Inputs needed for preparation:

1. ts_tlt directory containing the generated tilt series. This should contain your .rawtlt files and your .st files (This function only reads the default ts_tlt folder defined by TomoNet, and the output folder is also fixed as “eTomo” under the Recon Folder)

Output you will get:

Root directory

— Recon:

— ts_tlt: Directory storing the output of tilt series generation

— Trash: Directory storing deleted files

— eTomo: Directory storing eTomo reconstruction output

— Trash: Directory storing deleted files

Fig. 3: Updated table view.

This is the GUI for the reconstruction step. After a successful Tilt Series Generation, “Tomo Name” should be automatically populated. See Fig. 3 for an example.

• Double-click “View ST” to have a bin8 preview of the tilt series (for pre-scan)
• Double-click “Continue” to start/continue eTomo reconstruction.
• Double-click “Start Over”, if you want to redo something. Everything will be wiped clean, allowing you to do eTomo again.
• Double-click “Delete”, when you think this tomogram’s quality is bad and will not be used. If you change your mind after deleting, you can move your file back from the Trash folder.

After finishing each reconstruction

• “Tilts #”: shows how many tilts this tomogram has.
• “RE mean” and “RE range”: Populated after the “Fine Alignment” step in eTomo. They tell you how well your tilt images are aligned.
• “Binning”: If you used the binning function in eTomo, this will show the number you selected for binning.
• “Thickness”: thickness (in nanometers) for your reconstructed tomogram, not ice thickness.
• “Skipped view(s)”: Lists any views you skipped during “Fiducial Model Generation” and “Tomogram Generation”
• “Notes”: You can type in some notes associated with each reconstruction.