The goal of this step is to generate a 3D reconstruction from 2D tomogram images.

I will demo using 20211105_NEC_WT_24, one tomogram I have.

In GUI “eTomo Reconstruction” Tab, click “continue”

If you successfully run the code, a window should pop up. The window looks like this. Click “Build Tomogram”.

A new window should pop up and look like this.

This window is used to set some parameters. For tomogram, you generally need to do the following:

1. Click the button that looks like a folder to select the .st file. Now, you should see the blank on the right of “Dataset name” should be filled with your .st file’s name.
2. Click the dropdown button next to “System template” and “No selection (2 available). Then click “cryoSample.adoc”. After this, you should see some areas become gray. That’s normal.
3. Click “Scan Header” to scan the header of your .st file. You should see the blank on the right of “Pixel size (nm)” is filled with your tomogram’s resolution.
4. Type the size of the gold beads you used inside the blank on the right of “Fiducial diameter (nm)”. In my sample, I used 5nm gold beads.
5. Type the image rotation degrees you want. Your sample may be different and you can always manipulate the values to see the resulted reconstruction and determine which is better.
   1. This should stay the same when you used the same microscope.
   2. The value will decide the handedness of your reconstruction.
6. Check “Tilt angles in existing rawtlt file”
7. If you already know there are some views in the .st file that you don’t want to use, you can specify the #views in “Exclude views” and check “Remove excluded views”, so the following steps won’t use those frames.

At this point, your window should look like this:

1. Click “Create Com Scripts”.