Top level LLS folder
A typical lattice light sheet experiment will yield a single folder that will contain some or all of the following files/folders:
- Top level folder (e.g. “cell1”)
- many “raw” (pre-processed)
TIFF
files. See below for the naming convention. - a
Settings.txt
file with metadata about acquisition settings. - a
Deskewed
folder that contains the deskewed data. - a
GPUdecon
orCPPdecon
folder that contains any deconvolved data. This directory may not include full deconvolved Z-stacks depending post-processing parameters, but will likely include a max intensity projection “MIP” file for all channels & time points for easy viewing (scroll to the bottom of the folder), the MIP files may also be separated inside a MIP folder. To retain or retrieve the complete deconvolved data during processing, see here. - a
ProcessingLog.txt
file with JSON-formatted data about the data and post-processing
- many “raw” (pre-processed)
To combine separate timepoint and/or channel stacks/MIPS into a single 4-5D hyperstack, see here.
File naming convention
All TIFF files follow the following naming convention:
name_channel#_stack#_laser_relativeTime_absoluteTime.tif
The name may additionally include one or more of the following flags:
COR
means that the image has been corrected for bad/residual pixelsdeskewed
means the image has been deskewddecon
means the image has been deconvolvedMIP_axis
means the image is a maximum intensity projection along the specified axis