@synsci/cli-darwin-x64-baseline 1.1.71 → 1.1.72

package/bin/skills/scientific-schematics/SKILL.md

@@ -0,0 +1,615 @@
+---
+name: scientific-schematics
+description: "Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations."
+allowed-tools: [Read, Write, Edit, Bash]
+---
+
+# Scientific Schematics and Diagrams
+
+## Overview
+
+Scientific schematics and diagrams transform complex concepts into clear visual representations for publication. **This skill uses Nano Banana Pro AI for diagram generation with Gemini 3 Pro quality review.**
+
+**How it works:**
+- Describe your diagram in natural language
+- Nano Banana Pro generates publication-quality images automatically
+- **Gemini 3 Pro reviews quality** against document-type thresholds
+- **Smart iteration**: Only regenerates if quality is below threshold
+- Publication-ready output in minutes
+- No coding, templates, or manual drawing required
+
+**Quality Thresholds by Document Type:**
+| Document Type | Threshold | Description |
+|---------------|-----------|-------------|
+| journal | 8.5/10 | Nature, Science, peer-reviewed journals |
+| conference | 8.0/10 | Conference papers |
+| thesis | 8.0/10 | Dissertations, theses |
+| grant | 8.0/10 | Grant proposals |
+| preprint | 7.5/10 | arXiv, bioRxiv, etc. |
+| report | 7.5/10 | Technical reports |
+| poster | 7.0/10 | Academic posters |
+| presentation | 6.5/10 | Slides, talks |
+| default | 7.5/10 | General purpose |
+
+**Simply describe what you want, and Nano Banana Pro creates it.** All diagrams are stored in the figures/ subfolder and referenced in papers/posters.
+
+## Quick Start: Generate Any Diagram
+
+Create any scientific diagram by simply describing it. Nano Banana Pro handles everything automatically with **smart iteration**:
+
+```bash
+# Generate for journal paper (highest quality threshold: 8.5/10)
+python scripts/generate_schematic.py "CONSORT participant flow diagram with 500 screened, 150 excluded, 350 randomized" -o figures/consort.png --doc-type journal
+
+# Generate for presentation (lower threshold: 6.5/10 - faster)
+python scripts/generate_schematic.py "Transformer encoder-decoder architecture showing multi-head attention" -o figures/transformer.png --doc-type presentation
+
+# Generate for poster (moderate threshold: 7.0/10)
+python scripts/generate_schematic.py "MAPK signaling pathway from EGFR to gene transcription" -o figures/mapk_pathway.png --doc-type poster
+
+# Custom max iterations (max 2)
+python scripts/generate_schematic.py "Complex circuit diagram with op-amp, resistors, and capacitors" -o figures/circuit.png --iterations 2 --doc-type journal
+```
+
+**What happens behind the scenes:**
+1. **Generation 1**: Nano Banana Pro creates initial image following scientific diagram best practices
+2. **Review 1**: **Gemini 3 Pro** evaluates quality against document-type threshold
+3. **Decision**: If quality >= threshold → **DONE** (no more iterations needed!)
+4. **If below threshold**: Improved prompt based on critique, regenerate
+5. **Repeat**: Until quality meets threshold OR max iterations reached
+
+**Smart Iteration Benefits:**
+- ✅ Saves API calls if first generation is good enough
+- ✅ Higher quality standards for journal papers
+- ✅ Faster turnaround for presentations/posters
+- ✅ Appropriate quality for each use case
+
+**Output**: Versioned images plus a detailed review log with quality scores, critiques, and early-stop information.
+
+### Configuration
+
+Set your OpenRouter API key:
+```bash
+export OPENROUTER_API_KEY='your_api_key_here'
+```
+
+Get an API key at: https://openrouter.ai/keys
+
+### AI Generation Best Practices
+
+**Effective Prompts for Scientific Diagrams:**
+
+✓ **Good prompts** (specific, detailed):
+- "CONSORT flowchart showing participant flow from screening (n=500) through randomization to final analysis"
+- "Transformer neural network architecture with encoder stack on left, decoder stack on right, showing multi-head attention and cross-attention connections"
+- "Biological signaling cascade: EGFR receptor → RAS → RAF → MEK → ERK → nucleus, with phosphorylation steps labeled"
+- "Block diagram of IoT system: sensors → microcontroller → WiFi module → cloud server → mobile app"
+
+✗ **Avoid vague prompts**:
+- "Make a flowchart" (too generic)
+- "Neural network" (which type? what components?)
