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

Whole brain cell detection and registration