cellfinder documentation
The cellfinder documentation has now moved here. These pages will no longer be updated
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
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​