+- "Pathway diagram" (which pathway? what molecules?)
+
+**Key elements to include:**
+- **Type**: Flowchart, architecture diagram, pathway, circuit, etc.
+- **Components**: Specific elements to include
+- **Flow/Direction**: How elements connect (left-to-right, top-to-bottom)
+- **Labels**: Key annotations or text to include
+- **Style**: Any specific visual requirements
+
+**Scientific Quality Guidelines** (automatically applied):
+- Clean white/light background
+- High contrast for readability
+- Clear, readable labels (minimum 10pt)
+- Professional typography (sans-serif fonts)
+- Colorblind-friendly colors (Okabe-Ito palette)
+- Proper spacing to prevent crowding
+- Scale bars, legends, axes where appropriate
+
+## When to Use This Skill
+
+This skill should be used when:
+- Creating neural network architecture diagrams (Transformers, CNNs, RNNs, etc.)
+- Illustrating system architectures and data flow diagrams
+- Drawing methodology flowcharts for study design (CONSORT, PRISMA)
+- Visualizing algorithm workflows and processing pipelines
+- Creating circuit diagrams and electrical schematics
+- Depicting biological pathways and molecular interactions
+- Generating network topologies and hierarchical structures
+- Illustrating conceptual frameworks and theoretical models
+- Designing block diagrams for technical papers
+
+## How to Use This Skill
+
+**Simply describe your diagram in natural language.** Nano Banana Pro generates it automatically:
+
+```bash
+python scripts/generate_schematic.py "your diagram description" -o output.png
+```
+
+**That's it!** The AI handles:
+- ✓ Layout and composition
+- ✓ Labels and annotations
+- ✓ Colors and styling
+- ✓ Quality review and refinement
+- ✓ Publication-ready output
+
+**Works for all diagram types:**
+- Flowcharts (CONSORT, PRISMA, etc.)
+- Neural network architectures
+- Biological pathways
+- Circuit diagrams
+- System architectures
+- Block diagrams
+- Any scientific visualization
+
+**No coding, no templates, no manual drawing required.**
+
+---
+
+# AI Generation Mode (Nano Banana Pro + Gemini 3 Pro Review)
+
+## Smart Iterative Refinement Workflow
+
+The AI generation system uses **smart iteration** - it only regenerates if quality is below the threshold for your document type:
+
+### How Smart Iteration Works
+
+```
+┌─────────────────────────────────────────────────────┐
+│  1. Generate image with Nano Banana Pro             │
+│                    ↓                                │
+│  2. Review quality with Gemini 3 Pro                │
+│                    ↓                                │
+│  3. Score >= threshold?                             │
+│       YES → DONE! (early stop)                      │
+│       NO  → Improve prompt, go to step 1            │
+│                    ↓                                │
+│  4. Repeat until quality met OR max iterations      │
+└─────────────────────────────────────────────────────┘
+```
+
+### Iteration 1: Initial Generation
+**Prompt Construction:**
+```
+Scientific diagram guidelines + User request
+```
+
+**Output:** `diagram_v1.png`
+
+### Quality Review by Gemini 3 Pro
+
+Gemini 3 Pro evaluates the diagram on:
+1. **Scientific Accuracy** (0-2 points) - Correct concepts, notation, relationships
+2. **Clarity and Readability** (0-2 points) - Easy to understand, clear hierarchy
+3. **Label Quality** (0-2 points) - Complete, readable, consistent labels
+4. **Layout and Composition** (0-2 points) - Logical flow, balanced, no overlaps
+5. **Professional Appearance** (0-2 points) - Publication-ready quality
+
+**Example Review Output:**
+```
+SCORE: 8.0
+
+STRENGTHS:
+- Clear flow from top to bottom
+- All phases properly labeled
+- Professional typography
+
+ISSUES:
+- Participant counts slightly small
+- Minor overlap on exclusion box
+
+VERDICT: ACCEPTABLE (for poster, threshold 7.0)
+```
+
+### Decision Point: Continue or Stop?
