c-Fos expression levels were quantified from whole mouse-brain serial two-photon tomography data by automatically detecting somata and mapping them to different brain regions (resolution: 0.9 × 0.9 × 10 µm³)1. More than 1.8 million somata were automatically segmented. Quality scoring yielded an F1 score of greater than 0.97 and a false merger rate of less than 5% for both low- and high-density regions. In the first step, somata were detected individually and then mapped to the regions of a neuroanatomical reference atlas2. The video above is a visualization of the soma segmentation, color-coded per region (scale bar represents 1.4 mm).

Below: Soma visualization and navigation with our KNOSSOS plugin.

1 Mice whole-brain serial two-photon tomography stacks were prepared by Hassana Oyibo and Georg Keller (Friedrich Miescher Institute for Biomedical Research).

2 The Allen Reference Atlas: A digital color brain atlas of the C57Bl/6J male mouse (Reference Atlas, Version (2011)), Dong HW (2008). Wiley, Chichester