Operating CM12

Chen Xu

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This is a quick check list for the impatient user who already has a basic knowledge of the CM12. It gives the correct steps to align the scope and to set up the conditions for low-dose imaging. A pdf version of this document is also available.

For details on operating the scope and all other information, please refer to the original hard copy of the "Operating Instructions" that came with the scope.

A very brief, "condensed" version of this document can be found on this pdf and on the wall in the CM12 room.


Table of Contents
1 Check log book to see if there have been any problems
2 Check vacuum status
3 Add Liquid Nitrogen to the BIG anti-contaminator dewar
4 Apply High Tension
5 turn filament on
6 Check saturation and gun tilt, and then saturate the filament.
7 Check C2 aperture mechanical position and C2 stigmatism
8 Check specimen holder & load grid
9 Insert specimen holder into column
10 Adjust the specimen height to the eucentric position.
11 Put in objective aperture and center it
12 Check Objective Lens stigmatism
13 Check Pivot X, Y
14 Check voltage and current rotation centers
15 Re-center the objective aperture and check obj. stigmatism again
16 Typical Low-Dose setup parameters
17 Align an identified area under Exposure and Search
18 Check S1 and S2 parameters
19 Check exposure parameters
20 Taking Pictures On Film
21 CLosing Up

1 Check log book to see if there have been any problems

It is always a good idea to check the LOG book. You can find necessary information listed there, such as:


2 Check vacuum status

The status must be Ready before you can operate the scope. If not, you should ask for help and report it to the manager. Normally, if the vacuum is not ready, it is due to one of the following reasons:


3 Add Liquid Nitrogen to the BIG anti-contaminator dewar

LN2 in the cold trap dewar is necessary for vacuum recovery. It is very useful, especially when you need to change grids and/or do a cryo session.

Note: If you want to use 651N anti-contaminator, make sure it is in good vacuum condition by pumping it with heat before use. If you are unsure, but want to proceed in using the scope, you should not use the 651N small dewar.


4 Apply High Tension

Turn High Tension (H.T.) on if it is off by pressing the H.T. button on the panel. Set it to 120kV.


5 turn filament on

it is recommended to turn the filament on while on the configuration page where the actual filament current number is shown and the limit can be checked(highlighted).


6 Check saturation and gun tilt, and then saturate the filament.

The procedure is as follows:.


7 Check C2 aperture mechanical position and C2 stigmatism

Steps to adjust the C2 aperture mechanical position.

There are two ways to check and adjust the C2 stigmatism:


8 Check specimen holder & load grid

This is important. If you see any problem with any of the holders, report it to the manager immediately. Otherwise, you could be the one responsible for the problem. Several details about the holder must be checked before use:

Gently mount the specimen grid on its position. Use the tool pin to open and close the clamping device.


9 Insert specimen holder into column

Important: Be careful! Only at this stage, you might damage the scope or specimen holder mechanically. Be sure that you understand what you are doing. Should you feel any confusion about this procedure, please stop and ask for help.

Note: For the sake of filament crystal, it is REQUIRED to turn down the filament before inserting the specimen rod. That way, in case IGP shoots high, there will be no damage to the tip crystal. In general, filament should be kept DOWN until IGP recovers to below 26.


10 Adjust the specimen height to the eucentric position.

Unlock the geonimeter. While rotating the specimen stage around "0" degree, adjust Z screw to get the minimum translation movement induced by the rotating. Lock the geonimeter.


11 Put in objective aperture and center it

It is very important to know what size of the obj. aperture you are using. The position of the aperture will affect the obj. lens stigmatism. Here are the steps:


12 Check Objective Lens stigmatism

The obj. stigmatism should be corrected as much as possible, and it should be checked for every netative stain low-dose image that you are taking. Follow the steps:


13 Check Pivot X, Y

Note: The prerequisites for Pivot-Point is specimen being at eucentric height and objective being preceisly at focus level.


14 Check voltage and current rotation centers

This step is to align the beam to make it parallel to the axis of the columm. Make sure the obj. aperture is inserted and centered.

Note: The step size button on "Focus" is used to control the amplitude of the beam wobbling.

The steps used here only give "roughly" parallel beam to the axis. If you need very acurate "0" tilt beam, some extra tools and step will be needed, such as "Coma-Free" which is available on FEG scopes.


15 Re-center the objective aperture and check obj. stigmatism again

Because the beam tilt condition may have changed after the previous step, you could find that the obj. aperture position has changed also. If that is the case, recenter it.


16 Typical Low-Dose setup parameters

Here are some typical setup for Low-Dose condition.


17 Align an identified area under Exposure and Search

This step is to insure that what you see under low mag. (Search mode) will be the same area you get under imaging mag. Here is how I do it:

Note: You can use a corner of a mesh as the identified spot for a negative stain specimet or to use an ice burn mark in the cryo case.


18 Check S1 and S2 parameters

In Focus mode, S1 and S2 are linked to the positions of the beam which is deflected away from the center of the imaging area on the specimen. When highlighted, their parameters can be changed by the Multi-function keys.

Normally, we use 175kX as the magnification. The radius of the spot is about 1.5 microns. Depending on the specimen, you can change those parameters to fit your needs.


19 Check exposure parameters

Here I assume you are only going to take low-dose images.


20 Taking Pictures On Film

This is what I usually do to take a picture.


21 CLosing Up