moco: Fast Motion Correction for Calcium Imaging

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 expe...

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Bibliographic Details
Published in:Frontiers in neuroinformatics Vol. 10; p. 6
Main Authors: Dubbs, Alexander, Guevara, James, Yuste, Rafael
Format: Journal Article
Language:English
Published: Switzerland Frontiers Research Foundation 16.02.2016
Frontiers Media S.A
Subjects:
Algorithms
Calcium imaging
Conflicts of interest
Dynamic Programming
Fourier Transform
Fourier transforms
Information processing
Mesoscale Neuroscience
Microscopy
Motion Correction
Neurons
Neuroscience
United States > US
dynamic programming
Machine Vision Algorithms 150.1135
motion correction
calcium imaging
fourier transform
mesoscale neuroscience
ISSN:1662-5196, 1662-5196
Online Access:Get full text
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Summary: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.
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Reviewed by: Steve Poelzing, Virginia Tech, USA; Shaoqun Zeng, HUST, China
Edited by: Qingming Luo, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, China
ISSN:1662-5196
1662-5196
DOI:10.3389/fninf.2016.00006