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

Analysing cell distributions
Analysing cell distributions in the brain with napari

Retraining cellfinder
Retraining the cellfinder cell classification network in napari

Atlas download
Download an atlas with 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

Aligning samples
Aligning samples to image axes for template building (experimental!)
