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