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).

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​

Installation

pip install cellfinder

Usage

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