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scientific_writer/.claude/skills/scientific-schematics/SKILL.md

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+---
+name: scientific-schematics
+description: "Create publication-quality scientific diagrams, flowcharts, and schematics using Python (graphviz, matplotlib, schemdraw, networkx). Specialized in neural network architectures, system diagrams, and flowcharts. Generates SVG/EPS in figures/ folder with automated quality verification."
+---
+
+# Scientific Schematics and Diagrams
+
+## Overview
+
+Scientific schematics and diagrams transform complex concepts into clear visual representations for publication. Generate neural network architectures, flowcharts, circuit diagrams, biological pathways, and system diagrams using best-in-class Python libraries. **All diagrams are created as SVG/EPS files, stored in the figures/ subfolder, and referenced in papers/posters** - never embedded directly in LaTeX.
+
+## Zero-Shot Diagram Generation Workflow
+
+**Standard workflow for ALL diagrams:**
+
+1. **Analyze requirements** - Identify diagram type and components
+2. **Choose optimal library** - Select best tool for the specific diagram type
+3. **Generate vector graphic** - Create SVG/EPS with proper spacing and layout
+4. **Store in figures/** - Save to `figures/` subfolder with descriptive name
+5. **Run quality checks** - Verify no overlaps, good contrast, proper resolution
+6. **Reference in document** - Use `\includegraphics{figures/diagram_name.pdf}` in LaTeX
+
+**Key principle:** Generate standalone vector graphics first, then integrate into documents.
+
+## 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
+
+## Best Libraries by Diagram Type
+
+Choose the optimal library for your specific diagram type:
+
+### Neural Network Architectures (Transformers, CNNs, etc.)
+**Best library:** `graphviz` via Python's `pygraphviz` or `pydot`
+- Excellent automatic layout algorithms
+- Clean, professional appearance
+- Perfect for layer stacks and connections
+- Handles complex cross-connections well
+
+**Alternative:** Custom `matplotlib` with careful positioning
+- More control over exact placement
+- Better for highly customized designs
+- Requires more manual positioning
+
+### Flowcharts and Process Diagrams
+**Best library:** `graphviz` with `dot` or `flowchart` layout
+- Automatic optimal positioning
+- Standard flowchart shapes
+- Clean arrow routing
+- Minimal overlap issues
+
+**Alternative:** `diagrams` library (for cloud/system architecture style)
+
+### Circuit Diagrams
+**Best library:** `schemdraw`
+- Purpose-built for electrical circuits
+- Extensive component library
+- Automatic wire routing
+- Professional engineering standard output
+
+### Biological Pathways
+**Best library:** `networkx` with custom rendering
+- Graph-based pathway representation
+- Algorithm-driven layout
+- Flexible node/edge styling
+
+### Block Diagrams and System Architecture
+**Best library:** `graphviz` or `diagrams`
+- Clean hierarchical layouts
+- Automatic spacing
+- Professional appearance
+
+## Zero-Shot Examples for Common Diagram Types
+
+### Example 1: Transformer Architecture (Neural Network)
+
+Creating a Transformer encoder-decoder diagram like in "Attention Is All You Need":
+
+```python
+import graphviz
+from pathlib import Path
+
+def create_transformer_diagram(output_dir='figures'):
+    """
+    Create a Transformer architecture diagram.
+    Zero-shot generation with automatic layout.
+    """
+    Path(output_dir).mkdir(exist_ok=True)
+    
+    # Create directed graph with TB (top-to-bottom) layout
+    dot = graphviz.Digraph(
+        'transformer',
+        format='pdf',
+        graph_attr={
+            'rankdir': 'BT',  # Bottom to top (like the original paper)
+            'splines': 'ortho',  # Orthogonal edges
+            'nodesep': '0.5',
+            'ranksep': '0.8',
+            'bgcolor': 'white',
+            'dpi': '300'
+        },
+        node_attr={
+            'shape': 'box',
+            'style': 'rounded,filled',
+            'fillcolor': 'lightgray',
+            'fontname': 'Arial',
+            'fontsize': '11',
+            'width': '2.5',
+            'height': '0.5'
+        },
+        edge_attr={
+            'color': 'black',
+            'penwidth': '1.5'
+        }
+    )
+    
+    # ENCODER STACK (left side)
+    with dot.subgraph(name='cluster_encoder') as enc:
+        enc.attr(label='Encoder', fontsize='14', fontname='Arial-Bold')
+        enc.attr(style='rounded', color='blue', penwidth='2')
+        
+        # Encoder layers (bottom to top)
+        enc.node('enc_input_emb', 'Input Embedding', fillcolor='#E8F4F8')
+        enc.node('enc_pos', 'Positional Encoding', fillcolor='#E8F4F8')
+        enc.node('enc_mha', 'Multi-Head\nAttention', fillcolor='#B3D9E6')
+        enc.node('enc_an1', 'Add & Norm', fillcolor='#CCE5FF')
+        enc.node('enc_ff', 'Feed Forward', fillcolor='#B3D9E6')
+        enc.node('enc_an2', 'Add & Norm', fillcolor='#CCE5FF')
+        
+        # Encoder flow
+        enc.edge('enc_input_emb', 'enc_pos')
+        enc.edge('enc_pos', 'enc_mha')
+        enc.edge('enc_mha', 'enc_an1')
+        enc.edge('enc_an1', 'enc_ff')
+        enc.edge('enc_ff', 'enc_an2')
+    
+    # DECODER STACK (right side)
+    with dot.subgraph(name='cluster_decoder') as dec:
+        dec.attr(label='Decoder', fontsize='14', fontname='Arial-Bold')
+        dec.attr(style='rounded', color='red', penwidth='2')
+        
+        # Decoder layers (bottom to top)
+        dec.node('dec_output_emb', 'Output Embedding', fillcolor='#FFE8E8')
+        dec.node('dec_pos', 'Positional Encoding', fillcolor='#FFE8E8')
+        dec.node('dec_mmha', 'Masked Self-\nAttention', fillcolor='#FFB3B3')
+        dec.node('dec_an1', 'Add & Norm', fillcolor='#FFCCCC')
+        dec.node('dec_cross', 'Cross-Attention', fillcolor='#FFB3B3')
+        dec.node('dec_an2', 'Add & Norm', fillcolor='#FFCCCC')
+        dec.node('dec_ff', 'Feed Forward', fillcolor='#FFB3B3')
+        dec.node('dec_an3', 'Add & Norm', fillcolor='#FFCCCC')
+        dec.node('dec_linear', 'Linear & Softmax', fillcolor='#FF9999')
+        dec.node('dec_output', 'Output\nProbabilities', fillcolor='#FFE8E8')
+        
+        # Decoder flow
+        dec.edge('dec_output_emb', 'dec_pos')
+        dec.edge('dec_pos', 'dec_mmha')
+        dec.edge('dec_mmha', 'dec_an1')
+        dec.edge('dec_an1', 'dec_cross')
+        dec.edge('dec_cross', 'dec_an2')
+        dec.edge('dec_an2', 'dec_ff')
+        dec.edge('dec_ff', 'dec_an3')
+        dec.edge('dec_an3', 'dec_linear')
+        dec.edge('dec_linear', 'dec_output')
+    
+    # Cross-attention connection (encoder to decoder)
+    dot.edge('enc_an2', 'dec_cross', 
+             style='dashed', 
+             color='purple', 
+             label='  context  ',
+             fontsize='9')
+    
+    # Input and output labels
+    dot.node('input_seq', 'Input Sequence', 
+             shape='ellipse', fillcolor='lightgreen')
+    dot.node('target_seq', 'Target Sequence', 
+             shape='ellipse', fillcolor='lightgreen')
+    
+    dot.edge('input_seq', 'enc_input_emb')
+    dot.edge('target_seq', 'dec_output_emb')
+    
+    # Render to files
+    output_path = f'{output_dir}/transformer_architecture'
+    dot.render(output_path, cleanup=True)
+    
+    # Also save as SVG and EPS
+    dot.format = 'svg'
+    dot.render(output_path, cleanup=True)
+    dot.format = 'eps'
+    dot.render(output_path, cleanup=True)
+    
+    print(f"✓ Transformer diagram created:")
+    print(f"  - {output_path}.pdf")
+    print(f"  - {output_path}.svg")
+    print(f"  - {output_path}.eps")
+    
+    return f"{output_path}.pdf"
+
+# Usage
+if __name__ == '__main__':
+    diagram_path = create_transformer_diagram('figures')
+    
+    # Run quality checks
+    from quality_checker import run_quality_checks
+    run_quality_checks(diagram_path.replace('.pdf', '.png'))
+```
+
+**LaTeX integration:**
+```latex
+\begin{figure}[htbp]
+\centering
+\includegraphics[width=0.9\textwidth]{figures/transformer_architecture.pdf}
+\caption{Transformer encoder-decoder architecture showing multi-head attention,
+         feed-forward layers, and cross-attention mechanism.}
+\label{fig:transformer}
+\end{figure}
+```
+
+### Example 2: Simple Flowchart (CONSORT-style)
+
+```python
+import graphviz
+from pathlib import Path
+
+def create_consort_flowchart(output_dir='figures'):
+    """Create a CONSORT participant flow diagram."""
