Explanation
These pages explain how the GUI works and why it works that way. Unlike the tutorials and how-to guides, they aren’t step-by-step instructions. They cover the concepts the GUI is built on, such as how a fit is calculated or how coordinates are defined. They’re especially useful when an alignment doesn’t behave as you expect, or when you’re deciding how to set up your own data.
The pages are grouped by topic:
- The alignment itself
How alignment works, from reference lines to a location for every channel.
- Positions in the brain
Coordinate systems, how bregma-relative and Allen CCF coordinates relate, and Brain region mappings, the three levels of detail the brain regions can be shown at.
- Organising your data
Shanks, probes and configurations, How session YAML paths are resolved, and Offline and online modes, working from local files or from the IBL Alyx database.
- The region prediction models
The channel prediction models, what the models predict, how to read their output, and their limits.