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).
{% hint style="info" %} The underlying cell detection algorithm is available for use (e.g. for use with other types of data) as a Python package (cellfinder-core) or as a Napari plugin. {% endhint %}
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 %}
For information on how to use cellfinder, see the User guide, or for a step-by step walkthrough, see the Tutorial.