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BP: Fachverband Biologische Physik
BP 9: Bioimaging
BP 9.7: Vortrag
Dienstag, 6. September 2022, 11:15–11:30, H16
Extraction of Calcium Traces from Volumetric Lightsheet Images of 3D Neuron Ensembles — •Filippo Kiessler1, Paulina Wysmolek4, Katja Salbaum1,2, Elijah Shelton1, Selina Sonntag1, and Friedhelm Serwane1,2,3 — 1Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich — 2Graduate School of Systemic Neuroscience (GSN), Munich, Germany — 3Munich Cluster for Systems Neurology (SyNergy), Germany — 4Max Planck Institute for Medical Research, Heidelberg, Germany
In vitro systems resembling brain regions, such as brain organoids, are slowly changing the field of neuroscience. However, characterization of their electrical activity has remained a challenge as this requires electrophysiological readout in 3D at single-neuron resolution. We use a custom-built single-photon light-sheet microscope to record calcium activity in 3D neuron ensembles which we grow from mouse embryonic stem cells. To extract calcium intensities from the volumetric light-sheet data, we developed a custom software pipeline that augments the CaImAn software. Our pipeline includes a median filter to remove sample bleaching effects. In addition, typical artifacts arising from the illumination of of our light-sheet microscope are removed with a custom Fourier filter. With this setup we obtained connectivity graphs based on correlation of the extracted calcium traces. We envision this platform as a non-invasive toy-model to understand neuronal information generation and processing.