AUTHOR=Dubbs Alexander , Guevara James , Yuste Rafael 

TITLE=moco: Fast Motion Correction for Calcium Imaging

JOURNAL=Frontiers in Neuroinformatics

VOLUME=10

YEAR=2016

URL=https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2016.00006

DOI=10.3389/fninf.2016.00006

ISSN=1662-5196

ABSTRACT=<p>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 <italic>L</italic><sub>2</sub> 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.</p>