Tutorials#
Getting started#
Atlas visualisation
Visualise atlas data in napari
3D registration
Registering a whole-brain dataset to an atlas.
Track segmentation
Manually segmenting a 1d track.
Structure segmentation
Manually segmenting a 3d structure
3D cell detection
Detecting cells in 3D with cellfinder in napari
Retraining cellfinder
Retraining the cellfinder cell classification network in napari
Specific applications#
Probe segmentation
Analysis of silicon probe tracks (e.g. Neuropixels)
Bulk tracing analysis
Analyze and visualize bulk fluorescence tracing data
Cell detection via brainmapper
Whole brain cell detection and registration
