Tilt Series Acquisition with SerialEM
SerialEM is a program to acquire tilt series for electron tomography on Tecnai
and JEOL microscopes.
It uses an approach based on prediction of specimen position
during the tilt series from the position at previous tilts. It does not count
on the microscope or the specimen being particularly well-behaved, so unless a
prediction appears reliable, it falls back to measuring and adjusting defocus
and/or specimen position when necessary. With this method, it achieves both
the robustness of the older approach to tilt series acquisition (track and focus at every tilt) and the
speed of the newer precalibration approach.
A 2Kx2K, 1 degree tilt series can be acquired in about 45 minutes with a
single-port readout camera or 20-25 minutes with a four-port readout camera.
The method and the program are described in this
Mastronarde, D.N. 2005. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152:36-51.
The prediction method was first described in this abstract from the 2003 MSA meeting,
Mastronarde, D.N. 2003. SerialEM: A program for automated tilt series acquisition on Tecnai microscopes using prediction of specimen position. Microscopy and Microanalysis Vol. 9, Suppl. 2, 1182CD.
In addition to automating tilt series acquisition, the program provides an
integrated user interface for image acquisition, display, and storage. It
looks like this:
Other notable features include:
SerialEM works on both modern FEI microscopes (Tecnai, Titan, Spirit) and JEOL microscopes with the TEMCON interface (e.g., 1400, 2100, 2200, 2500, 3100, 3200, ARM200). The program is built and tested with the version 3 of Tecnai but it apparently still works on a G1 Tecnai.
SerialEM works with CCD cameras from Gatan, TVIPS (Tietz Video and Image Processing Systems), FEI, and AMT, and some cameras from DirectElectron and OSIS (Olympus Soft Imaging Solutions). We have extensive experience with several models of Gatan cameras. Many other labs are using the program successfully with various models of Tietz cameras, a few labs are using FEI or AMT cameras. Some OSIS cameras work through a plugin available from OSIS.
Program and configuration files are available on our ftp site. Follow the
instructions in the README
file to get started. Your first step is to fill out the
and send it to David Mastronarde, who will prepare an initial configuration
Installations on new JEOL microscopes are usually done with the assistance of Jaap Brink from JEOL, so he should be contacted in those cases (jbrink at jeol dot com).
This software is provided free for non-commercial purposes. By downloading the software, you agree that you will use it for research rather than commercial purposes, and that you will not distribute it outside of your own institution.
SerialEM and the Microscope
SerialEM is written in Visual C++ using Microsoft Foundation Classes (MFC).
It controls FEI microscopes using the TEM scripting interface; this must be
installed and activated for the program to work. There is an installer script but
no formal Windows
installation procedure; the program is essentially just placed on the computer and run.
SerialEM obtains images from DigitalMicrograph using a plugin that is placed
in a Gatan Plugins folder and registered with the system. It
obtains images from Tietz cameras using the CAMC4 module provided by TVIPS;
from FEI cameras through the TEM scripting interface; from Direct Electron
cameras through an interface to their server program; from AMT and OSIS
cameras through modules supplied by them.
The program has been used exclusively for data acquisition in our lab since May 2002. It currently runs over 3000 hours per year on our two Tecnai microscopes and has been installed on over 110 FEI and 90 JEOL microscopes. There has been no history of it impairing the operation of the microscope hardware or software, or the operation of DigitalMicrograph. If necessary, it can be run on a support computer and control the microscope over the network, as long as it is the same computer that hosts the CCD camera.
SerialEM Discussion List
The SerialEM discussion listserver provides a means for users and people
managing the program to ask questions and share their experiences, as well as
a way to receive notification of new releases and other news.
The list is not moderated, but joining requires approval.
To subscribe to this list, send a message to listproc@lists.Colorado.EDU with the contents of your message being:
subscribe serialem your-full-name
where your-full-name is your name, including spaces. After your request is reviewed, you will be added to the list and receive an email with more instructions on using the list.
To remove yourself from the list, send a message to listproc@lists.Colorado.EDU with the contents of the message being:
To access the list archives, see these instructions.
Other Helpful Materials
A copy of 3dmod and associated files that can be run on Windows without
installing IMOD or Cygwin is available
here. The package unpacks
to C:\Program Files\3dmod and a shortcut can be set up to run 3dmod from
there. The package also includes midas, which can be useful to have on the
microscope for checking rotations between magnifications.
Our YouTube channel has a series of videos of the lectures on SerialEM presented in a webinar in September 2012, plus some tutorial videos prepared by Cindi Schwartz.
Here are some training documents written by Cindi Schwartz, to provide concrete guidance for doing room temperature and cryo tomography.
Here are Powerpoint presentations from a workshop on SerialEM given in December 2006. The slides have a lot of words, but there are many fewer words than in the help manual, so they may be helpful by highlighting the most important points.
And again, here are the: