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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).
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.
Detected labelled cells, overlaid on a segmented coronal brain section
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

1
pip install cellfinder
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For detailed instructions see Installation

Usage

For information on how to use cellfinder, see the User guide, or for a step-by step walkthrough, see the Tutorial.
Last modified 3mo ago
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