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).

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


pip install cellfinder

For more detailed instructions, see the documentation or ask a question


We’re interested in supporting as many applications as possible. If you have ideas, or want to contribute please get in touch or raise an issue on the GitHub repository