+
+| If Score... | Action |
+|-------------|--------|
+| >= threshold | **STOP** - Quality is good enough for this document type |
+| < threshold | Continue to next iteration with improved prompt |
+
+**Example:**
+- For a **poster** (threshold 7.0): Score of 7.5 → **DONE after 1 iteration!**
+- For a **journal** (threshold 8.5): Score of 7.5 → Continue improving
+
+### Subsequent Iterations (Only If Needed)
+
+If quality is below threshold, the system:
+1. Extracts specific issues from Gemini 3 Pro's review
+2. Enhances the prompt with improvement instructions
+3. Regenerates with Nano Banana Pro
+4. Reviews again with Gemini 3 Pro
+5. Repeats until threshold met or max iterations reached
+
+### Review Log
+All iterations are saved with a JSON review log that includes early-stop information:
+```json
+{
+  "user_prompt": "CONSORT participant flow diagram...",
+  "doc_type": "poster",
+  "quality_threshold": 7.0,
+  "iterations": [
+    {
+      "iteration": 1,
+      "image_path": "figures/consort_v1.png",
+      "score": 7.5,
+      "needs_improvement": false,
+      "critique": "SCORE: 7.5\nSTRENGTHS:..."
+    }
+  ],
+  "final_score": 7.5,
+  "early_stop": true,
+  "early_stop_reason": "Quality score 7.5 meets threshold 7.0 for poster"
+}
+```
+
+**Note:** With smart iteration, you may see only 1 iteration instead of the full 2 if quality is achieved early!
+
+## Advanced AI Generation Usage
+
+### Python API
+
+```python
+from scripts.generate_schematic_ai import ScientificSchematicGenerator
+
+# Initialize generator
+generator = ScientificSchematicGenerator(
+    api_key="your_openrouter_key",
+    verbose=True
+)
+
+# Generate with iterative refinement (max 2 iterations)
+results = generator.generate_iterative(
+    user_prompt="Transformer architecture diagram",
+    output_path="figures/transformer.png",
+    iterations=2
+)
+
+# Access results
+print(f"Final score: {results['final_score']}/10")
+print(f"Final image: {results['final_image']}")
+
+# Review individual iterations
+for iteration in results['iterations']:
+    print(f"Iteration {iteration['iteration']}: {iteration['score']}/10")
+    print(f"Critique: {iteration['critique']}")
+```
+
+### Command-Line Options
+
+```bash
+# Basic usage (default threshold 7.5/10)
+python scripts/generate_schematic.py "diagram description" -o output.png
+
+# Specify document type for appropriate quality threshold
+python scripts/generate_schematic.py "diagram" -o out.png --doc-type journal      # 8.5/10
+python scripts/generate_schematic.py "diagram" -o out.png --doc-type conference   # 8.0/10
+python scripts/generate_schematic.py "diagram" -o out.png --doc-type poster       # 7.0/10
+python scripts/generate_schematic.py "diagram" -o out.png --doc-type presentation # 6.5/10
+
+# Custom max iterations (1-2)
+python scripts/generate_schematic.py "complex diagram" -o diagram.png --iterations 2
+
+# Verbose output (see all API calls and reviews)
+python scripts/generate_schematic.py "flowchart" -o flow.png -v
+
+# Provide API key via flag
+python scripts/generate_schematic.py "diagram" -o out.png --api-key "sk-or-v1-..."
