Send to

Choose Destination
Front Neuroinform. 2016 Feb 16;10:6. doi: 10.3389/fninf.2016.00006. eCollection 2016.

moco: Fast Motion Correction for Calcium Imaging.

Author information

Departments of Mathematics and CSE, University of Michigan Ann Arbor, MI, USA.
Neurotechnology Center, Department of Biological Sciences, Columbia University New York, NY, USA.


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.


Machine Vision Algorithms 150.1135; calcium imaging; dynamic programming; fourier transform; mesoscale neuroscience; motion correction

Supplemental Content

Full text links

Icon for Frontiers Media SA Icon for PubMed Central
Loading ...
Support Center