Cellfinder is a collection of tools from the Margrie Lab and others at the Sainsbury Wellcome Centre for the analysis of whole-brain imaging data such as serial-section imaging and lightsheet imaging in cleared tissue.

The aim is to provide a single solution for:
  • Cell detection (initial cell candidate detection and refinement using deep learning implemented in Keras)

  • Atlas registration (using aMAP)

  • Analysis of cell positions in a common space