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Mesoscopic calcium imaging enables studies of cell-type specific neural activity over large areas. A growing body of literature suggests that neural activity can be different when animals are free to move compared to when they are restrained. Unfortunately, existing systems for imaging calcium dynamics over large areas in non-human primates (NHPs) are table-top devices that require restraint of the animal’s head. Here, we demonstrate an imaging device capable of imaging mesoscale calcium activity in a head-unrestrained male non-human primate. We successfully miniaturize our system by replacing lenses with an optical mask and computational algorithms. The resulting lensless microscope can fit comfortably on an NHP, allowing its head to move freely while imaging. We are able to measure orientation columns maps over a 20 mm²field-of-view in a head-unrestrained macaque. Our work establishes mesoscopic imaging using a lensless microscope as a powerful approach for studying neural activity under more naturalistic conditions.

 

Deep Learning (DL) has recently enabled unprecedented advances in one of the grand challenges in computational biology: the half-century-old problem of protein structure prediction. In this paper we discuss recent advances, limitations, and future perspectives of DL on five broad areas: protein structure prediction, protein function prediction, genome engineering, systems biology and data integration, and phylogenetic inference. We discuss each application area and cover the main bottlenecks of DL approaches, such as training data, problem scope, and the ability to leverage existing DL architectures in new contexts. To conclude, we provide a summary of the subject-specific and general challenges for DL across the biosciences.

 

DeepTensor is a computationally efficient framework for low-rank decomposition of matrices and tensors using deep generative networks. We decompose a tensor as the product of low-rank tensor factors where each low-rank tensor is generated by a deep network (DN) that is trained in a self-supervised manner to minimize the mean-square approximation error. Our key observation is that the implicit regularization inherent in DNs enables them to capture nonlinear signal structures that are out of the reach of classical linear methods like the singular value decomposition (SVD) and principal components analysis (PCA). We demonstrate that the performance of DeepTensor is robust to a wide range of distributions and a computationally efficient drop-in replacement for the SVD, PCA, nonnegative matrix factorization (NMF), and similar decompositions by exploring a range of real-world applications, including hyperspectral image denoising, 3D MRI tomography, and image classification.