gh-k-dense-ai-claude-scientific-writer-claude-scientific-writer/skills/scientific-schematics/references/best_practices.md

Best Practices for Scientific Diagrams

Overview

This guide provides publication standards, accessibility guidelines, and best practices for creating high-quality scientific diagrams that meet journal requirements and communicate effectively to all readers.

Publication Standards

1. File Format Requirements

Vector Formats (Preferred)

• PDF: Universal acceptance, preserves quality, works with LaTeX

  • Use for: Line drawings, flowcharts, block diagrams, circuit diagrams
  • Advantages: Scalable, small file size, embeds fonts
  • Standard for LaTeX workflows

• EPS (Encapsulated PostScript): Legacy format, still accepted

  • Use for: Older publishing systems
  • Compatible with most journals
  • Can be converted from PDF

• SVG (Scalable Vector Graphics): Web-friendly, increasingly accepted

  • Use for: Online publications, interactive figures
  • Can be edited in vector graphics software
  • Not all journals accept SVG

Raster Formats (When Necessary)

• TIFF: Professional standard for raster graphics

  • Use for: Microscopy images, photographs combined with diagrams
  • Minimum 300 DPI at final print size
  • Lossless compression (LZW)

• PNG: Web-friendly, lossless compression

  • Use for: Online supplementary materials, presentations
  • Minimum 300 DPI for print
  • Supports transparency

Never Use

• JPEG: Lossy compression creates artifacts in diagrams
• GIF: Limited colors, inappropriate for scientific figures
• BMP: Uncompressed, unnecessarily large files

2. Resolution Requirements

Vector Graphics

• Infinite resolution (scalable)
• Recommended: Always use vector when possible

Raster Graphics (when vector not possible)

• Publication quality: 300-600 DPI
• Line art: 600-1200 DPI
• Web/screen: 150 DPI acceptable
• Never: Below 300 DPI for print

Calculating DPI

DPI = pixels / (inches at final size)

Example:
Image size: 2400 × 1800 pixels
Final print size: 8 × 6 inches
DPI = 2400 / 8 = 300 ✓ (acceptable)

3. Size and Dimensions

Journal-Specific Column Widths

• Nature: Single column 89 mm (3.5 in), Double 183 mm (7.2 in)
• Science: Single column 55 mm (2.17 in), Double 120 mm (4.72 in)
• Cell: Single column 85 mm (3.35 in), Double 178 mm (7 in)
• PLOS: Single column 83 mm (3.27 in), Double 173 mm (6.83 in)
• IEEE: Single column 3.5 in, Double 7.16 in

Best Practices

• Design at final print size (avoid scaling)
• Use journal templates when available
• Allow margins for cropping
• Test appearance at final size before submission

4. Typography Standards

Font Selection

• Recommended: Arial, Helvetica, Calibri (sans-serif)
• Acceptable: Times New Roman (serif) for mathematics-heavy
• Avoid: Decorative fonts, script fonts, system fonts that may not embed

Font Sizes (at final print size)

• Minimum: 6-7 pt (journal dependent)
• Axis labels: 8-9 pt
• Figure labels: 10-12 pt
• Panel labels (A, B, C): 10-14 pt, bold
• Main text: Should match manuscript body text

Text Clarity

• Use sentence case: "Time (seconds)" not "TIME (SECONDS)"
• Include units in parentheses: "Temperature (°C)"
• Spell out abbreviations in figure caption
• Avoid rotated text when possible (exception: y-axis labels)

5. Line Weights and Strokes

Recommended Line Widths

• Diagram outlines: 0.5-1.0 pt
• Connection lines/arrows: 1.0-2.0 pt
• Emphasis elements: 2.0-3.0 pt
• Minimum visible: 0.25 pt at final size

Consistency

• Use same line weight for similar elements
• Vary line weight to show hierarchy
• Avoid hairline rules (too thin to print reliably)

