Fix Scripting Beam Blank

Chen Xu

$BrandeisEM: ~/emdoc-xml/en_US.ISO8859-1/articles/SerialEM-howto:fix-scripting-beam-blank/article.xml 1 2013-02-11 07:54:59 xuchen Exp$

It happened to us twice, both after Tecnai software upgrade. I feel that it is useful to document this so we know how to deal with it if it happens again. And it might be helpful for other sites who run into the same issue.

It is important to have this issue fixed. Otherwise, all the CCD shots from SerialEM will have dark image problem and some SerialEM functions won't even work because of this.

You can also get pdf version of this document here.

Table of Contents
1 Problem description
2 Background
3 The Fix

1 Problem description

The easiest way to see if your system has this issue is to use Low Dose mode of SerialEM. If you toggle the check box next to "blank beam when screen is down", the beam can always be seen on the large screen, then you do have this problem. The "blanked" beam might be far away from the center of large screen and can only be seen partially at the edge of screen, but as along as it doesn't completely disappear, i.e. blanked, we have to fix it.

2 Background

Tecnai scope uses beam blanker all the time. When you change the magnification, the beam is blanked momentarily. In Tencai Low-Dose module, there even is a "blank" button for you to click. Usually, gun coils are used to perform this task. A large offsets to gun coil(s) will make beam disappear, so the beam gets "blanked".

In fact, when one starts a new account on Tecnai computer and the blanker in Low-Dose mode might not work at all. You still see beam or part of the beam on large screen. Gun coil gets a offset but not big enough. Fortunately, one can calibrate the blanker in Low-Dose mode so that the offset to gun coil can be sufficient to blank the beam completely. The calibration result will update into registry of computer so that next time you start TUI interface the blanker will simply work. This result can also be saved into a file separately.

The information used to blank beam in Low-Dose mode is stored in the registry, but it is not part of alignment file. Therefore, different user has to calibrate this again. Alternatively, they can load the saved beam blank calibration file. In any case, this information is only available for blanking purpose within Low-Dose mode.

SerialEM and other program that communicate with scope via scripting interface also need to blank beam from time to time. It uses the same gun coil, but the default amplitude for this gun coil change might not be correct, as it has never been touched before. This is the part that needs to be fixed.

3 The Fix

Here are steps to make the change. The snapshot below shows where to modify in user's registry.

As part of alignment, this amplitude can be passed to other users by loading the saved alignment file.