Neural network imaging

3D Random-access point scanning

The Femto3D Atlas enables the spatial and temporal complexity of neuronal coding to be resolved by scanning distributed points as regions of interest (ROIs) in a large 3D volume. The high speed of random-access point scanning (30 kHz/ROI) facilitates to measure several thousand cells near-simultaneously by restricting the imaging to sub-regions of the 3D volume. The Cell3DFinder software module finds cell centers in 3D image stacks automatically and can display them as a set of points. Ratio imaging software module allows real-time ratio metric analysis by calculating relative fluorescence, and contains also batch analysis tools. The figure (A-D) shows the changes in Ca2+ concentration of 2000 cells from the visual cortex of a GCaMP-expressing mouse as a function of time. See more Wertz et al., Science, 2015; Katona et al., Nat Meth, 2012.

3D Chessboard scanning

Chessboard scanning allows scanning of small squares located anywhere in a near cubic millimeter volume. The squares include the somata with the surrounding area, therefore this scanning mode allows preserving the fluorescence during motions caused by vessel pulsing, respiration, locomotion, or behavior and using the data for motion correction. The scanning speed can reach the 3 kHz and up to 300 somata can be measured simultaneously. Fluent software interface allows real-time visualization of the recorded 3D fluorescent data. Using direct data access and MATLAB’s 3D rendering capabilities, any custom 3D visualization or animation can be easily constructed. The figure shows in vivo neuronal activity, Ca2+ transients from 100 neuronal somata from the mouse V1 region, labeled with GCaMP6. See also Szalay et al., Neuron, 2016.



3D Multi-cube scanning

Multi-cube scanning is a spatially extended mode of chessboard scanning, where a Z dimension is added to the aforementioned squares to cover the whole extent of the somata, therefore preserving all fluorescent information even during large amplitude movements. Figure shows simultaneous measurements of 10 GCaMP6-labeled somata. The ROIs were ordered next to each other for visualization, and transients were derived from each cube using small sub volumes. The imaging was performed from 8.2 up to 25.2 Hz using relatively large cubes (each cube was between 46 x 14 x 15 voxels and 46 x 32 x 20 voxels, where one voxel was 1.5 x 3 x 4 µm and 1.5 x 1.5 x 4 µm). This spatial and temporal resolution made it possible to resolve the subcellular Ca2+ dynamic. The measurement can be improved: for example, 50 somata can be recorded at 50 Hz when using cubes made of 50 x 10 x 5 voxels. Szalay et al., Neuron, 2016.



We want to open new perspectives in microscopic imaging

The best of our knowledge was poured into the Femto3D AcoustoOptic microscope and the exceptional measurement and analysis software package that enables scientists to reveal 3D neural networks and dendritic activities in the brain of awake animal models during behavior.

Follow Us