Introduction

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​

Installation

pip install cellfinder

Usage

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