Many neurological and digestive diseases have been linked to dysfunctions of the Enteric Nervous System (ENS) or gut microbiome imbalances. However, to this day, no tool allows a comprehensive in-vivo interrogation of the ENS. To address this lack of such technology, we performed a complete characterization and monitoring of the ENS to design an optogenetic endomicroscope based on Optical Coherence Tomography, capable of in-vivo mapping the ENS's morphology and functionality as well as in-situ microbiota sampling. We anticipate that researchers and clinicians would benefit from such a device to gain new insights into the microbiota-gut-brain axis and improve standards of care.
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.
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