run_ConvertToTiff

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Exports imaging data to .TIF files.

Description

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This function exports imaging data created in umIT to a multi-frame .TIF file. For 3D datasets, the function will create a single .TIF file containing the image series. For image time series split by trials (4D arrays with dimensions E,Y,X,T), a .TIF file will be created for each trial. This function does not have optional parameters.

Output

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For 3D data:
A multi-frame .TIF file will be created in the SaveFolder with the name of the .dat file prepended with the string 'img_'. For instance, the .TIF file from the file fluo.dat will be named img_fluo.tif.

For 4D data:
One multi-frame .TIF file will be created in the SaveFolder for each trial. the filename will be appended with the condition (C) and repetition(R) indices as so: 'img_<FILENAME>_C<index>_R<index>.tif'. For example, for a recording with name DF_F.dat with one condition and 10 repetitions the TIF files will be created as so: img_DF_F_C1_R1.tif, img_DF_F_C1_R2.tif, ..., img_DF_F_C1_R10.tif.

Default output file name

The output file name of this function is extracted from the variable datFile stored in the .mat meta data file associated with the .dat file. In the eventuality that this variable is empty, a default filename 'img_out.tif' will be used.

The algorithm

This function uses the code from this Git repo to write to TIF files. As stated in their documentation: the algorithm writes "the image data first, and end the file with IFD's". The accepted data formats are: uint8, uint16 and single precision. No compression is applied.