+    Path(output_dir).mkdir(exist_ok=True)
+    
+    dot = graphviz.Digraph(
+        'consort',
+        format='pdf',
+        graph_attr={
+            'rankdir': 'TB',
+            'splines': 'ortho',
+            'nodesep': '0.6',
+            'ranksep': '0.8',
+            'bgcolor': 'white'
+        },
+        node_attr={
+            'shape': 'box',
+            'style': 'rounded,filled',
+            'fillcolor': '#E8F4F8',
+            'fontname': 'Arial',
+            'fontsize': '10',
+            'width': '3',
+            'height': '0.6'
+        }
+    )
+    
+    # Enrollment
+    dot.node('assessed', 'Assessed for eligibility\n(n=500)')
+    dot.node('excluded', 'Excluded (n=150)\n• Age < 18: n=80\n• Declined: n=50\n• Other: n=20')
+    dot.node('randomized', 'Randomized\n(n=350)')
+    
+    # Allocation
+    dot.node('treatment', 'Allocated to treatment\n(n=175)', fillcolor='#C8E6C9')
+    dot.node('control', 'Allocated to control\n(n=175)', fillcolor='#FFECB3')
+    
+    # Follow-up
+    dot.node('treat_lost', 'Lost to follow-up (n=15)', fillcolor='#FFCDD2')
+    dot.node('ctrl_lost', 'Lost to follow-up (n=10)', fillcolor='#FFCDD2')
+    
+    # Analysis
+    dot.node('treat_analyzed', 'Analyzed (n=160)', fillcolor='#C8E6C9')
+    dot.node('ctrl_analyzed', 'Analyzed (n=165)', fillcolor='#FFECB3')
+    
+    # Connect nodes
+    dot.edge('assessed', 'excluded')
+    dot.edge('assessed', 'randomized')
+    dot.edge('randomized', 'treatment')
+    dot.edge('randomized', 'control')
+    dot.edge('treatment', 'treat_lost')
+    dot.edge('treatment', 'treat_analyzed')
+    dot.edge('control', 'ctrl_lost')
+    dot.edge('control', 'ctrl_analyzed')
+    
+    # Render
+    output_path = f'{output_dir}/consort_flowchart'
+    dot.render(output_path, cleanup=True)
+    
+    print(f"✓ CONSORT flowchart created: {output_path}.pdf")
+    return f"{output_path}.pdf"
+```
+
+### Example 3: CNN Architecture
+
+```python
+def create_cnn_architecture(output_dir='figures'):
+    """Create a CNN architecture diagram."""
+    dot = graphviz.Digraph(
+        'cnn',
+        format='pdf',
+        graph_attr={'rankdir': 'LR', 'bgcolor': 'white'}
+    )
+    
+    # Define layers
+    layers = [
+        ('input', 'Input\n32×32×3', '#FFE8E8'),
+        ('conv1', 'Conv 3×3\n32 filters', '#B3D9E6'),
+        ('pool1', 'MaxPool\n2×2', '#FFE5B3'),
+        ('conv2', 'Conv 3×3\n64 filters', '#B3D9E6'),
+        ('pool2', 'MaxPool\n2×2', '#FFE5B3'),
+        ('flatten', 'Flatten', '#D4E8D4'),
+        ('fc1', 'FC 128', '#C8B3E6'),
+        ('fc2', 'FC 10', '#C8B3E6'),
+        ('softmax', 'Softmax', '#FFC8C8')
+    ]
+    
+    # Create nodes
+    for node_id, label, color in layers:
+        dot.node(node_id, label, 
+                shape='box', style='rounded,filled', 
+                fillcolor=color, fontname='Arial')
+    
+    # Connect layers
+    for i in range(len(layers) - 1):
+        dot.edge(layers[i][0], layers[i+1][0])
+    
+    output_path = f'{output_dir}/cnn_architecture'
+    dot.render(output_path, cleanup=True)
+    
+    print(f"✓ CNN diagram created: {output_path}.pdf")
+    return f"{output_path}.pdf"
+```
+
+## Core Capabilities
+
+### 1. Diagram Types Supported
+
+**Neural Network Architectures**
+- Transformer encoder-decoder models
+- Convolutional Neural Networks (CNNs)
+- Recurrent networks (LSTM, GRU)
+- Attention mechanisms and variants
+- Custom deep learning architectures
+
+**Methodology Flowcharts**
+- CONSORT participant flow diagrams
+- PRISMA systematic review flows
+- Data processing pipelines
+- Algorithm workflows
+- Subject enrollment flows
+
+**Circuit Diagrams**
+- Analog and digital electronic circuits
+- Signal processing block diagrams
+- Control system diagrams
+
+**Biological Diagrams**
+- Signaling pathways
+- Metabolic pathway diagrams
+- Gene regulatory networks
+- Protein interaction networks
+
+**System Architecture Diagrams**
+- Software architecture and components
+- Data flow diagrams
+- Network topology diagrams
+- Hierarchical organization charts
+
+## Required Libraries and Installation
+
+### Primary Library: Graphviz (Recommended for 90% of diagrams)
+
+Graphviz is the best tool for most scientific diagrams due to automatic layout, clean rendering, and zero-overlap guarantee.
+
+**Installation:**
+```bash
+# Install Graphviz binary (required)
+# macOS
+brew install graphviz
+
+# Ubuntu/Debian
+sudo apt-get install graphviz
+
+# Install Python bindings
+pip install graphviz
+```
+
+**Why Graphviz is optimal:**
+- ✓ Automatic optimal layout (no manual positioning needed)
+- ✓ Zero overlaps guaranteed by layout algorithms
+- ✓ Professional appearance out of the box
+- ✓ Supports complex hierarchies and cross-connections
+- ✓ Native SVG, PDF, EPS output
+- ✓ Minimal code for maximum quality
+
+### Specialized Libraries
+
+**Schemdraw** - Circuit diagrams only
+```bash
+pip install schemdraw
+```
+
+**NetworkX** - Complex network analysis + visualization
+```bash
+pip install networkx matplotlib
+```
+
+**Matplotlib** - Custom manual diagrams (when you need exact control)
+```bash
+pip install matplotlib
+```
+
+## Quick Start Guide for Zero-Shot Diagram Creation
+
+Follow this systematic approach for any diagram type:
+
+### Step 1: Identify Diagram Structure
+
+Ask yourself:
+- **Is it a hierarchy?** → Use `rankdir='TB'` or `'BT'` (top-to-bottom or bottom-to-top)
+- **Is it a sequence?** → Use `rankdir='LR'` (left-to-right)
+- **Does it have parallel branches?** → Use subgraphs/clusters
+- **Does it have cross-connections?** → Graphviz handles this automatically
+
+### Step 2: Set Up Base Template
+
+Start with this template and customize:
+
+```python
+import graphviz
+from pathlib import Path
+
+def create_diagram(output_dir='figures', diagram_name='my_diagram'):
+    """Universal diagram creation template."""
+    Path(output_dir).mkdir(exist_ok=True, parents=True)
+    
+    dot = graphviz.Digraph(
+        name=diagram_name,
+        format='pdf',
+        graph_attr={
+            'rankdir': 'TB',      # TB, BT, LR, or RL
+            'splines': 'ortho',   # ortho (straight) or curved
+            'nodesep': '0.6',     # horizontal spacing
+            'ranksep': '0.8',     # vertical spacing
+            'bgcolor': 'white',
+            'dpi': '300'
+        },
+        node_attr={
+            'shape': 'box',       # box, ellipse, diamond, etc.
