SerialEM HowTo: Off-line Target Picking

Chen Xu

$BrandeisEM: ~emdoc-xml/en_US.ISO8859-1/articles/SerialEM-howto:align-to-hole/article.xml 1 2014-10-06 12:07:48 xuchen Exp$

In this document, I try to show you how to setup a dummy instance of SerialEM for picking more target points while main instance of SerialEM is busy collecting data for the points previously defined. With the latest beta version of SerialEM, one can easily add more target points off-line: either from the same computer or from a local computer at user site.

You can also get pdf version of this document here.


Table of Contents
1 The Background
2 The Setup
3 How to use it

1 The Background

One of the ways to define target for data collection is to manually pick good points in a medium mag montage map. Later, SerialEM drives stage to these positions using Realign routine which is very robust and reliable. It might take some time to pick all the interested point, but it is perhaps the only way to make sure you will be on the target precisely. For filament object, this way is also preferred.

It would be ideal to be able to pick good target positions while SerialEM is collecting data. And, for SerialEM running on a stable microscope like Titan Krios, data collection can be fully automatic, user is no longer required to babysit the data collection session on site. It could be very attractive to let user pick their preferred positions remotely without too much trouble of delay and lagging. Therefore, a setup which allows off-line picking becomes reasonably needed.

However, one could not do this with previous version of SerialEM. While SerialEM is busy collecting data, the navigator dialog window is gray out unless the action is stopped or pulsed. Fortunately, this is available with the latest beta version of SerialEM which allows more than one instance for this particular purpose.


2 The Setup

There are two cases: one is on the same computer of running SerialEM, and the other is to setup on a off-line, remote computer.


2.1 Setup on the same computer

Setting up this on the same computer is easy. We need to make another alias to SerialEM icon, on Desktop, for example. From the properties window of the icon, define an argument "/DUMMY" in the "Target" area, as below.


C:\Program Files\SerialEM\SerialEM /DUMMY

And we should use a different setting file for this second instance of SerialEM so that it doesn't interfere with setting file of running software, in "Start In" area like this:


C:\Program Files\SerialEM\SEM-settings-for-DUMMY 

Here the SEM-settings-for-DUMMY is a the name of a folder where the setting file sits. Apparently, it needs to exsit.

In this case, the DUMMY instance of SerialEM uses the same set of property file and calibration file. It doesn't connects to scope and doesn't initiate camera object either. It is really a DUMMY instance.


2.2 Setup on a remote computer

For a remote computer on user side, to setup this would need to install SerialEM and its running library etc. into normal location, C:\Programs Files\SerialEM and setup DUMMY version as above. The property and calibration files from host computer would also be needed.


3 How to use it

On the same computer, while main SerialEM is collecting, one can start the DUMMY instance of SerialEM and read the available Nav file. Load map, and off you go to pick all the target positions. In the end, save the nav file to a different filename like nav1.nav. This file can later be read by main instance of SerialEM and continue the data collecting session.

Note: If you launch the DUMMY instance but could not load the map, it is likely due to the map stack file is still open at main instance of SerialEM. Closing it would solve this issue.

On a remote computer at user site, one has to get the nav file and MMM maps to local. And after all the target picking is finished, transfer the final saved nav file back to host scope computer and resume there. This way, there is no delay or lagging like with a real online remote session.