title: moco: Fast Motion Correction for Calcium Imaging.
abstract: Motion correction is the first step in a pipeline of algorithms to analyze calcium imaging videos and extract biologically relevant information, for example the network structure of the neurons therein. Fast motion correction is especially critical for closed-loop activity triggered stimulation experiments, where accurate detection and targeting of specific cells in necessary. We introduce a novel motion-correction algorithm which uses a Fourier-transform approach, and a combination of judicious downsampling and the accelerated computation of many L 2 norms using dynamic programming and two-dimensional, fft-accelerated convolutions, to enhance its efficiency. Its accuracy is comparable to that of established community-used algorithms, and it is more stable to large translational motions. It is programmed in Java and is compatible with ImageJ.
authors.affiliation: Departments of Mathematics and CSE, University of Michigan Ann Arbor, MI, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Dubbs
authors.affiliation: Neurotechnology Center, Department of Biological Sciences, Columbia University New York, NY, USA.
authors.forename: James
authors.initials: J
authors.lastname: Guevara
authors.affiliation: Neurotechnology Center, Department of Biological Sciences, Columbia University New York, NY, USA.
authors.forename: Rafael
authors.initials: R
authors.lastname: Yuste
keywords: Machine Vision Algorithms 150.1135; calcium imaging; dynamic programming; fourier transform; mesoscale neuroscience; motion correction