+            'style': 'rounded,filled',
+            'fillcolor': 'lightgray',
+            'fontname': 'Arial',
+            'fontsize': '11',
+            'margin': '0.2',
+            'width': '2',         # minimum width
+            'height': '0.5'       # minimum height
+        },
+        edge_attr={
+            'color': 'black',
+            'penwidth': '1.5',
+            'arrowsize': '0.8'
+        }
+    )
+    
+    # Add your nodes and edges here
+    dot.node('node1', 'Label 1')
+    dot.node('node2', 'Label 2')
+    dot.edge('node1', 'node2')
+    
+    # Render to multiple formats
+    output_path = f'{output_dir}/{diagram_name}'
+    dot.render(output_path, cleanup=True)  # PDF
+    dot.format = 'svg'
+    dot.render(output_path, cleanup=True)  # SVG
+    dot.format = 'eps'
+    dot.render(output_path, cleanup=True)  # EPS
+    
+    print(f"✓ Diagram saved: {output_path}.{{pdf,svg,eps}}")
+    return f"{output_path}.pdf"
+```
+
+### Step 3: Add Nodes with Clear Labels
+
+**Best practices:**
+- Use descriptive node IDs: `'encoder_layer1'` not `'n1'`
+- Use `\n` for multi-line labels
+- Use fill colors to group related components
+- Keep labels concise (3-5 words max per line)
+
+```python
+# Good node definitions
+dot.node('input_layer', 'Input Layer\n(512 dims)', fillcolor='#E8F4F8')
+dot.node('attention', 'Multi-Head\nAttention', fillcolor='#B3D9E6')
+dot.node('output', 'Output', fillcolor='#C8E6C9')
+```
+
+### Step 4: Connect Nodes with Edges
+
+**Edge types:**
+```python
+# Standard arrow
+dot.edge('node1', 'node2')
+
+# Dashed line (for information flow)
+dot.edge('encoder', 'decoder', style='dashed')
+
+# Bidirectional
+dot.edge('node1', 'node2', dir='both')
+
+# With label
+dot.edge('layer1', 'layer2', label='  ReLU  ')
+
+# Different color
+dot.edge('input', 'output', color='red', penwidth='2')
+```
+
+### Step 5: Use Subgraphs for Grouping
+
+**For parallel structures (like Encoder/Decoder):**
+```python
+# Encoder cluster
+with dot.subgraph(name='cluster_encoder') as enc:
+    enc.attr(label='Encoder', style='rounded', color='blue')
+    enc.node('enc1', 'Encoder Layer 1')
+    enc.node('enc2', 'Encoder Layer 2')
+    enc.edge('enc1', 'enc2')
+
+# Decoder cluster
+with dot.subgraph(name='cluster_decoder') as dec:
+    dec.attr(label='Decoder', style='rounded', color='red')
+    dec.node('dec1', 'Decoder Layer 1')
+    dec.node('dec2', 'Decoder Layer 2')
+    dec.edge('dec1', 'dec2')
+
+# Cross-connection between clusters
+dot.edge('enc2', 'dec1', style='dashed', color='purple')
+```
+
+### Step 6: Render and Verify
+
+```python
+# Always render to PDF (for LaTeX) and SVG (for web/slides)
+output_path = f'{output_dir}/{diagram_name}'
+
+# PDF for papers
+dot.format = 'pdf'
+dot.render(output_path, cleanup=True)
+
+# SVG for posters/slides
+dot.format = 'svg'
+dot.render(output_path, cleanup=True)
+
+# EPS for some journals
+dot.format = 'eps'
+dot.render(output_path, cleanup=True)
+```
+
+## Common Graphviz Attributes Quick Reference
+
+### Graph Attributes (overall layout)
+```python
+graph_attr={
+    'rankdir': 'TB',        # Direction: TB, BT, LR, RL
+    'splines': 'ortho',     # Edge style: ortho, curved, line, polyline
+    'nodesep': '0.5',       # Space between nodes (inches)
+    'ranksep': '0.8',       # Space between ranks (inches)
+    'bgcolor': 'white',     # Background color
+    'dpi': '300',           # Resolution for raster output
+    'compound': 'true',     # Allow edges between clusters
+    'concentrate': 'true'   # Merge multiple edges
+}
+```
+
+### Node Attributes (boxes/shapes)
+```python
+node_attr={
+    'shape': 'box',         # box, ellipse, circle, diamond, plaintext
+    'style': 'rounded,filled',  # rounded, filled, dashed, bold
+    'fillcolor': '#E8F4F8', # Fill color (hex or name)
+    'color': 'black',       # Border color
+    'penwidth': '1.5',      # Border width
+    'fontname': 'Arial',    # Font family
+    'fontsize': '11',       # Font size (points)
+    'fontcolor': 'black',   # Text color
+    'width': '2',           # Minimum width (inches)
+    'height': '0.5',        # Minimum height (inches)
+    'margin': '0.2'         # Internal padding
+}
+```
+
+### Edge Attributes (arrows/connections)
+```python
+edge_attr={
+    'color': 'black',       # Line color
+    'penwidth': '1.5',      # Line width
+    'style': 'solid',       # solid, dashed, dotted, bold
+    'arrowsize': '1.0',     # Arrow head size
+    'dir': 'forward',       # forward, back, both, none
+    'arrowhead': 'normal'   # normal, vee, diamond, dot, none
+}
+```
+
+## Colorblind-Safe Palettes
+
+Use these color sets to ensure accessibility:
+
+### Okabe-Ito Palette (8 colors)
+```python
+OKABE_ITO = {
+    'orange': '#E69F00',
+    'sky_blue': '#56B4E9',
+    'green': '#009E73',
+    'yellow': '#F0E442',
+    'blue': '#0072B2',
+    'vermillion': '#D55E00',
+    'purple': '#CC79A7',
+    'black': '#000000'
+}
+```
+
+### Light Backgrounds (for filled nodes)
+```python
+LIGHT_FILLS = {
+    'blue': '#E8F4F8',
+    'green': '#E8F5E9',
+    'orange': '#FFF3E0',
+    'purple': '#F3E5F5',
+    'red': '#FFEBEE',
+    'yellow': '#FFFDE7',
+    'gray': '#F5F5F5'
+}
+```
+
+### 4. Publication Standards
+
+All diagrams follow scientific publication best practices:
+
+**Vector Format Output**
+- PDF for LaTeX integration (preferred)
+- SVG for web and presentations
+- EPS for legacy publishing systems
+- High-resolution PNG as fallback (300+ DPI)
+
+**Colorblind-Friendly Design**
+- Okabe-Ito palette for categorical elements
+- Perceptually uniform colormaps for continuous data
+- Redundant encoding (shapes + colors)
+- Grayscale compatibility verification
+
+**Typography Standards**
+- Sans-serif fonts (Arial, Helvetica) for consistency
+- Minimum 7-8 pt text at final print size
+- Clear, readable labels with units
+- Consistent notation throughout
+
+**Accessibility**
+- High contrast between elements
+- Adequate line weights (0.5-1 pt minimum)
+- Clear visual hierarchy
+- Descriptive captions and alt text
+
+For comprehensive publication guidelines, see `references/best_practices.md`.
