Spatially downsample raw movies or convert to HDF5 with modelDownsampleRawMovies

Users have the ability to spatially downsample raw movies, often necessary to denoise the data, save storage space, and improve runtimes of later processing steps. For most data, users can downsample 2 or 4 times in each spatial dimension while still retaining sufficient pixels per cell to facilitate cell-extraction.

To run, either select modelDownsampleRawMovies in the GUI menu or type the below command after initializing a CIAtah obj.

obj.modelDownsampleRawMovies;

This will pop-up the following screen. Users can - input several folders where ISXD files are by separating each folder path with a comma (Folder(s) where raw HDF5s are located), - specify a common root folder to save files to (Folder to save downsampled HDF5s to:), - and input a root directory that contains the sub-folders with the raw data (Decompression source root folder(s)). The function will automatically put each file in its corresponding folder, make sure folder names are unique (this should be done anyways for data analysis reasons).

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Converting Inscopix ISXD files to HDF5

To convert from Inscopix ISXD file format (output by nVista v3+ and nVoke) to HDF5 run modelDownsampleRawMovies without changing the regular expression or make sure it looks for .*.isxd or similar. Users will need the latest version of the Inscopix Data Processing Software as these functions take advantage of their API. If CIAtah cannot automatically find the API, it will ask the user to direct it to the root location of the Inscopix Data Processing Software (see below).

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