Research project
Human Brain Heatmap Generator
A Python tool for generating publication-quality SVG and PNG heatmaps from brain anatomical templates. Supports intensity and density visualisations across Brodmann areas with scientific colour palettes including magma and viridis.
- My role
- Solo Developer
- Duration
- 3 weeks
- Discipline
- Research project
- Year
- 2024
Project Overview
A command-line Python tool that generates publication-quality brain region heatmaps from synaptome data. Used to create figures for published neuroscience research papers, transforming numerical data into visual representations overlaid on anatomical brain templates.
Project Details
Technologies Used
- Python 3
- CairoSVG (SVG rendering)
- PIL/Pillow (image processing)
- NumPy (data processing)
- Matplotlib colour maps (magma, viridis, inferno)
Key Features
- Dual Visualisation Modes: Intensity-based and density-based colour gradients
- Brodmann Area Mapping: Precise anatomical region identification and colouring
- Scientific Colour Palettes: Perceptually uniform colour maps (magma, viridis) for accurate data representation
- Scale Bar Generation: Automatic colour scale bars with min/max labels for publication figures
- SVG to PNG Pipeline: High-resolution SVG rendering to publication-quality PNG
- Batch Processing: Process multiple datasets and generate comparative visualisations
Technical Highlights
- Template-Based Rendering: Parses SVG brain atlas templates and dynamically applies colours based on data values
- Colour Normalisation: Proper min-max normalisation across brain regions for accurate scientific representation
- Publication Quality: Output designed to meet journal figure requirements — high DPI, clean labels, consistent styling
Impact
Heatmaps generated by this tool have been used in published research figures, providing visual evidence for synaptome architecture findings across different brain regions.