+
+## Quick Start Examples
+
+### Example 1: Simple Flowchart in TikZ
+
+```latex
+\documentclass{article}
+\usepackage{tikz}
+\usetikzlibrary{shapes.geometric, arrows.meta}
+
+% Load colorblind-safe colors
+\input{tikz_styles.tex}
+
+\begin{document}
+
+\begin{figure}[h]
+\centering
+\begin{tikzpicture}[
+    node distance=2cm,
+    process/.style={rectangle, rounded corners, draw=black, thick, 
+                    fill=okabe-blue!20, minimum width=3cm, minimum height=1cm},
+    decision/.style={diamond, draw=black, thick, fill=okabe-orange!20, 
+                     minimum width=2cm, aspect=2},
+    arrow/.style={-Stealth, thick}
+]
+
+% Nodes
+\node (start) [process] {Screen Participants\\(n=500)};
+\node (exclude) [process, below of=start] {Exclude (n=150)\\Age $<$ 18 years};
+\node (randomize) [process, below of=exclude] {Randomize (n=350)};
+\node (treatment) [process, below left=1.5cm and 2cm of randomize] 
+                  {Treatment Group\\(n=175)};
+\node (control) [process, below right=1.5cm and 2cm of randomize] 
+                {Control Group\\(n=175)};
+\node (analyze) [process, below=3cm of randomize] {Analyze Data};
+
+% Arrows
+\draw [arrow] (start) -- (exclude);
+\draw [arrow] (exclude) -- (randomize);
+\draw [arrow] (randomize) -| (treatment);
+\draw [arrow] (randomize) -| (control);
+\draw [arrow] (treatment) |- (analyze);
+\draw [arrow] (control) |- (analyze);
+
+\end{tikzpicture}
+\caption{Study participant flow diagram following CONSORT guidelines.}
+\label{fig:consort}
+\end{figure}
+
+\end{document}
+```
+
+### Example 2: Circuit Diagram with Schemdraw
+
+```python
+import schemdraw
+import schemdraw.elements as elm
+
+# Create drawing with colorblind-safe colors
+d = schemdraw.Drawing()
+
+# Voltage source
+d += elm.SourceV().label('$V_s$')
+
+# Resistors in series
+d += elm.Resistor().right().label('$R_1$\n1kΩ')
+d += elm.Resistor().label('$R_2$\n2kΩ')
+
+# Capacitor
+d += elm.Capacitor().down().label('$C_1$\n10µF')
+
+# Close the circuit
+d += elm.Line().left().tox(d.elements[0].start)
+
+# Add ground
+d += elm.Ground()
+
+# Save as vector graphics
+d.save('circuit_diagram.svg')
+d.save('circuit_diagram.pdf')
+```
+
+### Example 3: Biological Pathway with Python
+
+```python
+import matplotlib.pyplot as plt
+import matplotlib.patches as mpatches
+from matplotlib.patches import FancyBboxPatch, FancyArrowPatch
+
+# Okabe-Ito colorblind-safe palette
+colors = {
+    'protein': '#56B4E9',    # Blue
+    'gene': '#009E73',       # Green
+    'process': '#F0E442',    # Yellow
+    'inhibition': '#D55E00'  # Orange
+}
+
+fig, ax = plt.subplots(figsize=(8, 6))
+
+# Define proteins as rounded rectangles
+proteins = [
+    ('Receptor', 1, 5),
+    ('Kinase A', 3, 5),
+    ('Kinase B', 5, 5),
+    ('TF', 7, 5),
+    ('Gene', 7, 3)
+]
+
+for name, x, y in proteins:
+    color = colors['gene'] if name == 'Gene' else colors['protein']
+    box = FancyBboxPatch((x-0.4, y-0.3), 0.8, 0.6, 
+                         boxstyle="round,pad=0.1", 
+                         facecolor=color, edgecolor='black', linewidth=2)
+    ax.add_patch(box)
+    ax.text(x, y, name, ha='center', va='center', fontsize=10, fontweight='bold')
+
+# Add activation arrows
+arrows = [
+    (1.5, 5, 2.5, 5, 'black'),   # Receptor -> Kinase A
+    (3.5, 5, 4.5, 5, 'black'),   # Kinase A -> Kinase B
+    (5.5, 5, 6.5, 5, 'black'),   # Kinase B -> TF
+    (7, 4.7, 7, 3.6, 'black')    # TF -> Gene
+]
+
+for x1, y1, x2, y2, color in arrows:
+    arrow = FancyArrowPatch((x1, y1), (x2, y2),
+                           arrowstyle='->', mutation_scale=20, 
+                           linewidth=2, color=color)
+    ax.add_patch(arrow)
+
+# Configure axes
+ax.set_xlim(0, 8.5)
+ax.set_ylim(2, 6)
+ax.set_aspect('equal')
+ax.axis('off')
+
+plt.tight_layout()
+plt.savefig('signaling_pathway.pdf', bbox_inches='tight', dpi=300)
+plt.savefig('signaling_pathway.png', bbox_inches='tight', dpi=300)
+```
+
+## Production Workflow (From Concept to Publication)
+
+Follow this systematic workflow for all diagrams:
+
+### Phase 1: Analysis (2 minutes)
+
+1. **Identify diagram type** - What are you visualizing?
+   - Neural network architecture? → Use graphviz
+   - Flowchart (CONSORT, PRISMA)? → Use graphviz
+   - Circuit diagram? → Use schemdraw
+   - Complex network? → Use networkx + graphviz
+
+2. **Determine layout direction**
+   - Vertical flow (top-to-bottom)? → `rankdir='TB'`
+   - Bottom-up (like Transformer)? → `rankdir='BT'`  
+   - Left-to-right sequence? → `rankdir='LR'`
+   - Right-to-left? → `rankdir='RL'`
+
+3. **Identify groupings**
+   - Parallel structures (encoder/decoder)? → Use clusters/subgraphs
+   - Sequential only? → Simple node chain
+   - Cross-connections? → Graphviz handles automatically
+
+### Phase 2: Implementation (10-15 minutes)
+
+**Standard procedure for 95% of diagrams:**
+
+```python
+import graphviz
+from pathlib import Path
+
+# 1. Set up output directory
+output_dir = 'figures'
+Path(output_dir).mkdir(exist_ok=True, parents=True)
+
+# 2. Create diagram with base template
+dot = graphviz.Digraph(
+    'my_diagram',
+    format='pdf',
+    graph_attr={
+        'rankdir': 'TB',      # Adjust based on Phase 1
+        'splines': 'ortho',   # Clean orthogonal edges
+        'nodesep': '0.6',     # Good default spacing
+        'ranksep': '0.8',
+        'bgcolor': 'white',
+        'dpi': '300'
+    },
+    node_attr={
+        'shape': 'box',
+        'style': 'rounded,filled',
+        'fillcolor': 'lightgray',
+        'fontname': 'Arial',
+        'fontsize': '11'
+    },
+    edge_attr={'color': 'black', 'penwidth': '1.5'}
+)
+
+# 3. Add nodes (with descriptive IDs and clear labels)
+dot.node('input', 'Input Layer', fillcolor='#E8F4F8')
+dot.node('hidden', 'Hidden Layer', fillcolor='#B3D9E6')
+dot.node('output', 'Output Layer', fillcolor='#C8E6C9')
+
+# 4. Add edges
+dot.edge('input', 'hidden')
+dot.edge('hidden', 'output')
+
+# 5. Render to figures/ folder
+output_path = f'{output_dir}/my_diagram'
+dot.render(output_path, cleanup=True)  # Creates PDF
+dot.format = 'svg'
+dot.render(output_path, cleanup=True)  # Creates SVG
+dot.format = 'eps'
+dot.render(output_path, cleanup=True)  # Creates EPS
+
+print(f"✓ Saved to: {output_path}.{{pdf,svg,eps}}")
+```
+
+### Phase 3: Quality Verification (5 minutes)
+
+**Automatic checks:**
+```python
+# Convert PDF to PNG for quality checking
+from pdf2image import convert_from_path
+
+pages = convert_from_path(f'{output_path}.pdf', dpi=300)
+pages[0].save(f'{output_path}.png')
+
+# Run quality checks
+from quality_checker import run_quality_checks
+report = run_quality_checks(f'{output_path}.png')
+
+if report['overall_status'] != 'PASS':
+    print("⚠️ Issues detected - review quality_reports/")
+    # Adjust spacing: increase nodesep or ranksep
+    # Adjust colors: check accessibility report
+else:
+    print("✓ Quality checks passed!")
+```
+
+**Manual verification:**
+1. Open PDF in viewer - check for overlaps
+2. Verify text is readable (zoom to 100%)
+3. Check alignment and spacing looks professional
+4. Ensure colors are distinguishable
+
+### Phase 4: LaTeX Integration (2 minutes)
+
+**In your LaTeX document:**
+
+```latex
+% In preamble
+\usepackage{graphicx}
+
+% In document
+\begin{figure}[htbp]
+\centering
+\includegraphics[width=0.8\textwidth]{figures/my_diagram.pdf}
+\caption{Clear, descriptive caption explaining all components and abbreviations.
+         Define any non-standard notation used in the diagram.}
+\label{fig:my_diagram}
+\end{figure}
+
+% Reference in text
+As shown in Figure~\ref{fig:my_diagram}, the architecture consists of...
