Video rate volumetric Ca2+ imaging across cortical layers using Seeded Iterative Demixing (SID) microscopy

Light-field microscopy (LFM) is a scalable approach for volumetric Ca 2+ imaging with the highest volumetric acquisition rates (up to 100 Hz). While this has enabled high-speed whole-brain Ca 2+ imaging in small semi-transparent specimen, tissue scattering has limited its application in the rodent brain. Here we introduce Seeded Iterative Demixing (SID), a computational source extraction technique that extends LFM to the scattering mammalian cortex. Using GCaMP-expressing mice we demonstrate SID’s ability to capture neuronal dynamics in vivo within a volume of 900×900×260μm located as deep as 380 μm in the mouse cortex and hippocampus at 30 Hz volume rate while faithfully discriminating signals from neurons as close as 20 μm, at three orders of magnitude reduced computational cost. The simplicity and scalability of LFM, coupled with the performance of SID opens up a range of new applications including closed-loop experiments and is expected to propel its wide dissemination within the neuroscience community.