Please use the online documentation website going forward: https://bahanonu.github.io/ciatah/

Inscopix

Documentation related to Inscopix-specific functions on the repository.

Converting ISXD files to HDF5

To convert ISXD files to HDF5, see convertInscopixIsxdToHdf5 function in the inscopix folder or modelDownsampleRawMovies module in calciumImagingAnalysis.

Note: By default the Inscopix API gives out a frame full of 0s for dropped frames. So those 0s frames are maintained after converting/downsampling to HDF5 or you will also get a frame with 0s if you use loadMovieList to read frames that were dropped from isxd files. Adjust analysis accordingly.

To use this function call it as below:

moviePath = 'PATH_TO_ISXD';
opts.maxChunkSize = 5000; % Max chunk size in Mb to load into RAM.
opts.downsampleFactor = 4; % How much to downsample original movie, set to 1 for no downsampling.
convertInscopixIsxdToHdf5(moviePath,'options',opts);

If you want to save to a custom folder, use saveFolder input.

moviePath = 'PATH_TO_ISXD';
opts.maxChunkSize = 5000; % Max chunk size in Mb to load into RAM.
opts.downsampleFactor = 4; % How much to downsample original movie, set to 1 for no downsampling.
opts.saveFolder = 'ALT_FOLDER_PATH'; % Char: alternative file path
convertInscopixIsxdToHdf5(moviePath,'options',opts);

The same functionality can be achieved by loading a calciumImagingAnalysis module using the below commands. By default modelDownsampleRawMovies module will see .isxd files and call convertInscopixIsxdToHdf5. This can be done on multiple folders by separating them with commas in the modelDownsampleRawMovies menu.

obj = calciumImagingAnalysis;
obj.modelDownsampleRawMovies;