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)
  • Register the image to an atlas (such as the Allen Mouse Brain Atlas)
  • Segment the brain based on the reference atlas
  • Calculate the volume of each brain area, and the number of labelled cells within it
  • Transform everything into standard space for analysis and visualisation
For more information see the website or GitHub repository


pip install cellfinder
For detailed instructions see Installation


For information on how to use cellfinder, see the User guide, or for a step-by step walkthrough, see the Tutorial.