Accessibility and Colorblindness

1. Colorblind-Safe Palettes

Okabe-Ito Palette (Recommended) Most distinguishable by all types of colorblindness:

% RGB values
Orange:     #E69F00 (230, 159,   0)
Sky Blue:   #56B4E9 ( 86, 180, 233)
Green:      #009E73 (  0, 158, 115)
Yellow:     #F0E442 (240, 228,  66)
Blue:       #0072B2 (  0, 114, 178)
Vermillion: #D55E00 (213,  94,   0)
Purple:     #CC79A7 (204, 121, 167)
Black:      #000000 (  0,   0,   0)

Alternative: ColorBrewer Palettes

• Qualitative: Set2, Paired, Dark2
• Sequential: Blues, Greens, Oranges (avoid Reds/Greens together)
• Diverging: RdBu (Red-Blue), PuOr (Purple-Orange)

Colors to Avoid Together

• Red-Green combinations (8% of males cannot distinguish)
• Blue-Purple combinations
• Yellow-Light green combinations

2. Redundant Encoding

Don't rely on color alone. Use multiple visual channels:

Shape + Color

Circle + Blue   = Condition A
Square + Orange = Condition B
Triangle + Green = Condition C

Line Style + Color

Solid + Blue = Treatment 1
Dashed + Orange = Treatment 2
Dotted + Green = Control

Pattern Fill + Color

Solid fill + Blue = Group A
Diagonal stripes + Orange = Group B
Cross-hatch + Green = Group C

3. Grayscale Compatibility

Test Requirement: All diagrams must be interpretable in grayscale

Strategies

• Use different shades (light, medium, dark)
• Add patterns or textures to filled areas
• Vary line styles (solid, dashed, dotted)
• Use labels directly on elements
• Include text annotations

Grayscale Test

# Convert to grayscale to test
convert diagram.pdf -colorspace gray diagram_gray.pdf

4. Contrast Requirements

Minimum Contrast Ratios (WCAG Guidelines)

• Normal text: 4.5:1
• Large text (≥18pt): 3:1
• Graphical elements: 3:1

High Contrast Practices

• Dark text on light background (or vice versa)
• Avoid low-contrast color pairs (yellow on white, light gray on white)
• Use black or dark gray for critical text
• White text on dark backgrounds needs larger font size

5. Alternative Text and Descriptions

Figure Captions Must Include

• Description of diagram type
• All abbreviations spelled out
• Explanation of symbols and colors
• Sample sizes (n) where relevant
• Statistical annotations explained
• Reference to detailed methods if applicable

Example Caption "Participant flow diagram following CONSORT guidelines. Rectangles represent study stages, with participant numbers (n) shown. Exclusion criteria are listed beside each screening stage. Final analysis included n=350 participants across two groups."

Design Principles

1. Simplicity and Clarity

Occam's Razor for Diagrams

• Remove every element that doesn't add information
• Simplify complex relationships
• Break complex diagrams into multiple panels
• Use consistent layouts across related figures

Visual Hierarchy

• Most important elements: Largest, darkest, central
• Supporting elements: Smaller, lighter, peripheral
• Annotations: Minimal, clear labels only

2. Consistency

Within a Figure

• Same shape/color represents same concept
• Consistent arrow styles for same relationships
• Uniform spacing and alignment
• Matching font sizes for similar elements

Across Figures in a Paper

• Reuse color schemes
• Maintain consistent node styles
• Use same notation system
• Apply same layout principles

3. Professional Appearance

Alignment

• Use grids for node placement
• Align nodes horizontally or vertically
• Evenly space elements
• Center labels within shapes

White Space

• Don't overcrowd diagrams
• Leave breathing room around elements
• Use white space to group related items
• Margins around entire diagram

Polish

• No jagged lines or misaligned elements
• Smooth curves and precise angles
• Clean connection points
• No overlapping text

Common Pitfalls and Solutions

Pitfall 1: Overcomplicated Diagrams

Problem: Too much information in one diagram Solution:

