Run TranSPHIRE - MPI-Dortmund/transphire GitHub Wiki

To run TranSPHIRE, type in the terminal:

transphire

If TranSPHIRE is not started for the first time, the settings of the last closed session or started TranSPHIRE run are saved and can be loaded.
TranSPHIRE asks you, if the default settings should be loaded or not.

The recommendation is:
If one wants to start a new run, load the default settings.
If the GUI is started for a continuation or for monitoring, load the previous settings.

Setup a session

The general procedure is as follows:

  1. Mount necessary mount points
  2. Specify all settings
  3. Specify users for notifications
  4. Press the Start button
  5. Visualize the results

Mount tab

Mount all necessary mount points that are required for the run.

In our case, we have different file servers for our cluster and one backup server. The user mounts the file server that contains the home directory, the backup server and the microscope's camera pc.

Settings tab

Specify all necessary settings to make each program work.
For the meaning of each settings, please refer to the programs manual.

In addition to the external program settings, there is another option in the Motion tab under Frames.
Here, one can specify a sub-range of frames that will be averaged to a motion corrected and dose unweighted average image.

Start TranSPHIRE

Press the Start button to start the process.

In case you want to continue an old run, TranSPHIRE will ask you if you really want to continue.
The Start number needs to be adjusted to the next valid number.

Since TranSPHIRE will not overwrite any files, the easiest way to find the next valid number is to start TranSPHIRE in the continue mode and let TranSPHIRE tell you the next valid number.

Visualization

After the Start button is clicked, the visualization tab will show the results of the different TranSPHRIE steps.

Monitor mode

To run the GUI in monitor mode, start another TranSPHIRE instance on the same computer.
Do not load the default settings and instead of Start, click the Monitor button.

The real time progress can be accessed in the visualization tab.