{% hint style="danger" %} The cellfinder documentation has now moved here. These pages will no longer be updated {% endhint %}
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
{% hint style="info" %} For detailed instructions see Installation {% endhint %}
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
{% hint style="info" %} For more information and other options or analysis see Getting started {% endhint %}