Creating TIFF series of ZaP window with segmentations in IMOD

Instructions

1. Open the .mrc and .mod files in 3dmod:

   3dmod basename.mrc basename.mod

2. In the 3dmod window, select File --> Set Snap Dir
   1. Select the directory to save the output TIFF series to. This needs to be a directory that already exists.
3. In the 3dmod window, select File --> Movie/Montage
   1. Axis to Control = Z
   2. Start = 1
   3. End = max value for the volume
   4. Increment = 1
   5. Rate = Default (UNTESTED, but worked on my dataset)
   6. Looping = One way
   7. Snapshot = TIFF
   8. Start at = Start/end
   9. Zap montage snapshots --> Check the 'Montage' and 'Whole image at 1:1 zoom' boxes
4. Bring the ZaP window to the front, and make sure all other windows are behind it (including other imod windows)
5. Middle click anywhere on the ZaP window to begin the process.

Import to Amira

To import the TIF stack to Amira and have it load properly with respect to any models or other MRC files, follow the following steps:

1. Each TIF file must be mirrored, which can be done in a batch process using Image Magick:

   for file in zap*.tif; do convert $file -flip $file; done

2. With Amira open, press the 'Open Data' button.
3. Navigate to the folder containing your TIF series, select all of them, and press Open.
4. Enter the proper data in the Voxel Spacing field. These should be the same values output when you run the IMOD program 'header' on your original MRC stack, and are typically in Angstroms.