+```
+
+**For posters (beamer):**
+```latex
+\begin{frame}{Architecture}
+\begin{center}
+\includegraphics[width=0.9\textwidth]{figures/my_diagram.pdf}
+\end{center}
+\end{frame}
+```
+
+### Phase 5: Version Control (1 minute)
+
+**Always commit:**
+1. Python source code (`create_my_diagram.py`)
+2. Generated outputs (`figures/my_diagram.{pdf,svg,eps}`)
+3. Quality reports (`my_diagram_quality_reports/`)
+
+```bash
+git add create_my_diagram.py
+git add figures/my_diagram.*
+git add my_diagram_quality_reports/
+git commit -m "Add architecture diagram with quality verification"
+```
+
+## Troubleshooting Common Issues
+
+### Graphviz-Specific Problems
+
+**Problem:** Nodes overlap or are too close
+```python
+# Solution: Increase spacing
+graph_attr={
+    'nodesep': '1.0',   # Increase from default 0.6
+    'ranksep': '1.2'    # Increase from default 0.8
+}
+```
+
+**Problem:** Edges cross in confusing ways
+```python
+# Solution 1: Use orthogonal splines
+graph_attr={'splines': 'ortho'}
+
+# Solution 2: Adjust rank direction
+graph_attr={'rankdir': 'LR'}  # Try different directions
+```
+
+**Problem:** Labels are cut off or too small
+```python
+# Solution: Adjust node size and font
+node_attr={
+    'fontsize': '12',      # Increase from 11
+    'margin': '0.3',       # More internal padding
+    'width': '2.5',        # Wider boxes
+    'height': '0.6'        # Taller boxes
+}
+```
+
+**Problem:** Clusters/subgraphs not appearing
+```python
+# Solution: Cluster names MUST start with 'cluster_'
+with dot.subgraph(name='cluster_encoder') as enc:  # ✓ Correct
+    enc.attr(label='Encoder')
+
+with dot.subgraph(name='encoder') as enc:  # ✗ Won't show as cluster
+    enc.attr(label='Encoder')
+```
+
+**Problem:** Cross-cluster edges not working
+```python
+# Solution: Enable compound edges
+dot.attr(compound='true')
+
+# Then use lhead/ltail for cluster connections
+dot.edge('node1', 'node2', lhead='cluster_decoder')
+```
+
+**Problem:** Graphviz not found error
+```bash
+# Solution: Install graphviz binary (not just Python package)
+# macOS
+brew install graphviz
+
+# Ubuntu
+sudo apt-get install graphviz
+
+# Then install Python bindings
+pip install graphviz
+```
+
+### Visual Quality Issues
+
+**Problem:** Colors not colorblind-safe
+```python
+# Solution: Use Okabe-Ito palette
+COLORS = {
+    'blue': '#56B4E9',
+    'green': '#009E73',
+    'orange': '#E69F00',
+    'purple': '#CC79A7'
+}
+dot.node('n1', 'Node', fillcolor=COLORS['blue'])
+```
+
+**Problem:** Text too small when printed
+```python
+# Solution: Increase font size and DPI
+node_attr={'fontsize': '12'}  # Minimum 11-12 for print
+graph_attr={'dpi': '300'}     # Publication quality
+```
+
+**Problem:** PDF too large
+```python
+# Solution 1: Use simpler edge routing
+graph_attr={'splines': 'line'}  # Simpler than 'ortho'
+
+# Solution 2: Reduce DPI for drafts
+graph_attr={'dpi': '150'}  # For drafts only
+```
+
+### Workflow Issues
+
+**Problem:** Need to regenerate diagram after changes
+```python
+# Solution: Make diagram generation a function
+def create_diagram(params):
+    # ... diagram code ...
+    return output_path
+
+# Easy to regenerate with different parameters
+create_diagram({'nodesep': '0.8', 'ranksep': '1.0'})
+```
+
+**Problem:** Diagram doesn't match paper figures style
+```python
+# Solution: Create a reusable style configuration
+PAPER_STYLE = {
+    'graph_attr': {
+        'rankdir': 'TB',
+        'bgcolor': 'white',
+        'dpi': '300'
+    },
+    'node_attr': {
+        'fontname': 'Arial',
+        'fontsize': '11',
+        'style': 'rounded,filled',
+        'fillcolor': '#E8F4F8'
+    },
+    'edge_attr': {
+        'color': 'black',
+        'penwidth': '1.5'
+    }
+}
+
+# Use for all diagrams
+dot = graphviz.Digraph(**PAPER_STYLE)
+```
+
+## Visual Verification and Quality Control
+
+All diagrams undergo automated visual quality checks to prevent overlaps, ensure readability, and verify accessibility. This multi-stage verification process uses computer vision techniques to detect common issues.
+
+### Stage 1: Overlap Detection
+
+Automatically detect overlapping elements that reduce clarity:
+
+```python
+import numpy as np
+from PIL import Image
+import json
+from pathlib import Path
+
+def detect_overlaps(image_path, threshold=0.95):
+    """
+    Detect potential overlapping regions in a diagram.
+    
+    Args:
+        image_path: Path to the rendered diagram (PNG/PDF)
+        threshold: Similarity threshold for detecting overlaps (0-1)
+        
+    Returns:
+        dict: Overlap report with locations and severity
+    """
+    # Load image
+    img = Image.open(image_path).convert('RGB')
+    img_array = np.array(img)
+    
+    # Detect dense regions (potential overlaps)
+    gray = np.mean(img_array, axis=2)
+    
+    # Edge detection to find boundaries
+    from scipy.ndimage import sobel
+    edges_x = sobel(gray, axis=0)
+    edges_y = sobel(gray, axis=1)
+    edge_magnitude = np.hypot(edges_x, edges_y)
+    
+    # Find regions with high edge density (overlaps)
+    from scipy.ndimage import label, find_objects
+    binary_edges = edge_magnitude > np.percentile(edge_magnitude, 85)
+    labeled_regions, num_features = label(binary_edges)
+    
+    overlaps = []
+    slices = find_objects(labeled_regions)
+    
+    for i, slice_obj in enumerate(slices):
+        if slice_obj is not None:
+            region = edge_magnitude[slice_obj]
+            density = np.mean(region)
+            
+            # High density suggests potential overlap
+            if density > threshold * np.max(edge_magnitude):
+                y_center = (slice_obj[0].start + slice_obj[0].stop) // 2
+                x_center = (slice_obj[1].start + slice_obj[1].stop) // 2
+                
+                overlaps.append({
+                    'region_id': i + 1,
+                    'position': (x_center, y_center),
+                    'density': float(density),
+                    'severity': 'high' if density > 0.98 * np.max(edge_magnitude) else 'medium'
+                })
+    
+    report = {
+        'image': str(image_path),
+        'overlaps_detected': len(overlaps),
+        'overlap_regions': overlaps,
+        'status': 'PASS' if len(overlaps) == 0 else 'WARNING'
+    }
+    
+    return report
+
+def save_overlap_report(report, output_path='overlap_report.json'):
+    """Save overlap detection report to JSON."""
+    with open(output_path, 'w') as f:
+        json.dump(report, indent=2, fp=f)
+    
+    print(f"Overlap Report: {report['status']}")
+    print(f"  - Overlaps detected: {report['overlaps_detected']}")
+    if report['overlap_regions']:
+        print("  - Regions requiring review:")
+        for region in report['overlap_regions']:
+            print(f"    * Region {region['region_id']}: "
+                  f"Position {region['position']}, Severity: {region['severity']}")
+```
+
+### Stage 2: Contrast and Accessibility Verification
+
+Ensure diagrams meet accessibility standards for colorblind readers:
+
+```python
+def verify_accessibility(image_path):
+    """
+    Verify diagram meets accessibility standards.
+    
+    Checks:
+    - Sufficient contrast ratios
+    - Grayscale readability
+    - Text size adequacy
+    """
+    from PIL import ImageFilter, ImageStat
+    
+    img = Image.open(image_path).convert('RGB')
+    
+    # Test 1: Grayscale conversion
+    grayscale = img.convert('L')
+    gray_stat = ImageStat.Stat(grayscale)
+    
+    # Calculate contrast (std dev of grayscale)
+    contrast = gray_stat.stddev[0]
+    min_contrast = 30  # Minimum standard deviation for good contrast
+    
+    # Test 2: Color distribution
+    rgb_array = np.array(img)
+    unique_colors = len(np.unique(rgb_array.reshape(-1, 3), axis=0))
+    
+    # Test 3: Simulate common color blindness (deuteranopia)
+    def simulate_colorblind(img_array):
+        # Simplified deuteranopia simulation
+        colorblind = img_array.copy().astype(float)
+        colorblind[:, :, 0] = 0.625 * img_array[:, :, 0] + 0.375 * img_array[:, :, 1]
+        colorblind[:, :, 1] = 0.7 * img_array[:, :, 1] + 0.3 * img_array[:, :, 0]
+        return colorblind.astype(np.uint8)
+    
+    colorblind_img = simulate_colorblind(np.array(img))
+    cb_image = Image.fromarray(colorblind_img)
+    cb_gray = cb_image.convert('L')
+    cb_stat = ImageStat.Stat(cb_gray)
+    cb_contrast = cb_stat.stddev[0]
+    
+    report = {
+        'image': str(image_path),
+        'checks': {
+            'grayscale_contrast': {
+                'value': contrast,
+                'threshold': min_contrast,
+                'status': 'PASS' if contrast >= min_contrast else 'FAIL'
+            },
+            'colorblind_contrast': {
+                'value': cb_contrast,
+                'threshold': min_contrast * 0.8,
+                'status': 'PASS' if cb_contrast >= min_contrast * 0.8 else 'FAIL'
+            },
+            'color_diversity': {
+                'unique_colors': unique_colors,
+                'status': 'INFO'
+            }
+        },
+        'overall_status': 'PASS' if (contrast >= min_contrast and 
+                                     cb_contrast >= min_contrast * 0.8) else 'FAIL'
+    }
+    
+    return report
+
+def save_accessibility_report(report, output_path='accessibility_report.json'):
+    """Save accessibility report to JSON."""
