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Using the llsinfo over an ssh connection, you can also preview lattice light sheet data remotely.  This is useful when you want to verify the data contained in an LLS folder, perhaps before downloading/processing, etc…  You can view either the MIP file, or the Z stack for a specific channel/timepoint.

  1. Log in to the CBMF server using X11 forwarding.
    • Note: remotely previewing data requires X11 forwarding. You must add the -X flag to your ssh connection and install a local Xserver:
    • ssh -X user@cbmf-latwork.med.harvard.edu

Show MIP file

  1. Use the --showmip or -s flags with the llsinfo command to get a preview of the maximum-intensity-projection (assuming a MIP exists).
    • llsinfo /path/to/LLS/folder --showmip
  2. A window should appear on your local computer with a preview of the dataset.  You can click and drag on the sliders at the bottom to change the channel, or the timepoint.
preview lattice light sheet data

Previewing an image with the llsinfo --show command

Note: this function can usually be used to preview the MIP file for data that has been compressed for long term storage.

Show Z stack for specific channel/timepoint

  1. Use the --showz or -z flags with the llsinfo command to get a preview of a Zstack for a specific channel/timepoint (assuming the file exists).  This flag accepts up to three additional numbers, seperated by spaces representing: [channel, timepoint, deskewed(0)/deconvolved(1)].   Remember, the filenames are zero-indexed, which means the first channel is number “0” and the second channel is number “1”.  The --showz flag should come at the end of the command.  Here are a couple examples:
    • show channel 1, timepoint 1, deskewed:
      • llsinfo /path/to/LLS/folder --showz
    • show channel 1, timepoint 6, deskewed:
      • llsinfo /path/to/LLS/folder --showz 0 5
    • show channel 2, timepoint 1, deconvolved:
      • llsinfo /path/to/LLS/folder -z 1 0 1
  2. A window should appear on your local computer with a preview of the dataset (or an alert may appear saying the file cannot be found).  You can click and drag on the slider at the bottom to change the z position.
2017-02-14T11:08:48-05:00