Inscopix¶
Documentation related to Inscopix-specific functions on the repository.
Visualizing ISXD files¶
ISXD files can be directly visualized from disk by running playMovie
from MATLAB command line:
playMovie('path\to\youMovie.isxd');
Converting ISXD files to HDF5¶
To convert ISXD files to HDF5, see convertInscopixIsxdToHdf5
function in the inscopix
folder or modelDownsampleRawMovies
module in CIAtah.
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 CIAtah
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 = ciatah;
obj.modelDownsampleRawMovies;