cellfinder

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

Installation

pip install cellfinder

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

Contributing

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