• Split into multiple panels (A, B, C)
• Create overview + detailed diagrams
• Move details to supplementary figures
• Use hierarchical presentation

Pitfall 2: Inconsistent Styling

Problem: Different styles for same elements across figures Solution:

• Create and use style templates
• Use the same color palette throughout
• Document your style choices

Pitfall 3: Poor Label Placement

Problem: Labels overlap elements or are hard to read Solution:

• Place labels outside shapes when possible
• Use leader lines for distant labels
• Rotate text only when necessary
• Ensure adequate contrast with background

Pitfall 4: Tiny Text

Problem: Text too small to read at final print size Solution:

• Design at final size from the start
• Test print at final size
• Minimum 7-8 pt font
• Simplify labels if space is limited

Pitfall 5: Ambiguous Arrows

Problem: Unclear what arrows represent or where they point Solution:

• Use different arrow styles for different meanings
• Add labels to arrows
• Include legend for arrow types
• Use anchor points for precise connections

Pitfall 6: Color Overuse

Problem: Too many colors, confusing or inaccessible Solution:

• Limit to 3-5 colors maximum
• Use color purposefully (categories, emphasis)
• Stick to colorblind-safe palette
• Provide redundant encoding

Quality Control Checklist

Before Submission

Technical Requirements

• Correct file format (PDF/EPS preferred for diagrams)
• Sufficient resolution (vector or 300+ DPI)
• Appropriate size (matches journal column width)
• Fonts embedded in PDF
• No compression artifacts

Accessibility

• Colorblind-safe palette used
• Works in grayscale (tested)
• Text minimum 7-8 pt at final size
• High contrast between elements
• Redundant encoding (not color alone)

Design Quality

• Elements aligned properly
• Consistent spacing and layout
• No overlapping text or elements
• Clear visual hierarchy
• Professional appearance

Content

• All elements labeled
• Abbreviations defined
• Units included where relevant
• Legend provided if needed
• Caption comprehensive

Consistency

• Matches other figures in style
• Same notation as text
• Consistent with journal guidelines
• Cross-references work

Journal-Specific Guidelines

Nature

Figure Requirements

• Size: 89 mm (single) or 183 mm (double column)
• Format: PDF, EPS, or high-res TIFF
• Fonts: Sans-serif preferred
• File size: <10 MB per file
• Resolution: 300 DPI minimum for raster

Style Notes

• Panel labels: lowercase bold (a, b, c)
• Simple, clean design
• Minimal colors
• Clear captions

Science

Figure Requirements

• Size: 55 mm (single) or 120 mm (double column)
• Format: PDF, EPS, TIFF, or JPEG (high quality)
• Resolution: 300 DPI for photos, 600 DPI for line art
• File size: <10 MB
• Fonts: 6-7 pt minimum

Style Notes

• Panel labels: capital bold (A, B, C)
• High contrast
• Readable at small size

Cell

Figure Requirements

• Size: 85 mm (single) or 178 mm (double column)
• Format: PDF preferred, TIFF, EPS acceptable
• Resolution: 300 DPI minimum
• Fonts: 8-10 pt for labels
• Line weight: 0.5 pt minimum

Style Notes

• Clean, professional
• Color or grayscale
• Panel labels capital (A, B, C)

IEEE

Figure Requirements

• Size: 3.5 in (single) or 7.16 in (double column)
• Format: PDF, EPS (vector preferred)
• Resolution: 600 DPI for line art, 300 DPI for halftone
• Fonts: 8-10 pt minimum
• Color: Grayscale in print, color in digital

Style Notes

• Follow IEEE Graphics Manual
• Standard symbols for circuits
• Technical precision
• Clear axis labels

Software-Specific Export Settings

AI-Generated Images

AI-generated diagrams are exported as PNG images and can be included in LaTeX documents using:

