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Tutorial: How to use Ot2Rec Previewer

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Neville Yee edited this page Apr 5, 2023 · 4 revisions

RFI Users

If you have your own installation of Ot2Rec (see install guide), you can skip this section.

On Guacamole (any virtual machine which has access to the /ceph/groups/structbio/ folder),

  1. Open a terminal
  2. Launch the Ot2Rec loading script. This activate the Ot2Rec conda environment and module loads all the relevant plugins.
source /ceph/groups/structbio/Ot2Rec/load_ot2rec.sh

Using Ot2Rec Previewer

Ot2Rec Previewer runs motion correction, alignment and reconstruction of tomograms for a pre-set workflow (motioncor2 -> AreTomo), and produces a report to summarise the processes. It is useful for previewing all of your collected tomograms in one place so you can assess which tomograms to take forward for further analysis, e.g., discarding the tomograms which do not contain your feature of interest.

To run Ot2Rec Previewer, in the same terminal as before,

  1. Navigate to where your images are stored.
  2. Run Ot2Rec Previewer, a GUI should pop up for you to enter your parameters.
o2r.previewer

Note to RFI users: If you use the above method to load Ot2Rec, there may be a slight delay of GUI appearance due to the conda environment being held in a network (remote) drive.

The fields to be filled in are:

  • Project name: project name of your data, e.g., if your images are named Position_x_x_x.mrc, your project name is Position.
  • Source folder: path to where your micrographs are stored.
  • Mdocs folder: path to where your mdocs are stored.
  • Image file extension: tiff, mrc, or eer.
  • Stack index field #: Index of the field after project name in your filename that describes the stack number. e.g., if your images are in the format Position_stacknumber_tiltimage_tiltangle.mrc, then your stack index field # is 0.
  • Image index field #: Index of the field after project name in your filename that describes the image number within the tilt series. Following the previous example, your image index field is 1.
  • Tilt angle field #: Index of the field after project name in your filename that describes the tilt angle. Following the previous example, your tilt angle field is 2.
  • Lamella thickness: Estimated lamella thickness in nm, this estimates the VolZ parameter in AreTomo, taking pixel size into account. This parameter controls the z-size of the reconstructed tomogram.
  • Output tomogram binning factor: Bin factor to apply to the tomograms in x-y. E.g., if your micrograph is 4096 x 4096, and bin factor is 4, then your final tomogram x-y dimension will be 1024 x 1024.
  • AreTomo executable: path to a specific AreTomo executable if you want to use a particular version. Otherwise, if left as "AreTomo" it will use the module loaded version. (RFI Users: There is a group installation of AreTomo 1.3.4 - use /ceph/groups/structbio/AreTomo_1.3.4/AreTomo_1.3.4_Cuda113_Feb22_2023)

Once you are happy, click on "Create config file" and close the GUI. Everything should start running and you can monitor the progress in the terminal.

Once complete, there will be a report.slides.html file in the images directory which you can open in a browser to see the results of the reconstruction.

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