cellfinder documentation


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).

Detected labelled cells, overlaid on a segmented coronal brain section

It's a work in progress, but 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


To run the cell detection just do:

cellfinder -s signal_channel_images optional_signal_channel_images -b background_channel_images -o /path/to/output_directory -x 2 -y 2 -z 5

For more information and other options or analysis see Getting started