+    with open(output_path, 'w') as f:
+        json.dump(report, indent=2, fp=f)
+    
+    print(f"Accessibility Report: {report['overall_status']}")
+    for check_name, check_data in report['checks'].items():
+        print(f"  - {check_name}: {check_data['status']}")
+        if 'value' in check_data and 'threshold' in check_data:
+            print(f"    Value: {check_data['value']:.2f}, Threshold: {check_data['threshold']:.2f}")
+```
+
+### Stage 3: Text Size and Resolution Validation
+
+Verify text is readable at publication size:
+
+```python
+def validate_resolution(image_path, target_dpi=300, min_text_size_pt=7):
+    """
+    Validate image resolution and estimated text size.
+    
+    Args:
+        image_path: Path to diagram image
+        target_dpi: Target DPI for publication (default 300)
+        min_text_size_pt: Minimum acceptable text size in points
+    """
+    from PIL import Image
+    import pytesseract
+    
+    img = Image.open(image_path)
+    
+    # Check DPI
+    dpi = img.info.get('dpi', (72, 72))
+    actual_dpi = dpi[0] if isinstance(dpi, tuple) else dpi
+    
+    # Estimate text size (simplified - assumes text detection)
+    # For production, use OCR or PDF text extraction
+    width, height = img.size
+    dpi_ratio = actual_dpi / 72  # Convert to screen pixels
+    
+    # Calculate physical size in inches
+    width_inches = width / actual_dpi if actual_dpi > 0 else width / 72
+    height_inches = height / actual_dpi if actual_dpi > 0 else height / 72
+    
+    report = {
+        'image': str(image_path),
+        'resolution': {
+            'dpi': actual_dpi,
+            'target_dpi': target_dpi,
+            'status': 'PASS' if actual_dpi >= target_dpi else 'WARNING'
+        },
+        'dimensions': {
+            'pixels': {'width': width, 'height': height},
+            'inches': {'width': round(width_inches, 2), 
+                      'height': round(height_inches, 2)}
+        },
+        'recommendations': []
+    }
+    
+    if actual_dpi < target_dpi:
+        report['recommendations'].append(
+            f"Increase resolution to {target_dpi} DPI for publication quality"
+        )
+    
+    if width_inches > 7:
+        report['recommendations'].append(
+            "Image width exceeds typical single-column width (7 inches)"
+        )
+    
+    return report
+```
+
+### Stage 4: Comprehensive Quality Check Pipeline
+
+Run all verification stages in sequence:
+
+```python
+def run_quality_checks(image_path, output_dir='quality_reports'):
+    """
+    Run comprehensive quality checks on diagram.
+    
+    Args:
+        image_path: Path to diagram to verify
+        output_dir: Directory to save reports
+        
+    Returns:
+        dict: Comprehensive quality report
+    """
+    import os
+    from datetime import datetime
+    
+    Path(output_dir).mkdir(exist_ok=True)
+    
+    print(f"Running quality checks on: {image_path}")
+    print("=" * 60)
+    
+    # Stage 1: Overlap Detection
+    print("\n[Stage 1/4] Detecting overlaps...")
+    overlap_report = detect_overlaps(image_path)
+    save_overlap_report(
+        overlap_report, 
+        f"{output_dir}/overlap_report.json"
+    )
+    
+    # Stage 2: Accessibility
+    print("\n[Stage 2/4] Verifying accessibility...")
+    accessibility_report = verify_accessibility(image_path)
+    save_accessibility_report(
+        accessibility_report,
+        f"{output_dir}/accessibility_report.json"
+    )
+    
+    # Stage 3: Resolution
+    print("\n[Stage 3/4] Validating resolution...")
+    resolution_report = validate_resolution(image_path)
+    with open(f"{output_dir}/resolution_report.json", 'w') as f:
+        json.dump(resolution_report, f, indent=2)
+    
+    # Stage 4: Generate visual report
+    print("\n[Stage 4/4] Generating visual report...")
+    create_visual_report(
+        image_path,
+        overlap_report,
+        accessibility_report,
+        f"{output_dir}/visual_report.png"
+    )
+    
+    # Comprehensive summary
+    all_pass = (
+        overlap_report['status'] != 'FAIL' and
+        accessibility_report['overall_status'] != 'FAIL' and
+        resolution_report['resolution']['status'] != 'FAIL'
+    )
+    
+    summary = {
+        'timestamp': datetime.now().isoformat(),
+        'image': str(image_path),
+        'overall_status': 'PASS' if all_pass else 'NEEDS REVIEW',
+        'stage_results': {
+            'overlap_detection': overlap_report['status'],
+            'accessibility': accessibility_report['overall_status'],
+            'resolution': resolution_report['resolution']['status']
+        },
+        'reports_saved_to': output_dir
+    }
+    
+    with open(f"{output_dir}/summary.json", 'w') as f:
+        json.dump(summary, f, indent=2)
+    
+    print("\n" + "=" * 60)
+    print(f"OVERALL STATUS: {summary['overall_status']}")
+    print(f"Reports saved to: {output_dir}/")
+    print("=" * 60)
+    
+    return summary
+
+def create_visual_report(image_path, overlap_report, accessibility_report, output_path):
+    """Create visual report with annotations."""
+    import matplotlib.pyplot as plt
+    from matplotlib.patches import Circle
+    
+    fig, axes = plt.subplots(1, 3, figsize=(15, 5))
+    
+    # Load original image
+    img = Image.open(image_path)
+    
+    # Panel 1: Original with overlap markers
+    axes[0].imshow(img)
+    axes[0].set_title('Overlap Detection', fontsize=12, fontweight='bold')
+    if overlap_report['overlap_regions']:
+        for region in overlap_report['overlap_regions']:
+            x, y = region['position']
+            color = 'red' if region['severity'] == 'high' else 'orange'
+            circle = Circle((x, y), 20, color=color, fill=False, linewidth=2)
+            axes[0].add_patch(circle)
+    axes[0].axis('off')
+    axes[0].text(0.02, 0.98, f"Status: {overlap_report['status']}", 
+                transform=axes[0].transAxes, fontsize=10,
+                verticalalignment='top', bbox=dict(boxstyle='round', 
+                facecolor='wheat', alpha=0.5))
+    
+    # Panel 2: Grayscale version
+    gray_img = img.convert('L')
+    axes[1].imshow(gray_img, cmap='gray')
+    axes[1].set_title('Grayscale Preview', fontsize=12, fontweight='bold')
+    axes[1].axis('off')
+    gray_status = accessibility_report['checks']['grayscale_contrast']['status']
+    axes[1].text(0.02, 0.98, f"Status: {gray_status}", 
+                transform=axes[1].transAxes, fontsize=10,
+                verticalalignment='top', bbox=dict(boxstyle='round', 
+                facecolor='wheat', alpha=0.5))
+    
+    # Panel 3: Colorblind simulation
+    img_array = np.array(img)
+    colorblind = img_array.copy().astype(float)
+    colorblind[:, :, 0] = 0.625 * img_array[:, :, 0] + 0.375 * img_array[:, :, 1]
+    colorblind[:, :, 1] = 0.7 * img_array[:, :, 1] + 0.3 * img_array[:, :, 0]
+    axes[2].imshow(colorblind.astype(np.uint8))
+    axes[2].set_title('Colorblind Simulation', fontsize=12, fontweight='bold')
+    axes[2].axis('off')
+    cb_status = accessibility_report['checks']['colorblind_contrast']['status']
+    axes[2].text(0.02, 0.98, f"Status: {cb_status}", 
+                transform=axes[2].transAxes, fontsize=10,
+                verticalalignment='top', bbox=dict(boxstyle='round', 
+                facecolor='wheat', alpha=0.5))
+    
+    plt.tight_layout()
+    plt.savefig(output_path, dpi=150, bbox_inches='tight')
+    print(f"Visual report saved: {output_path}")
+    plt.close()
+```
+
+### Usage Example: Complete Workflow with Verification
+
+Here's how to create a diagram with full quality verification:
+
+```python
+import matplotlib.pyplot as plt
+from matplotlib.patches import FancyBboxPatch, FancyArrowPatch
+
+# Step 1: Create diagram
+def create_flowchart_with_verification(output_base='flowchart'):
+    """Create flowchart with automated quality checks."""
