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By default, the lls command will generate a Deskewed folder that contains the complete deskewed data and a GPUdecon folder with a single file that contains the combined maximum-intensity projections for all time points and all channels that can be easily opened in ImageJ/Fiji to view the dataset.  But the complete deconvolved Z-stacks will not be retained, in order to minimize unnecessary data size inflation.

To keep the complete deconvolved Z-stacks during (re-)processing, add the -i flag to the command and specify the number of desired iterations (5-10 is reasonable), including the -r or --reprocess flag if the dataset has already been processed before:

lls -r -i 8 /path/to/LLSfolder 

2017-02-14T14:00:18-04:00