Robust Estimation of Neural Signals in Calcium Imaging

Part of Advances in Neural Information Processing Systems 30 (NIPS 2017)

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Hakan Inan, Murat A. Erdogdu, Mark Schnitzer


Calcium imaging is a prominent technology in neuroscience research which allows for simultaneous recording of large numbers of neurons in awake animals. Automated extraction of neurons and their temporal activity from imaging datasets is an important step in the path to producing neuroscience results. However, nearly all imaging datasets contain gross contaminating sources which could originate from the technology used, or the underlying biological tissue. Although past work has considered the effects of contamination under limited circumstances, there has not been a general framework treating contamination and its effects on the statistical estimation of calcium signals. In this work, we proceed in a new direction and propose to extract cells and their activity using robust statistical estimation. Using the theory of M-estimation, we derive a minimax optimal robust loss, and also find a simple and practical optimization routine for this loss with provably fast convergence. We use our proposed robust loss in a matrix factorization framework to extract the neurons and their temporal activity in calcium imaging datasets. We demonstrate the superiority of our robust estimation approach over existing methods on both simulated and real datasets.