Neurosciences
Atlas Maker
Client - Neurome, Inc.
Dataset ingestion, contour authoring, XML export
(Circa 2004) Atlas Maker streamlines the creation of brain atlases by organizing serial sections, automating contour workflows, and packaging export-ready datasets for cross-lab collaboration on macOS and Windows.
Atlas Maker combines the ease of a photo-organizing interface with domain-specific authoring tools. Researchers can import serial sections from microscopes or scanners, annotate them with Bezier-based contours, and manage large datasets without losing track of progress or metadata.
Workflow Overview
The atlas creation process flows through datasets, thumbnails, sections, classification, normalization, and comparison.
Datasets
- Display NeuroMosaic or externally generated image sets
- Import from network sources and export to other formats
- Capture via attached video or TWAIN scanners
- Track species, strain, stain, and modeling phase metadata
Thumbnails
- Quick visual navigation inspired by iPhoto
- On-demand thumbnail generation with adjustable resolution
- Consistent overview of every file in the dataset
Sections
- View individual sections with layered contour overlays
- Authoring tools include selection, Bezier, vertex, transparency, and more
- All edits persist automatically to XML-based datasets
Classification
- Automatically convert unnamed contours into ROI masks
- Prompt authors to identify regions via pick lists or speech recognition
- Persist named ROIs back into the project dataset
- Maintain a 2D pixmap record for downstream analysis
