A Dedicated Light Sheet Fluorescence Microscopy Atlas for Mapping Neuronal Activity and Genetic Markers in the Mouse Brain

  • Johanna Perens (Guest lecturer)

Activity: Talks and presentationsConference presentations


The brain is the most complex organ in the body consisting of billions of neurons that are connected in a complex functional network of both long and short distance activating or inhibitory signals over long distances. Registration of anatomical features, neuronal connectivity and genetic markers into a common coordinate framework (CCF) has therefore greatly improved our understanding of the brain but also highlighted the spatial complexity and the need for high quality 3D reference maps.
In mice, Allen’s Institute of Brain Science has pioneered this effort by generating annotated average brain atlases based on Nissl staining’s and two-photon microscopy images. However, due to differences in tissue processing such atlases are not always suitable for registration of data obtained using other imaging modalities. Therefore, we developed a digital mouse brain atlas for automated analysis of intact iDISCO cleared brains scanned with light sheet fluorescence microscopy (LSFM).
The digital LSFM mouse brain atlas incorporates a variational average LSFM mouse brain image with 20 µm isotropic resolution, which was generated from LSFM autofluorescence images of 162 individual mice brains, and anatomical annotations of the brain regions. The variational LSFM mouse brain image was created through iterative multi-resolution image registration algorithm in order to avoid the bias towards a chosen reference brain and account for morphological differences between individual mouse brains. Anatomical annotations were imported from the Allen’s CCFv3 and aligned to the average LSFM mouse brain by dividing the brain areas into five parental regions and registering them separately to the average image.
In order to demonstrate the applicational value of our LSFM atlas we map physiological changes in the neuronal activity marker c-Fos in response to fasting and re-feeding. In correspondence with previously published data, whole brain quantification of the c-Fos activity show significant increases in the brain stem and hypothalamus.
Period1 Sept 20192 Sept 2019
Event title2019 International Neuroinformatics Coordinating Facility. Annual Congress
Event typeConference
LocationWarsaw, PolandShow on map