Automated 3D cell detection and registration of whole-brain images


cellfinder is software from the Margrie Lab at the Sainsbury Wellcome Centre, UCL for automated 3D cell detection and registration of whole-brain images (e.g. serial two-photon or lightsheet imaging).

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


cellfinder takes a stitched, but otherwise raw whole-brain dataset with at least two channels:

  • Background channel (i.e. autofluorescence)
  • Signal channel, the one with the cells to be detected:

raw Raw coronal serial two-photon mouse brain image showing labelled cells

Cell candidate detection

Classical image analysis (e.g. filters, thresholding) is used to find cell-like objects (with false positives):

raw Candidate cells (including many artefacts)

Cell candidate classification

A deep-learning network (ResNet) is used to classify cell candidates as true cells or artefacts:

raw Cassified cell candidates. Yellow - cells, Blue - artefacts

Registration and segmentation (brainreg)

Using brainreg, cellfinder aligns a template brain and atlas annotations (e.g. the Allen Reference Atlas, ARA) to the sample allowing detected cells to be assigned a brain region.

This transformation can be inverted, allowing detected cells to be transformed to a standard anatomical space.

raw ARA overlaid on sample image

Analysis of cell positions in a common anatomical space

Registration to a template allows for powerful group-level analysis of cellular disributions. (Example to come)


pip install cellfinder

For more detailed instructions, see the documentation or ask a question.


We’re interested in supporting as many applications as possible. If you have ideas, or want to contribute please get in touch or raise an issue on the GitHub repository.