. Study's own figures (ROC, flow diagram, representative image) — **always preferred**
   2. Free illustration from Servier Medical Art or NIAID BioArt
      (see `${CLAUDE_SKILL_DIR}/references/medical_illustration_sources.md`)
   3. Manual drawing in PPT/Keynote/Figma
   4. AI generation via `generate_image.py --style medical` (only if GEMINI_API_KEY set)
4. **Generate using the script:**
   ```bash
   python ${CLAUDE_SKILL_DIR}/scripts/generate_visual_abstract.py \
     --template medsci_default \
     --title "Article Title" \
     --hypothesis "Research question" \
     --methods "Method 1|Method 2|Method 3" \
     --finding "Main finding statement" \
     --citation "Eur Radiol (2026) Author A et al; DOI:..." \
     --visual figures/fig1_roc_curve.png \
     --badges "N=450|CT chest|Multi-center" \
     --output figures/visual_abstract.pptx
   ```
5. **Review with user.** Open the PPTX to verify layout and content. Iterate.
6. **Export.** PPTX is the primary deliverable. For PNG: open in PowerPoint/Keynote → export,
   or use LibreOffice CLI (`soffice --headless --convert-to png`).

Design: one page, landscape (16:9) or per the journal template; three sections (study question →
key method → main result); the study's actual figures rather than generic graphics; minimal text;
no decorative clip-art.

From Aperivue/medsci-skills, MIT.

More from Aperivue/medsci-skills