+
+# Combine options
+python scripts/generate_schematic.py "neural network" -o nn.png --doc-type journal --iterations 2 -v
+```
+
+### Prompt Engineering Tips
+
+**1. Be Specific About Layout:**
+```
+✓ "Flowchart with vertical flow, top to bottom"
+✓ "Architecture diagram with encoder on left, decoder on right"
+✓ "Circular pathway diagram with clockwise flow"
+```
+
+**2. Include Quantitative Details:**
+```
+✓ "Neural network with input layer (784 nodes), hidden layer (128 nodes), output (10 nodes)"
+✓ "Flowchart showing n=500 screened, n=150 excluded, n=350 randomized"
+✓ "Circuit with 1kΩ resistor, 10µF capacitor, 5V source"
+```
+
+**3. Specify Visual Style:**
+```
+✓ "Minimalist block diagram with clean lines"
+✓ "Detailed biological pathway with protein structures"
+✓ "Technical schematic with engineering notation"
+```
+
+**4. Request Specific Labels:**
+```
+✓ "Label all arrows with activation/inhibition"
+✓ "Include layer dimensions in each box"
+✓ "Show time progression with timestamps"
+```
+
+**5. Mention Color Requirements:**
+```
+✓ "Use colorblind-friendly colors"
+✓ "Grayscale-compatible design"
+✓ "Color-code by function: blue for input, green for processing, red for output"
+```
+
+## AI Generation Examples
+
+### Example 1: CONSORT Flowchart
+```bash
+python scripts/generate_schematic.py \
+  "CONSORT participant flow diagram for randomized controlled trial. \
+   Start with 'Assessed for eligibility (n=500)' at top. \
+   Show 'Excluded (n=150)' with reasons: age<18 (n=80), declined (n=50), other (n=20). \
+   Then 'Randomized (n=350)' splits into two arms: \
+   'Treatment group (n=175)' and 'Control group (n=175)'. \
+   Each arm shows 'Lost to follow-up' (n=15 and n=10). \
+   End with 'Analyzed' (n=160 and n=165). \
+   Use blue boxes for process steps, orange for exclusion, green for final analysis." \
+  -o figures/consort.png
+```
+
+### Example 2: Neural Network Architecture
+```bash
+python scripts/generate_schematic.py \
+  "Transformer encoder-decoder architecture diagram. \
+   Left side: Encoder stack with input embedding, positional encoding, \
+   multi-head self-attention, add & norm, feed-forward, add & norm. \
+   Right side: Decoder stack with output embedding, positional encoding, \
+   masked self-attention, add & norm, cross-attention (receiving from encoder), \
+   add & norm, feed-forward, add & norm, linear & softmax. \
+   Show cross-attention connection from encoder to decoder with dashed line. \
+   Use light blue for encoder, light red for decoder. \
+   Label all components clearly." \
+  -o figures/transformer.png --iterations 2
+```
+
+### Example 3: Biological Pathway
+```bash
+python scripts/generate_schematic.py \
+  "MAPK signaling pathway diagram. \
+   Start with EGFR receptor at cell membrane (top). \
+   Arrow down to RAS (with GTP label). \
+   Arrow to RAF kinase. \
+   Arrow to MEK kinase. \
+   Arrow to ERK kinase. \
+   Final arrow to nucleus showing gene transcription. \
+   Label each arrow with 'phosphorylation' or 'activation'. \
+   Use rounded rectangles for proteins, different colors for each. \
+   Include membrane boundary line at top." \
+  -o figures/mapk_pathway.png
+```
+
+### Example 4: System Architecture
+```bash
+python scripts/generate_schematic.py \
+  "IoT system architecture block diagram. \
+   Bottom layer: Sensors (temperature, humidity, motion) in green boxes. \
+   Middle layer: Microcontroller (ESP32) in blue box. \
+   Connections to WiFi module (orange box) and Display (purple box). \
+   Top layer: Cloud server (gray box) connected to mobile app (light blue box). \
+   Show data flow arrows between all components. \
+   Label connections with protocols: I2C, UART, WiFi, HTTPS." \
+  -o figures/iot_architecture.png
+```
+
+---
+
+## Command-Line Usage
+
+The main entry point for generating scientific schematics:
+
+```bash
+# Basic usage
+python scripts/generate_schematic.py "diagram description" -o output.png
+
+# Custom iterations (max 2)
+python scripts/generate_schematic.py "complex diagram" -o diagram.png --iterations 2
+
+# Verbose mode
+python scripts/generate_schematic.py "diagram" -o out.png -v
+```
+
+**Note:** The Nano Banana Pro AI generation system includes automatic quality review in its iterative refinement process. Each iteration is evaluated for scientific accuracy, clarity, and accessibility.
