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 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 L2 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.
Front. Neuroinform.