+    
+    # Okabe-Ito colorblind-safe palette
+    colors = {
+        'process': '#56B4E9',    # Blue
+        'decision': '#E69F00',   # Orange
+        'data': '#009E73',       # Green
+        'terminal': '#CC79A7'    # Purple
+    }
+    
+    fig, ax = plt.subplots(figsize=(8, 10))
+    
+    # Define flowchart elements with careful spacing
+    elements = [
+        ('Start', 4, 9, 'terminal'),
+        ('Input Data', 4, 7.5, 'data'),
+        ('Process A', 4, 6, 'process'),
+        ('Decision?', 4, 4.5, 'decision'),
+        ('Process B1', 2, 3, 'process'),
+        ('Process B2', 6, 3, 'process'),
+        ('Output', 4, 1.5, 'data'),
+        ('End', 4, 0, 'terminal')
+    ]
+    
+    # Draw boxes with adequate spacing
+    box_positions = {}
+    for label, x, y, element_type in elements:
+        color = colors[element_type]
+        width, height = (1.2, 0.6) if element_type != 'decision' else (1.5, 1.0)
+        
+        box = FancyBboxPatch(
+            (x - width/2, y - height/2), width, height,
+            boxstyle="round,pad=0.1" if element_type != 'decision' else "round,pad=0.05",
+            facecolor=color, edgecolor='black', linewidth=2
+        )
+        ax.add_patch(box)
+        ax.text(x, y, label, ha='center', va='center', 
+               fontsize=10, fontweight='bold')
+        box_positions[label] = (x, y)
+    
+    # Draw arrows with proper spacing
+    arrows = [
+        ('Start', 'Input Data'),
+        ('Input Data', 'Process A'),
+        ('Process A', 'Decision?'),
+        ('Decision?', 'Process B1'),
+        ('Decision?', 'Process B2'),
+        ('Process B1', 'Output'),
+        ('Process B2', 'Output'),
+        ('Output', 'End')
+    ]
+    
+    for start, end in arrows:
+        x1, y1 = box_positions[start]
+        x2, y2 = box_positions[end]
+        
+        # Calculate arrow start/end points to avoid overlap
+        if x1 == x2:  # Vertical arrow
+            y1_adj = y1 - 0.3 if y2 < y1 else y1 + 0.3
+            y2_adj = y2 + 0.3 if y2 < y1 else y2 - 0.3
+            arrow = FancyArrowPatch(
+                (x1, y1_adj), (x2, y2_adj),
+                arrowstyle='->', mutation_scale=20, linewidth=2, color='black'
+            )
+        else:  # Diagonal arrow
+            arrow = FancyArrowPatch(
+                (x1, y1 - 0.5), (x2, y2 + 0.3),
+                arrowstyle='->', mutation_scale=20, linewidth=2, color='black'
+            )
+        ax.add_patch(arrow)
+    
+    ax.set_xlim(0, 8)
+    ax.set_ylim(-0.5, 9.5)
+    ax.set_aspect('equal')
+    ax.axis('off')
+    
+    plt.tight_layout()
+    
+    # Save in multiple formats
+    plt.savefig(f'{output_base}.pdf', bbox_inches='tight', dpi=300)
+    plt.savefig(f'{output_base}.png', bbox_inches='tight', dpi=300)
+    plt.savefig(f'{output_base}.svg', bbox_inches='tight')
+    print(f"Diagram saved: {output_base}.pdf/.png/.svg")
+    plt.close()
+    
+    # Step 2: Run quality checks
+    print("\nRunning quality verification...")
+    quality_report = run_quality_checks(
+        f'{output_base}.png',
+        output_dir=f'{output_base}_quality_reports'
+    )
+    
+    # Step 3: Review and iterate if needed
+    if quality_report['overall_status'] != 'PASS':
+        print("\n⚠️  Diagram needs review. Check quality reports for details.")
+        return False
+    else:
+        print("\n✓ Diagram passed all quality checks!")
+        return True
+
+# Run complete workflow
+if __name__ == '__main__':
+    success = create_flowchart_with_verification('my_flowchart')
+```
+
+### Iterative Refinement Loop
+
+For complex diagrams, use an iterative refinement process:
+
+```python
+def iterative_diagram_refinement(create_function, max_iterations=3):
+    """
+    Iteratively refine diagram until it passes quality checks.
+    
+    Args:
+        create_function: Function that creates and saves diagram
+        max_iterations: Maximum refinement attempts
+    """
+    for iteration in range(1, max_iterations + 1):
+        print(f"\n{'='*60}")
+        print(f"ITERATION {iteration}/{max_iterations}")
+        print(f"{'='*60}")
+        
+        # Create diagram
+        diagram_path = create_function(iteration)
+        
+        # Run checks
+        quality_report = run_quality_checks(
+            diagram_path,
+            output_dir=f'iteration_{iteration}_reports'
+        )
+        
+        if quality_report['overall_status'] == 'PASS':
+            print(f"\n✓ Diagram approved after {iteration} iteration(s)")
+            return True
+        else:
+            print(f"\n⚠️  Issues found. Adjusting parameters for next iteration...")
+            # Here you would adjust spacing, colors, etc. based on reports
+    
+    print(f"\n❌ Maximum iterations reached. Manual review required.")
+    return False
+```
+
+## Common Use Cases
+
+### Use Case 1: CONSORT Participant Flow Diagram
+
+Clinical trials require standardized participant flow diagrams. Use the flowchart template:
+
+```latex
+% Load template
+\input{assets/flowchart_template.tex}
+
+% Customize with your numbers
+\begin{tikzpicture}[consort]
+  \node (assessed) [flowbox] {Assessed for eligibility (n=500)};
+  \node (excluded) [flowbox, below=of assessed] {Excluded (n=150)};
+  \node (reasons) [infobox, right=of excluded] {
+    \begin{tabular}{l}
+    Age $<$ 18: n=80 \\
+    Declined: n=50 \\
+    Other: n=20
+    \end{tabular}
+  };
+  % ... continue diagram
+\end{tikzpicture}
+```
+
+See `assets/flowchart_template.tex` for complete template.
+
+### Use Case 2: Electronics Circuit Schematic
+
+For electronics papers, use Schemdraw or CircuitikZ:
+
+```python
+# Python with Schemdraw - see scripts/circuit_generator.py
+from scripts.circuit_generator import create_circuit
+
+circuit = create_circuit(
+    components=['voltage_source', 'resistor', 'capacitor', 'ground'],
+    values=['5V', '1kΩ', '10µF', None],
+    layout='series'
+)
+circuit.save('my_circuit.pdf')
+```
+
+Or use CircuitikZ in LaTeX - see `assets/circuit_template.tex`.
+
+### Use Case 3: Biological Signaling Pathway
+
+Visualize molecular interactions and signaling cascades:
+
+```python
+# Python script - see scripts/pathway_diagram.py
+from scripts.pathway_diagram import PathwayGenerator
+
+pathway = PathwayGenerator()
+pathway.add_protein('EGFR', position=(1, 5))
+pathway.add_protein('RAS', position=(3, 5))
+pathway.add_protein('RAF', position=(5, 5))
+pathway.add_activation('EGFR', 'RAS')
+pathway.add_activation('RAS', 'RAF')
+pathway.save('mapk_pathway.pdf')
+```
+
+Or create in TikZ - see `assets/pathway_template.tex`.
