How to manually create a lamella boundary mask using IMOD

1. Open your tomogram in 3dmod (from IMOD):

3dmod tomogram.mrc

It should open the ZaP window first:

2. Make sure that 3dmod is in Model mode:

3. Open the Slicer window either by clicking the menu Image → Slicer or by pressing the \ key:

Tip: Make sure to click the "high resolution" interpolation button (the checkerboard)!

We will be using these slider controls in particular:

4. Now change the X rotation slider (the first one) all the way to the left (-90 degrees):

Tip: If your tomo is very noisy, you can increase the number of averaged slices via the Img button

5. Now change the View axis position slider (the last one) almost all the way to the left, i.e. somewhere the edges of the lamella are still clearly visible (the exact position does not matter):

6. You will now click 4 points defining the lamella boundary using the middle mouse button, in this order:

top left → top right → bottom left → bottom right

This order is very important! The points should form the letter Z in green.

You don't have to click exactly the "top left" corner of the lamella (say), just approximate positions are fine. See the example:

7. Now change the View axis position slider somewhere in the middle and repeat this process, always respecting the order of the points: top left → top right → bottom left → bottom right

8. Finally, change the View axis position slider almost all the way to the right and click the 4 points one last time, again in the same order:

9. Now go back to the 3dmod main window and save your model: File → Save Model As...

IMPORTANT: you can call your model whatever you like, but please use the .mod extension! In this example, we will call it tomogram_boundary.mod.

10. Now, using the Linux command line, go to where your model was saved and run the following IMOD command to convert your model to a plain text file containing the X,Y,Z coordinates of the twelve points:

Tip: this step is optional since Slabify can read .mod files directly

model2point tomogram_boundary.mod tomogram_boundary.txt

The contents of the .txt file should look something like this:

       38.67      968.00      388.00
     1013.33      968.00      334.67
       32.00      968.00      248.00
     1012.00      968.00      209.33
        4.00      488.00      324.00
     1014.67      488.00      305.33
        4.00      488.00      202.67
     1014.67      488.00      174.67
        8.00       89.00      260.00
      994.67       89.00      272.00
        4.00       89.00      142.67
      969.33       89.00      152.00

11. Now you can use Slabify to create a boundary mask by fitting two planes through the points that you've clicked:

slabify --input tomogram.mrc --output tomogram_slab_mask.mrc --points tomogram_boundary.txt

12. Finally, you should visualize the slab mask and certify that it matches your tomogram:

3dmod tomogram.mrc tomogram_slab_mask.mrc