\includegraphics[width=\textwidth]{diagram.png}

Python (Matplotlib) Export

import matplotlib.pyplot as plt

# Set publication quality
plt.rcParams['font.family'] = 'sans-serif'
plt.rcParams['font.sans-serif'] = ['Arial']
plt.rcParams['font.size'] = 8
plt.rcParams['pdf.fonttype'] = 42  # TrueType fonts in PDF

# Save with proper DPI and cropping
fig.savefig('diagram.pdf', dpi=300, bbox_inches='tight', 
            pad_inches=0.1, transparent=False)
fig.savefig('diagram.png', dpi=300, bbox_inches='tight')

Schemdraw Export

import schemdraw

d = schemdraw.Drawing()
# ... build circuit ...

# Export
d.save('circuit.svg')  # Vector
d.save('circuit.pdf')  # Vector
d.save('circuit.png', dpi=300)  # Raster

Inkscape Command Line

# PDF to high-res PNG
inkscape diagram.pdf --export-png=diagram.png --export-dpi=300

# SVG to PDF
inkscape diagram.svg --export-pdf=diagram.pdf

Version Control Best Practices

Keep Source Files

• Save original .tex, .py, or .svg files
• Use descriptive filenames with versions
• Document color palette and style choices
• Include README with regeneration instructions

Directory Structure

figures/
├── source/          # Editable source files
│   ├── diagram1.tex
│   ├── circuit.py
│   └── pathway.svg
├── generated/       # Auto-generated outputs
│   ├── diagram1.pdf
│   ├── circuit.pdf
│   └── pathway.pdf
└── final/          # Final submission versions
    ├── figure1.pdf
    └── figure2.pdf

Git Tracking

• Track source files (.tex, .py)
• Consider .gitignore for generated PDFs (large files)
• Use releases/tags for submission versions
• Document generation process in README

Testing and Validation

Pre-Submission Tests

Visual Tests

1. Print test: Print at final size, check readability
2. Grayscale test: Convert to grayscale, verify interpretability
3. Zoom test: View at 400% and 25% to check scalability
4. Screen test: View on different devices (phone, tablet, desktop)

Technical Tests

1. Font embedding: Check PDF properties
2. Resolution check: Verify DPI meets requirements
3. File size: Ensure under journal limits
4. Format compliance: Verify accepted format

Accessibility Tests

1. Colorblind simulation: Use tools like Color Oracle
2. Contrast checker: WCAG contrast ratio tools
3. Screen reader: Test alt text (for web figures)

Tools for Testing

Colorblind Simulation

• Color Oracle (free, cross-platform)
• Coblis (Color Blindness Simulator)
• Photoshop/GIMP colorblind preview modes

PDF Inspection

# Check PDF properties
pdfinfo diagram.pdf

# Check fonts
pdffonts diagram.pdf

# Check image resolution
identify -verbose diagram.pdf

Contrast Checking

• WebAIM Contrast Checker: https://webaim.org/resources/contrastchecker/
• Colorable: https://colorable.jxnblk.com/

Summary: Golden Rules

1. Vector first: Always use vector formats when possible
2. Design at final size: Avoid scaling after creation
3. Colorblind-safe palette: Use Okabe-Ito or similar
4. Test in grayscale: Diagrams must work without color
5. Minimum 7-8 pt text: At final print size
6. Consistent styling: Across all figures in paper
7. Keep it simple: Remove unnecessary elements
8. High contrast: Ensure readability
9. Align elements: Professional appearance matters
10. Comprehensive caption: Explain everything

Further Resources

• Nature Figure Preparation: https://www.nature.com/nature/for-authors/final-submission
• Science Figure Guidelines: https://www.science.org/content/page/instructions-preparing-initial-manuscript
• WCAG Accessibility Standards: https://www.w3.org/WAI/WCAG21/quickref/
• Color Universal Design (CUD): https://jfly.uni-koeln.de/color/
• ColorBrewer: https://colorbrewer2.org/

Following these best practices ensures your diagrams meet publication standards and effectively communicate to all readers, regardless of colorblindness or viewing conditions.