We propose an end-to-end image analysis pipeline based on the Adaptive Particle Representation (APR) for analyzing large 3D cleared tissue samples such as whole mouse brains or large human brain sections, achieving 100+ times faster computation. Our pipeline is compatible with real-time use, i.e. analysis can be done during acquisition. In addition to faster processing, using APR yields memory and storage compression ratios ranging from dozens to thousands depending on the labeling sparsity, saving costs on the storage and computing infrastructures.
We present a video-rate optical microscope that allows simultaneous imaging of two-photon excited fluorescence
(TPEF), second harmonic generation (SHG) and reflectance. The ms time resolution of the system together with its
submicrometer spatial resolution make it an ideal tool for studying fast neuronal activity and signaling, to understand
how action potentials are decoded molecularly. Transient trans-membrane potentials are measured with SHG, while the
evoked calcium oscillations are monitored with TPEF. The ability of this system to monitor both signals simultaneously
in multiple sub-compartments of living neurons should open the way to study how the electrical activity of neurons is
encoded intracellularly.
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