Topic: volumetric cell extraction

Introduction: Spontaneous activity in visual cortex is high-dimensional and state-dependent, yet its organizing principles are unclear (Stringer et al. Science 2019; Berkes et al. Science 2011). We combine large-scale imaging, modelling, and theory to ask: 1. Does spontaneous activity share the structure of evoked activity? 2. Is spontaneous activity organized spatially? Methods: We constructed a modified Light Beads Microscope (Demas et al. Nature Methods 2021) to image Ca2+ transients in excitatory neurons from large volumes. We developed an open-source, GPU-accelerated volumetric cell extra

[Aims] Neurons in mouse visual cortex encode high-dimensional sensory information and lower-dimensional behavioral variables. Here we asked how behavioral signals are organized across the cortical volume, and whether they follow the organization of visual activity.[Methods] We used Light Beads Microscopy (Demas et al, 2021) to functionally image Ca2+ transients at cellular resolution from large volumes of cortex (3 x 3 x 0.5 mm^3) in awake, headfixed transgenic mice expressing GCaMP6s. To segment individual cells, we developed a novel volumetric cell extraction pipeline by accelerating and ext