IMOD - edmont

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About

NOTE: This page is a daughter page of: IMOD


Edmont/blendmont is a command-line program which is distributed as part of the IMOD tomography suite and is used to cross-correlate montage files. For full information on edmont, visit the edmont man page.

To create a montage in IMOD the steps are:

  1. Copy montage file (eg: 2_4d2) into its own folder.
  2. Open a terminal window and change to that folder.
  3. Enter "edmont" and run through interactive program (this program outputs a piece list) (see below)
  4. Copy "Blend.com" com script to the directory and change values (see below)
  5. Enter/run "subm Blend.com" & wait for it to finish (this com script generated the blended montage).
  6. Open blended montage file (type "3dmod 2_4d2.bl"), check it is okay, do auto contrast (Shift+A), take note of black & white values.
  7. To make the final montage 1/2 as small run mrcbyte:
    1. mrcbyte -c 40,140 2_4d2.bl 2_4d2.byte.bl (NOTE: 40,140 = appropriate black & white values)
  8. Clean up all unnecessary files (can delete all but original stack and final blend - "2_4d2" and "2_4d2.byte.bl")


Interactive program:

prompt>  edmont
# of input files (or -1 to read list of input files from file):     1
Name of input image file:         2_4d2
Name of file with list of piece coordinates (or Return to use piece
coordinates in image header):
Enter list of sections to read from file (1st sec is 0; ranges may be entered)
0
# of output files (or -1 to read list of output files from file):      1
Name of output image file:       test
Name of output piece list file (or Return for none, if image headers
have piece coordinates):      2_4d2.pl
Enter Min X, Max X, Min Y, & Max Y; pieces outside this range will be excluded
  from output file (enter / to include all pieces):      /
1 to enter a list of points specifying pieces to exclude, 0 not to: 0
Output file data mode (/ for same as first input file):      /
0 for no floating, or 1 or 2 to float sections to common range or mean:      1
1 to renumber sections in output file(s) sequentially from zero, 0 not to:    0

Input only (copy and paste this into the command window after changing "2_4d2")

edmont
1
2_4d2.st

0
1
test
2_4d2.pl
/
0
/
1
0

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