Analyzing large movies¶

Some movies are larger than the available RAM on users analysis computer. Below are several ways that the underlying functions in CIAPKG can be used to analyze large movies.

Playing large movies from disk¶

To directly and quickly visualize large or long movies from disk, directly input the movie path into playMovie as below.

% Full path to the movie
inputMoviePath = 'path/to/movie.h5';

playMovie(inputMoviePath);

Which will produce a GUI as below that will play the movie back.

ROI signal extraction¶

The below code is an example ROI signal extraction for large movie in chunks from disk after analyzing a small chunk with PCA-ICA to obtain reference masks. Modify inputMoviePath to a full path to your movie (HDF5, TIF, AVI, and ISXD supported).

% Full path to the movie
inputMoviePath = 'path/to/movie.h5';

%% =======PCA-ICA
% Run PCA-ICA on only a subset of frames.
% OPTIONS
    % Vector of frames to analyze for PCA-ICA
    framesToAnalyzePcaIca = 1:300;
    % Number of PCs and ICs to request
    nPCs = 250; nICs = 200;
[pcaicaAnalysisOutput] = ciapkg.signal_extraction.runPcaIca(inputMoviePath,nPCs,nICs,'frameList',framesToAnalyzePcaIca,'mu',0.1,'max_iter',1e3);

%% =======ROI extraction new version
% OPTIONS
    % Number of frames to chunk from movie when doing ROI estimation, to reduce RAM usage.
    movieChunks = 100;
% Normal PCA-ICA, binary masks
[roiSignals, ~] = ciapkg.signal_extraction.computeSignalsFromImages(pcaicaAnalysisOutput.IcaFilters,inputMoviePath,'frameList',[],'readMovieChunks',1,'threshold',0.4,'nFramesPerChunk',movieChunks,'weightSignalByImage',0);
% Weighted PCA-ICA, trace based on weighted pixel values of eahc ROI
[roiSignalsWeighted, ~] = ciapkg.signal_extraction.computeSignalsFromImages(pcaicaAnalysisOutput.IcaFilters,inputMoviePath,'frameList',[],'readMovieChunks',1,'threshold',0.4,'nFramesPerChunk',movieChunks,'weightSignalByImage',1);