+
+### Use Case 4: System Architecture Diagram
+
+Illustrate software/hardware components and relationships:
+
+```latex
+% Use block diagram template
+\input{assets/block_diagram_template.tex}
+
+\begin{tikzpicture}[architecture]
+  \node (sensor) [component] {Sensor};
+  \node (adc) [component, right=of sensor] {ADC};
+  \node (micro) [component, right=of adc] {Microcontroller};
+  \node (wifi) [component, above right=of micro] {WiFi Module};
+  \node (display) [component, below right=of micro] {Display};
+  
+  \draw [dataflow] (sensor) -- node[above] {Analog} (adc);
+  \draw [dataflow] (adc) -- node[above] {Digital} (micro);
+  \draw [dataflow] (micro) -- (wifi);
+  \draw [dataflow] (micro) -- (display);
+\end{tikzpicture}
+```
+
+See `assets/block_diagram_template.tex` for complete template.
+
+## Helper Scripts
+
+The `scripts/` directory contains Python utilities for automated diagram generation and quality verification:
+
+### `generate_flowchart.py`
+
+Convert text descriptions into TikZ flowcharts with automatic quality checks:
+
+```python
+from scripts.generate_flowchart import text_to_flowchart, create_with_verification
+
+description = """
+1. Screen participants (n=500)
+2. Exclude if age < 18 (n=150)
+3. Randomize remaining (n=350)
+4. Treatment group (n=175)
+5. Control group (n=175)
+6. Follow up at 3 months
+7. Analyze data
+"""
+
+# Generate TikZ code
+tikz_code = text_to_flowchart(description)
+with open('methodology_flow.tex', 'w') as f:
+    f.write(tikz_code)
+
+# Or create with automatic verification
+success = create_with_verification(
+    description, 
+    output='methodology_flow',
+    verify=True
+)
+```
+
+### `circuit_generator.py`
+
+Generate circuit diagrams using Schemdraw with quality verification:
+
+```python
+from scripts.circuit_generator import CircuitBuilder
+
+builder = CircuitBuilder()
+builder.add_voltage_source('Vs', '5V')
+builder.add_resistor('R1', '1kΩ')
+builder.add_capacitor('C1', '10µF')
+builder.add_ground()
+
+# Save with automatic quality checks
+builder.save('circuit.pdf', verify=True)
+
+# Access quality report
+print(builder.quality_report)
+```
+
+### `pathway_diagram.py`
+
+Create biological pathway diagrams with overlap detection:
+
+```python
+from scripts.pathway_diagram import PathwayGenerator
+
+gen = PathwayGenerator(
+    colorblind_safe=True,
+    auto_spacing=True  # Automatically adjust spacing to prevent overlaps
+)
+
+gen.add_node('Receptor', type='protein', position=(1, 5))
+gen.add_node('Kinase', type='protein', position=(3, 5))
+gen.add_edge('Receptor', 'Kinase', interaction='activation')
+
+# Save with quality verification
+quality_report = gen.save('pathway.pdf', verify=True)
+
+# Iteratively refine if needed
+if quality_report['status'] != 'PASS':
+    gen.auto_adjust_spacing()
+    gen.save('pathway.pdf', verify=True)
+```
+
+### `compile_tikz.py`
+
+Standalone TikZ compilation utility with quality checks:
+
+```bash
+# Compile TikZ to PDF with verification
+python scripts/compile_tikz.py flowchart.tex -o flowchart.pdf --verify
+
+# Generate PNG with quality report
+python scripts/compile_tikz.py flowchart.tex -o flowchart.pdf --png --dpi 300 --verify
+
+# Preview with quality overlay
+python scripts/compile_tikz.py flowchart.tex --preview --show-quality
+```
+
+### `quality_checker.py`
+
+Standalone quality verification tool for any diagram:
+
+```bash
+# Check single diagram
+python scripts/quality_checker.py diagram.png
+
+# Check with detailed report
+python scripts/quality_checker.py diagram.png --detailed --output-dir reports/
+
+# Batch check multiple diagrams
+python scripts/quality_checker.py figures/*.png --batch
+
+# Export visual comparison report
+python scripts/quality_checker.py diagram.png --visual-report
+```
+
+```python
+# Python API
+from scripts.quality_checker import DiagramQualityChecker
+
+checker = DiagramQualityChecker()
+
+# Run all checks
+report = checker.check_diagram('diagram.png')
+
+# Access specific checks
+overlap_report = checker.check_overlaps('diagram.png')
+accessibility_report = checker.check_accessibility('diagram.png')
+resolution_report = checker.check_resolution('diagram.png')
+
+# Generate visual report
+checker.create_visual_report('diagram.png', output='quality_report.png')
+
+# Batch processing
+results = checker.batch_check(['fig1.png', 'fig2.png', 'fig3.png'])
+checker.save_batch_report(results, 'batch_quality_report.json')
+```
+
+## Templates and Assets
+
+Pre-built templates in `assets/` directory provide starting points:
+
+- **`flowchart_template.tex`** - Methodology flowcharts (CONSORT style)
+- **`circuit_template.tex`** - Electrical circuit diagrams
+- **`pathway_template.tex`** - Biological pathway diagrams
+- **`block_diagram_template.tex`** - System architecture diagrams
+- **`tikz_styles.tex`** - Reusable style definitions (ALWAYS load this)
+
+All templates use colorblind-safe Okabe-Ito palette and publication-ready styling.
+
+## 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 `\input{}` for TikZ, `\includegraphics{}` for external
+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 source files (.tex, .py) in repository
+
+## Troubleshooting Common Issues
+
+### TikZ Compilation Errors
+
+**Problem**: `! Package tikz Error: I do not know the key '/tikz/...`
+- **Solution**: Missing library - add `\usetikzlibrary{...}` to preamble
+
+**Problem**: Overlapping text or elements
+- **Solution**: Run quality checker to identify overlaps: `python scripts/quality_checker.py diagram.png`
+- **Solution**: Increase `node distance`, adjust positioning manually based on overlap report
+- **Solution**: Use `auto_spacing=True` in pathway generator for automatic adjustment
+
+**Problem**: Arrows not connecting properly
+- **Solution**: Use anchor points: `(node.east)`, `(node.north)`, etc.
+- **Solution**: Check overlap report for arrow/node intersections
+
+### Python Generation Issues
+
+**Problem**: Schemdraw elements not aligning
+- **Solution**: Use `.at()` method for precise positioning
+- **Solution**: Enable `auto_spacing` to prevent overlaps
+
+**Problem**: Matplotlib text rendering issues
+- **Solution**: Set `plt.rcParams['text.usetex'] = True` for LaTeX rendering
+- **Solution**: Ensure LaTeX installation is available
+
+**Problem**: Export quality poor
+- **Solution**: Increase DPI: `plt.savefig(..., dpi=300, bbox_inches='tight')`
+- **Solution**: Run resolution checker: `quality_checker.check_resolution(image_path, target_dpi=300)`
+
+**Problem**: Elements overlap after generation
+- **Solution**: Run `detect_overlaps()` function to identify problem regions
+- **Solution**: Use iterative refinement: `iterative_diagram_refinement(create_function)`
+- **Solution**: Increase spacing between elements by 20-30%
+
+### 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**: Quality checker fails on PDF files
+- **Solution**: Convert PDF to PNG first: `from pdf2image import convert_from_path`
+- **Solution**: Use PNG output format for quality checks
+
+**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/tikz_guide.md`** - Complete TikZ syntax, positioning, styles, and techniques
+- **`references/diagram_types.md`** - Catalog of scientific diagram types with examples
+- **`references/best_practices.md`** - Publication standards and accessibility guidelines
+- **`references/python_libraries.md`** - Guide to Schemdraw, NetworkX, and Matplotlib for diagrams
+
+### External Resources
+
+**TikZ and LaTeX**
+- TikZ & PGF Manual: https://pgf-tikz.github.io/pgf/pgfmanual.pdf
+- TeXample.net: http://www.texample.net/tikz/ (examples gallery)
+- CircuitikZ Manual: https://ctan.org/pkg/circuitikz
+
+**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** - Reuse TikZ styles for poster diagrams
+- **Research Grants** - Methodology diagrams for proposals
+- **Peer Review** - Evaluate diagram clarity and accessibility
+
+## Quick Reference Checklist
+
+Before submitting diagrams, verify:
+
+### Visual Quality
+- [ ] Vector format (PDF/SVG) or 300+ DPI raster
+- [ ] No overlapping elements (verified by quality checker)
+- [ ] Adequate spacing between all components
+- [ ] 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
+
+Use this skill to create clear, accessible, publication-quality diagrams that effectively communicate complex scientific concepts. The integrated quality verification workflow ensures all diagrams meet professional standards before publication.
+