A Computational toolbox for large scale Calcium Imaging Analysis* and behavioral analysis

Recent advances in calcium imaging acquisition techniques are creating datasets of the order of Terabytes/week. Memory and computationally efficient algorithms are required to analyze in reasonable amount of time terabytes of data. This projects implements a set of essential methods required in the calcium imaging movies analysis pipeline. Fast and scalable algorithms are implemented for motion correction, movie manipulation and source and spike extraction. CaImAn also contains some routine to the analyisi of behavior from video cameras. In summary, CaImAn provides a general purpose tool to handle large movies, with special emphasis tools for calcium imaging and behavioral datasets.

Features

Handling of very large datasets

Memory mapping
Frame-by-frame online processing (some functions)
opencv-based efficient movie playing and resizing
Motion correction

Fast parallelizable open-cv and fft-based motion correction of large movies
Run also in online mode (i.e. one frame at a time)
non rigid motion correction
Source extraction

identification of pixles associated to each neuron/neuronal structure
deals with heavily overlaping and neuroopil contaminated movies
separates different sources based on Nonnegative Matrix Factorization algorithms
Denoising, deconvolution and spike extraction

spikes can be inferred from fluorescence traces
also works in online mode (i.e. one sample at a time)
Behavioral Analysis (paper)

unsupervised algorithms based on optical flow and NMF to automatically extract motor kinetics
scales to large datasets since it exploits online dictionary learning (Mairal et. Al, link)
we also developed a tool for acquiring movies at high speed with low cost equipment (package)

Contributors:

Giovannucci, Andrea. Simons Foundation
Pnevmatikakis, Eftychios. Simons Foundation
Friedrich, Johannes. Columbia University and Janelia Farm
Cobos, Erick. Baylor College of Medicine
Staneva, Valentina. eScience Institute
Deverett, Ben. Princeton University
Kalfon, Jérémie. University of Kent , ECE paris
Please refer to the following wiki page or read in the testing section below.

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see [ Ссылка ].

Video from Sue Ann

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