+
+## Best Practices Summary
+
+### Design Principles
+
+1. **Clarity over complexity** - Simplify, remove unnecessary elements
+2. **Consistent styling** - Use templates and style files
+3. **Colorblind accessibility** - Use Okabe-Ito palette, redundant encoding
+4. **Appropriate typography** - Sans-serif fonts, minimum 7-8 pt
+5. **Vector format** - Always use PDF/SVG for publication
+
+### Technical Requirements
+
+1. **Resolution** - Vector preferred, or 300+ DPI for raster
+2. **File format** - PDF for LaTeX, SVG for web, PNG as fallback
+3. **Color space** - RGB for digital, CMYK for print (convert if needed)
+4. **Line weights** - Minimum 0.5 pt, typical 1-2 pt
+5. **Text size** - 7-8 pt minimum at final size
+
+### Integration Guidelines
+
+1. **Include in LaTeX** - Use `\includegraphics{}` for generated images
+2. **Caption thoroughly** - Describe all elements and abbreviations
+3. **Reference in text** - Explain diagram in narrative flow
+4. **Maintain consistency** - Same style across all figures in paper
+5. **Version control** - Keep prompts and generated images in repository
+
+## Troubleshooting Common Issues
+
+### AI Generation Issues
+
+**Problem**: Overlapping text or elements
+- **Solution**: AI generation automatically handles spacing
+- **Solution**: Increase iterations: `--iterations 2` for better refinement
+
+**Problem**: Elements not connecting properly
+- **Solution**: Make your prompt more specific about connections and layout
+- **Solution**: Increase iterations for better refinement
+
+### Image Quality Issues
+
+**Problem**: Export quality poor
+- **Solution**: AI generation produces high-quality images automatically
+- **Solution**: Increase iterations for better results: `--iterations 2`
+
+**Problem**: Elements overlap after generation
+- **Solution**: AI generation automatically handles spacing
+- **Solution**: Increase iterations: `--iterations 2` for better refinement
+- **Solution**: Make your prompt more specific about layout and spacing requirements
+
+### Quality Check Issues
+
+**Problem**: False positive overlap detection
+- **Solution**: Adjust threshold: `detect_overlaps(image_path, threshold=0.98)`
+- **Solution**: Manually review flagged regions in visual report
+
+**Problem**: Generated image quality is low
+- **Solution**: AI generation produces high-quality images by default
+- **Solution**: Increase iterations for better results: `--iterations 2`
+
+**Problem**: Colorblind simulation shows poor contrast
+- **Solution**: Switch to Okabe-Ito palette explicitly in code
+- **Solution**: Add redundant encoding (shapes, patterns, line styles)
+- **Solution**: Increase color saturation and lightness differences
+
+**Problem**: High-severity overlaps detected
+- **Solution**: Review overlap_report.json for exact positions
+- **Solution**: Increase spacing in those specific regions
+- **Solution**: Re-run with adjusted parameters and verify again
+
+**Problem**: Visual report generation fails
+- **Solution**: Check Pillow and matplotlib installations
+- **Solution**: Ensure image file is readable: `Image.open(path).verify()`
+- **Solution**: Check sufficient disk space for report generation
+
+### Accessibility Problems
+
+**Problem**: Colors indistinguishable in grayscale
+- **Solution**: Run accessibility checker: `verify_accessibility(image_path)`
+- **Solution**: Add patterns, shapes, or line styles for redundancy
+- **Solution**: Increase contrast between adjacent elements
+
+**Problem**: Text too small when printed
+- **Solution**: Run resolution validator: `validate_resolution(image_path)`
+- **Solution**: Design at final size, use minimum 7-8 pt fonts
+- **Solution**: Check physical dimensions in resolution report
+
+**Problem**: Accessibility checks consistently fail
+- **Solution**: Review accessibility_report.json for specific failures
+- **Solution**: Increase color contrast by at least 20%
+- **Solution**: Test with actual grayscale conversion before finalizing
+
+## Resources and References
+
