An end-to-end recurrent compressed sensing method to denoise, detect and demix calcium imaging data

Two-photon calcium imaging provides large-scale recordings of neuronal activities at cellular resolution. A robust, automated and high-speed pipeline to simultaneously segment the spatial footprints of neurons and extract their temporal activity traces while decontaminating them from background, noise and overlapping neurons is highly desirable to analyze calcium imaging data. In this paper, we demonstrate DeepCaImX, an end-to-end deep learning method based on an iterative shrinkage-thresholding algorithm and a long-short-term-memory neural network to achieve the above goals altogether at a very high speed and without any manually tuned hyper-parameter. DeepCaImX is a multi-task, multi-class and multi-label segmentation method composed of a compressed-sensing-inspired neural network with a recurrent layer and fully connected layers. It represents the first neural network that can simultaneously generate accurate neuronal footprints and extract clean neuronal activity traces from calcium imaging data. We trained the neural network with simulated datasets and benchmarked it against existing state-of-the-art methods with in vivo experimental data. DeepCaImX outperforms existing methods in the quality of segmentation and temporal trace extraction as well as processing speed. DeepCaImX is highly scalable and will benefit the analysis of mesoscale calcium imaging.