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 or CPPdecon 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

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 pixels
  • deskewed means the image has been deskewd
  • decon means the image has been deconvolved
  • MIP_axis means the image is a maximum intensity projection along the specified axis