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CaImAn

version 1.0.0.0 (33.7 MB) by Eftychios Pnevmatikakis
Complete Matlab pipeline for large scale calcium imaging data analysis

9 Downloads

Updated 16 Jun 2018

From GitHub

View license on GitHub

Matlab implementation of a source extraction and spike inference algorithm for large scale calcium imaging data analysis, based on a constrained matrix factorization approach (CNMF).

Cite As

Eftychios Pnevmatikakis (2021). CaImAn (https://github.com/flatironinstitute/CaImAn-MATLAB), GitHub. Retrieved .

Comments and Ratings (8)

Yojet Sharma

How to use this through matlab?

Jun Li

yuan yuan

Mao Ye

Suresh Kumar Jetti

I was trying to test the demo_dendritic code using the example data. I came across errors about lars_regression and spatial_comments. Trying to figure out the errors. Any suggestions would be great to know. Here is the error:

Error using lars_regression_noise (line 217)
An UndefinedFunction error was thrown on the workers for 'cvx_begin'. This might be because the file containing 'cvx_begin' is not accessible on the
workers. Use addAttachedFiles(pool, files) to specify the required files to be attached. See the documentation for 'parallel.Pool/addAttachedFiles'
for more details.

Error in update_spatial_components (line 127)
parfor px = 1:siz_row(nthr)

Error in demo_dendritic (line 64)
[A,b,Cin] = update_spatial_components(Yr,Cin,fin,Ain,P,options);

Caused by:
Undefined function 'cvx_begin' for input arguments of type 'char'.

Suresh Kumar Jetti

Excellent tool for analyzing calcium imaging data. However, there were several problems with the demo_dendritric codes. Would be great if someone help regarding it.

Putaro

fantastic!
can't wait axonal imaging ver.

Putaro

MATLAB Release Compatibility
Created with R2015a
Compatible with any release
Platform Compatibility
Windows macOS Linux
Acknowledgements

Inspired: Catrex GUI

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3D

@CNMF

Sources2D

deconvolution

deconvolution/MCMC

deconvolution/MCMC/utilities

deconvolution/examples

deconvolution/functions

deconvolution/oasis

endoscope

endoscope/cnmfe_scripts

endoscope/demos

tests

use_cases/2016_CSHL_Imaging

use_cases/2017_CSHL_NeuralDataScience

use_cases/2017_CajalCourse

utilities

utilities/GUI

utilities/memmap

use_cases/2017_CSHL_NeuralDataScience

use_cases/outdated/live scripts