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By default, data acquired on the lattice is saved as individual Z-stack TIFF files for each timepoint, for each channel.  Viewing an entire 5D dataset can be very challenging, and demands a computer with enough RAM to hold the full dataset (or the use of virtual stacks, which have drawbacks).  We strongly encourage contacting IDAC for assistance with visualization and analysis of datasets acquired on the lattice light sheet.  If you wish to view the full 5D dataset, the following procedure will arrange the data into a single hyperstack in ImageJ/Fiji.

  1. In Fiji, select File → Import → Image Sequence...
  2. Navigate to the folder containing the data (such as the Deskewed folder in your LLS folder), and click Open.
  3. In the Sequence Options window that pops up, you can either just click OK to select the full dataset, or change the options to select a subset of the data.
  4. Separate the resulting stack into the appropriate dimensions using Image → Hyperstacks → Stack to Hyperstack...
    • Order: typically ‘xyzct’ (but confirm that)
    • Enter the actual number of channels, slices, and frames in the data
      • Channels is easy to figure out
      • Number of frames can be quickly determined from the number of files that you opened (divided by the number of channels).
      • Number of slices can be determined by opening a single Z stack, or by dividing the number of planes in your combined stack by the number of channels multiplied by the number of frames.
      • channels xslices xframes must equal the number of planes in the imported combined stack.
    • Hit OK
  5. The resulting 5D Hyperstack is useful for extracting an ROI from a subset of the data in XYZC or T.
2017-02-05T23:29:18-05:00