cellfinder is software from the Margrie Lab at the Sainsbury Wellcome Centre for automated 3D cell detection and registration of whole-brain images (e.g. serial two-photon or lightsheet imaging).
The underlying cell detection algorithm is available for use (e.g. for use with other types of data) as a Python package (cellfinder-core) or as a Napari plugin.
Detected labelled cells, overlaid on a segmented coronal brain section
cellfinder can:
Detect labelled cells in 3D in whole-brain images (many hundreds of GB)