Scientific Diagram Generation

Scientific Diagram Generation

AI-powered scientific illustration generation using Gemini Image models. Creates publication-quality mechanism diagrams, pathway illustrations, and scientific figures.

API Configuration

API Call Structure

curl -X POST "${GEMINI_BASE_URL:-https://generativelanguage.googleapis.com/v1beta}/models/gemini-3.1-flash-image-preview:generateContent" \
  -H "Content-Type: application/json" \
  -H "Authorization: Bearer $LLM_API_KEY" \
  -d '{
    "contents": [{"role": "user", "parts": [{"text": "YOUR_PROMPT_HERE"}]}],
    "generationConfig": {
      "responseModalities": ["TEXT", "IMAGE"]
    }
  }'

Python Implementation

import httpx, base64

API_KEY = "your-gemini-key"
MODEL = "gemini-3.1-flash-image-preview"
BASE = os.environ.get("GEMINI_BASE_URL", "https://generativelanguage.googleapis.com/v1beta")
URL = f"{BASE}/models/{MODEL}:generateContent"

async def generate(prompt: str) -> bytes:
    payload = {
        "contents": [{"role": "user", "parts": [{"text": prompt}]}],
        "generationConfig": {"responseModalities": ["TEXT", "IMAGE"]}
    }
    async with httpx.AsyncClient(timeout=120) as c:
        r = await c.post(URL, json=payload,
            headers={"Content-Type": "application/json",
                     "Authorization": f"Bearer {API_KEY}"})
        r.raise_for_status()
        for cand in r.json().get("candidates", []):
            for part in cand["content"]["parts"]:
                if "inlineData" in part:
                    return base64.b64decode(part["inlineData"]["data"])
    return b""

Style Presets

Publication Style (default)

Cell/Nature/Science publication style. Realistic cell morphology with smooth
membranes. Activation arrows: solid black. Inhibition: red T-bar. Secretion:
dashed arrow. Proteins as colored ovals. Receptors as Y-shapes on membranes.
Clean, professional, suitable for journal figures.

Vector-Friendly Style

Flat vector style with clean outlines and solid color fills. No gradients,
textures, or noise. High contrast. Easy to edit in Adobe Illustrator or Inkscape.

Infographic Style

Modern infographic style with grid layout. Rounded rectangles for cells.
Circles for molecules. 3-5 accent colors maximum. Clean geometric shapes.

Core Prompt Rules (append to every prompt)

CRITICAL RULES FOR SCIENTIFIC DIAGRAM GENERATION:
1. BIOLOGICAL COMPLETENESS: Name all cell types, receptors, ligands, molecules,
   transcription factors. Include activation, inhibition, binding, phosphorylation,
   secretion, translocation.
2. VISUAL COMPOSITION: Describe spatial layout (top/bottom/left/right). Define
   compartments (membrane, cytoplasm, nucleus, extracellular). Choose layout flow.
3. FONT: Use Arial or clean sans-serif for ALL labels. Never decorative fonts.
4. TEXT LABELS: Title Case for all labels. Never ALL CAPS. Gene/protein
   abbreviations kept as-is (PD-L1, IFN-γ, JAK).
5. BACKGROUND: Pure white #FFFFFF. No gradients, textures, or vignettes.
6. EDITABILITY: Elements clearly separated with sharp edges. No overlapping.
   Easy post-editing.

SketchGraph Schema (for structured bio diagrams)

BioNode Types

cell, protein, receptor, mRNA, DNA, complex, small_molecule, vesicle, exosome, antibody, other

BioEdge Actions

activate, inhibit, bind, phosphorylate, secrete, recruit, translocate, transcribe, degrade, upregulate, downregulate

Compartments

membrane, cytoplasm, nucleus, extracellular_space, mitochondria, endoplasmic_reticulum, golgi

Prompt Templates

Template 1: Mechanism Diagram

Generate a scientific mechanism diagram:
[DESCRIPTION OF THE MECHANISM]

STYLE: [publication / vector_friendly / infographic]

[CORE_PROMPT_RULES]

EXACT TEXT LABELS to render (use these exact strings, do NOT change
capitalization): ["Label1", "Label2", ...]

Template 2: Signaling Pathway

Generate a signaling pathway diagram showing:
- Ligand: [name] binding to receptor: [name] on [cell type]
- Intracellular cascade: [kinase1] → [kinase2] → [transcription factor]
- Downstream effects: [gene expression changes]
- Compartments: extracellular, membrane, cytoplasm, nucleus

STYLE: publication
[CORE_PROMPT_RULES]

Template 3: Tumor Microenvironment

Generate a tumor microenvironment diagram showing:
- Central: tumor cells (irregular shape, dark)
- Surrounding: [immune cells, fibroblasts, endothelial cells]
- Key interactions: [list of interactions with arrow types]
- Secreted factors: [cytokines, chemokines with dashed arrows]

Layout: radial, tumor at center
STYLE: publication
[CORE_PROMPT_RULES]

Template 4: Cell Biology Overview

Generate a cell biology diagram showing:
- Cell with organelles: nucleus, mitochondria, ER, Golgi, lysosomes
- Process: [e.g., autophagy, apoptosis, protein trafficking]
- Key molecules at each step: [list]
- Arrows showing process flow

STYLE: publication
[CORE_PROMPT_RULES]

Template 5: Non-Bio Scientific Diagram (GENERAL)

Generate a scientific diagram (bypassing SketchGraph, direct prompting):
[DESCRIPTION — can be circuit diagram, chemical reaction scheme,
geological cross-section, physics experiment setup, etc.]

STYLE RULES:
- White background #FFFFFF
- Arial font for all labels
- Title Case for labels
- Clean, professional, publication quality
- No decorative elements

Retry Logic

The API may return 429 (rate limit) or 5xx errors. Recommended retry:

• Attempt 1: immediate
• Attempt 2: wait 15 seconds
• Attempt 3: wait 30 seconds
• Max 3 attempts

Output

• Format: PNG (default), can request JPEG
• Resolution: ~1024x1024 (model default)
• File size: typically 800KB-1.5MB
• Save to: ~/.scienceclaw/workspace/diagrams/diagram_{uuid}.png

Tips for Best Results

1. Be specific: "TREM2 receptor on macrophage" > "a receptor on a cell"
2. Name everything: Every molecule, cell, and arrow should have a label
3. Specify compartments: "extracellular space", "cytoplasm", "nucleus"
4. Use exact label injection: Always provide a list of exact text labels
5. Keep it focused: One mechanism per diagram, not an entire pathway map
6. Iterate: If the first result isn't perfect, refine the prompt and regenerate