+### Detailed References
+
+Load these files for comprehensive information on specific topics:
+
+- **`references/diagram_types.md`** - Catalog of scientific diagram types with examples
+- **`references/best_practices.md`** - Publication standards and accessibility guidelines
+
+### External Resources
+
+**Python Libraries**
+- Schemdraw Documentation: https://schemdraw.readthedocs.io/
+- NetworkX Documentation: https://networkx.org/documentation/
+- Matplotlib Documentation: https://matplotlib.org/
+
+**Publication Standards**
+- Nature Figure Guidelines: https://www.nature.com/nature/for-authors/final-submission
+- Science Figure Guidelines: https://www.science.org/content/page/instructions-preparing-initial-manuscript
+- CONSORT Diagram: http://www.consort-statement.org/consort-statement/flow-diagram
+
+## Integration with Other Skills
+
+This skill works synergistically with:
+
+- **Scientific Writing** - Diagrams follow figure best practices
+- **Scientific Visualization** - Shares color palettes and styling
+- **LaTeX Posters** - Generate diagrams for poster presentations
+- **Research Grants** - Methodology diagrams for proposals
+- **Peer Review** - Evaluate diagram clarity and accessibility
+
+## Quick Reference Checklist
+
+Before submitting diagrams, verify:
+
+### Visual Quality
+- [ ] High-quality image format (PNG from AI generation)
+- [ ] No overlapping elements (AI handles automatically)
+- [ ] Adequate spacing between all components (AI optimizes)
+- [ ] Clean, professional alignment
+- [ ] All arrows connect properly to intended targets
+
+### Accessibility
+- [ ] Colorblind-safe palette (Okabe-Ito) used
+- [ ] Works in grayscale (tested with accessibility checker)
+- [ ] Sufficient contrast between elements (verified)
+- [ ] Redundant encoding where appropriate (shapes + colors)
+- [ ] Colorblind simulation passes all checks
+
+### Typography and Readability
+- [ ] Text minimum 7-8 pt at final size
+- [ ] All elements labeled clearly and completely
+- [ ] Consistent font family and sizing
+- [ ] No text overlaps or cutoffs
+- [ ] Units included where applicable
+
+### Publication Standards
+- [ ] Consistent styling with other figures in manuscript
+- [ ] Comprehensive caption written with all abbreviations defined
+- [ ] Referenced appropriately in manuscript text
+- [ ] Meets journal-specific dimension requirements
+- [ ] Exported in required format for journal (PDF/EPS/TIFF)
+
+### Quality Verification (Required)
+- [ ] Ran `run_quality_checks()` and achieved PASS status
+- [ ] Reviewed overlap detection report (zero high-severity overlaps)
+- [ ] Passed accessibility verification (grayscale and colorblind)
+- [ ] Resolution validated at target DPI (300+ for print)
+- [ ] Visual quality report generated and reviewed
+- [ ] All quality reports saved with figure files
+
+### Documentation and Version Control
+- [ ] Source files (.tex, .py) saved for future revision
+- [ ] Quality reports archived in `quality_reports/` directory
+- [ ] Configuration parameters documented (colors, spacing, sizes)
+- [ ] Git commit includes source, output, and quality reports
+- [ ] README or comments explain how to regenerate figure
+
+### Final Integration Check
+- [ ] Figure displays correctly in compiled manuscript
+- [ ] Cross-references work (`\ref{}` points to correct figure)
+- [ ] Figure number matches text citations
+- [ ] Caption appears on correct page relative to figure
+- [ ] No compilation warnings or errors related to figure
+
+## Environment Setup
+
+```bash
+# Required
+export OPENROUTER_API_KEY='your_api_key_here'
+
+# Get key at: https://openrouter.ai/keys
+```
+
+## Getting Started
+
+**Simplest possible usage:**
+```bash
+python scripts/generate_schematic.py "your diagram description" -o output.png
+```
+
+---
+
+Use this skill to create clear, accessible, publication-quality diagrams that effectively communicate complex scientific concepts. The AI-powered workflow with iterative refinement ensures diagrams meet professional standards.
