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
--reprocess flag if the dataset has already been processed before:
lls -r -i 8 /path/to/LLSfolder