SerialEM Note: Make All LMM Maps Automatically

Author:

Chen Xu

Contact:

<chen.xu@umassmed.edu>

Date_Created:

Apr 3, 2018

Last_Updated:

Jan. 26, 2026

Abstract

We found that it was extremly useful to be able to make Low Mag Montage (LMM) maps for all the grids in autoloader cassette automatically. Since it can take a while for multiple grids, you should give yourself a good break while scope is busy working without feeling guilty.

Procedure

Here are steps to follow.

  1. Dock the cassette. After temperature in the autoloader recovers, do Inventory.

  2. Setup image condition. I do it inside or SerialEM Low-Dose mode. I use Search area for the job. On our Krios with GIF/K2, I set mag for Search as 220X (I cannot go lower as wish, because some hardware piece in lower portion of column will start to cut into image, unless with very large IS offset for LD_Search).

  3. Setup proper exposure and binning for Search parameter from camera control panel. I usually use binning 2, exposure 1 seconds, and in Linear mode (mP mode, Spotsize 8).

  4. Take a Search shot, make sure the count value is proper, no beam/aperture edge in the image.

  5. Navigator - Montaging & Grids - Setup Full Montage. Make sure Search is checked in the montage setup dialog window. Define a file like LMM.map.

  6. Edit script Cars to reflect cartridge and sample information, like below:

Cars.txt
 1 ScriptName Cars
 2
 3 # script of cartridges information
 4
 5 rootDir = X:\Munan_20180402
 6 cat = { 2 3 4 5 6 7 }
 7 name = { 56-g1 56-g2 56-g3 56-g4 54-g2 54-g4 }
 8
 9 SetDirectory $rootDir
10 ReportDirectory
11
12 If $#cat != $#name
13     Echo     >>> Arrays "cat" and "name" have different length, exit ...
14     Exit
15 else
16     echo     cat = { $cat }
17     echo name = { $name }
18 Endif

Here you define folder location, cartridge #, and sample names. The map filename will have the info in it, such as LMM-Car2-56-g1.st.

  1. Now run the Script LMMCars as below:

LMMCars.txt
 1 ScriptName LMMCars
 2 # LMM for multiple cartriges, assumes the montage file opened.
 3
 4 ##########################
 5 # navigator must be open
 6 ##########################
 7 Call Cars
 8
 9 ##### No editing Below ############
10 CallFunction LMMCars
11 ## in the end, rise mag to settle temp & Close the valves
12 #GoToLowDoseArea Search
13 SetColumnOrGunValve 0
14
15 ###############################################################
16 Function LMMCars 0 0
17
18 Loop $#cat index
19    LoadCartridge $cat[$index]
20    #SetNavRegistration $cat[$index]
21    SetColumnOrGunValve 1
22    SetApertureSize C2 150
23    SetApertureSize Obj 0
24    MoveStageTo 0 0
25    OpenNewMontage 0 0 LMM-Car$cat[$index]-$name[$index].st
26    Montage
27    NewMap
28    CloseFile
29 EndLoop
30
31 EndFunction

Convert LMM maps into JPEG format

For easy display and small file size, we usually convert all the maps in MRC format to JPEG.

  • Set Bin Overview to 1 on Montage control panel (default is usually higher than 1 with montage from command)

  • Load the map file, the overview will be displayed in a specific buffer such as Q

  • Run a small script

LMM->JPEG.txt
1ScriptName LMM->JPEG
2# convert to JPEG format for easy display
3
4SetDirectory X:\Munan_20180402
5
6# reduced image for good JPEG density range, redeuced one will be in A
7ReduceImage Q 2
8SaveToOtherFile A JPEG JPEG LMM-Car2-56-g1.jpeg

Note

  • The JPEG image generated from above script is true JEPG file, not a JPG compressed TIFF file as before. Compressed JPG cannot be displayed properly by Photoshop and ImageJ, although preview, paint and webbroser can show them nicely.

  • You can also convert MMM maps and single shot MRC image the same way.