+

package/bin/skills/scientific-schematics/example_usage.sh

@@ -0,0 +1,89 @@
+#!/bin/bash
+# Example usage of AI-powered scientific schematic generation
+# 
+# Prerequisites:
+# 1. Set OPENROUTER_API_KEY environment variable
+# 2. Ensure Python 3.10+ is installed
+# 3. Install requests: pip install requests
+
+set -e
+
+echo "=========================================="
+echo "Scientific Schematics - AI Generation"
+echo "Example Usage Demonstrations"
+echo "=========================================="
+echo ""
+
+# Check for API key
+if [ -z "$OPENROUTER_API_KEY" ]; then
+    echo "❌ Error: OPENROUTER_API_KEY environment variable not set"
+    echo ""
+    echo "Get an API key at: https://openrouter.ai/keys"
+    echo "Then set it with: export OPENROUTER_API_KEY='your_key'"
+    exit 1
+fi
+
+echo "✓ OPENROUTER_API_KEY is set"
+echo ""
+
+# Create output directory
+mkdir -p figures
+echo "✓ Created figures/ directory"
+echo ""
+
+# Example 1: Simple flowchart
+echo "Example 1: CONSORT Flowchart"
+echo "----------------------------"
+python scripts/generate_schematic.py \
+  "CONSORT participant flow diagram. Assessed for eligibility (n=500). Excluded (n=150) with reasons: age<18 (n=80), declined (n=50), other (n=20). Randomized (n=350) into Treatment (n=175) and Control (n=175). Lost to follow-up: 15 and 10. Final analysis: 160 and 165." \
+  -o figures/consort_example.png \
+  --iterations 2
+
+echo ""
+echo "✓ Generated: figures/consort_example.png"
+echo "  - Also created: consort_example_v1.png, v2.png, v3.png"
+echo "  - Review log: consort_example_review_log.json"
+echo ""
+
+# Example 2: Neural network (shorter for demo)
+echo "Example 2: Simple Neural Network"
+echo "--------------------------------"
+python scripts/generate_schematic.py \
+  "Simple feedforward neural network diagram. Input layer with 4 nodes, hidden layer with 6 nodes, output layer with 2 nodes. Show all connections. Label layers clearly." \
+  -o figures/neural_net_example.png \
+  --iterations 2
+
+echo ""
+echo "✓ Generated: figures/neural_net_example.png"
+echo ""
+
+# Example 3: Biological pathway (minimal)
+echo "Example 3: Signaling Pathway"
+echo "---------------------------"
+python scripts/generate_schematic.py \
+  "Simple signaling pathway: Receptor → Kinase A → Kinase B → Transcription Factor → Gene. Show arrows with 'activation' labels. Use different colors for each component." \
+  -o figures/pathway_example.png \
+  --iterations 2
+
+echo ""
+echo "✓ Generated: figures/pathway_example.png"
+echo ""
+
+echo "=========================================="
+echo "All examples completed successfully!"
+echo "=========================================="
+echo ""
+echo "Generated files in figures/:"
+ls -lh figures/*example*.png 2>/dev/null || echo "  (Files will appear after running with valid API key)"
+echo ""
+echo "Review the review_log.json files to see:"
+echo "  - Quality scores for each iteration"
+echo "  - Detailed critiques and suggestions"
+echo "  - Improvement progression"
+echo ""
+echo "Next steps:"
+echo "  1. View the generated images"
+echo "  2. Review the quality scores in *_review_log.json"
+echo "  3. Try your own prompts!"
+echo ""
+