Automated EM Data Acquisition with SerialEM


Contribute to the Continuation of SerialEM!
Tilt Series Acquisition with SerialEM
Program Features
Highlights of SerialEM 3.6
Availability of SerialEM for Various Hardware Configurations
Setting Up SerialEM
SerialEM Discussion Group
Other Helpful Materials
Source Code for SerialEM and SerialEMCCD Plugin
Download

Contribute to the Continuation of SerialEM!

SerialEM was originally developed with grant funding from NIH. It is now being maintained and developed with funding that comes from users, directly or indirectly, in order to maximize the time that can be spent on writing code and documentation instead of grant proposals.

You can help make SerialEM a community-supported resource by having your laboratory or microscope facility contribute to the further development and continued availability of the program. The mechanism for doing this is to purchase annual support, so that the expense represents a tangible item that can be paid from grant or institutional funds. We offer four options, allowing you to pick the size of your contribution based on your financial resources and the importance of SerialEM to your work. The options are:

  1. Basic bug support: Resolution of issues apparently arising from SerialEM bugs ($275 non-profit, $550 commercial).
  2. Priority bug support: Rapid resolution of issues apparently arising from SerialEM bugs ($550 non-profit, $1100 commercial).
  3. Priority software support: Consultation on and resolution of issues arising from configuration and calibration problems as well as SerialEM bugs ($1100 non-profit, $2200 commercial).
  4. Application support: In addition to software support, advice and consultation on how to get the most out of SerialEM for your applications ($2200 non-profit, $4400 commercial).

What happens if you do not contribute? Although the first three options represent the kind of support that we provide routinely, payment for this support is voluntary. We still answer questions and deal with problems from non-paying users, but may take longer to do so. Questions may be posted to the discussion list first.

Why is it important to contribute? Even though there are other sources of support for SerialEM continuation and development, user contributions are important both financially and because they are not tied to specific developments and represent the general user interest.

What does this mean for the future of SerialEM? This is not a move toward commercialization. We intend to keep the program freely available.

Click Here to see more details and contribute by check or purchase order.

Click Here to see more details and pay now by credit card.

Tilt Series Acquisition with SerialEM

SerialEM is a program that can acquire a variety of data from electron microscopes: tilt series for electron tomography, large image areas for 3-D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods.

The main focus of the program is automated tilt series acquisition. For this, 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 robustness and speed. For example, a 2Kx2K, 1 degree tilt series can be acquired in about 20-25 minutes with a four-port readout CCD camera.

The method and the program are described in this paper:
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.

Program Features

In addition to automating data acquisition, the program provides an integrated user interface for image acquisition, display, and storage. It looks like this:


Click image for full-sized view.

Other notable features include:

Highlights of SerialEM 3.6

The most notable features of the latest release, SerialEM 3.6, are:

Availability of SerialEM for Various Hardware Configurations

SerialEM works on modern FEI microscopes (Tecnai, Titan, Spirit, Talos), JEOL microscopes with the TEMCON interface (e.g., 1400, 2100, 2200, 2500, 2800, 3100, 3200, ARM200), and the Hitachi HT7700. The program is built and tested primarily with the version 2 of Titan but it still works on Tecnais under Windows 2000.

SerialEM works with CCD or CMOS cameras from Gatan, TVIPS (Tietz Video and Image Processing Systems), FEI, AMT, DirectElectron, and EMSIS (formerly OSIS, Olympus Soft Imaging Solutions); it also supports the JEOL Ruby camera. Direct detection cameras from Gatan, FEI, and DirectElectron are supported. All EMSIS cameras now work through a plugin available from EMSIS for either 32- or 64-bit versions. STEM acquisition is supported from Gatan's DigiScan or FEI's STEM imaging.

Falcon 3 cameras are now completely supported in the 3.7.0 beta versions of SerialEM. It will require upgrading to an FEI software version with a new scripting interface. An FEI release with a server version of 6.9 will provide this interface.

If necessary or advantageous, SerialEM can be run on a separate computer and control the microscope over the network. Such a configuration is standard on JEOL microscopes but is also possible for FEI and Hitachi microscopes. Version 3.5 of the program can access Gatan, Direct Electron, FEI, and JEOL Ruby cameras over the network from another computer, and version 3.6 can access Tietz cameras remotely as well, but for other kinds of cameras, SerialEM must run on the computer that hosts the camera.

For running on an FEI microscope, it is necessary to have the FEI scripting adapter installed. If you do not have the adapter, you need to purchase it from FEI. To check whether it is installed, do the following:

  1. Locate and run the "Delphi Scripting Exampler". For Tecnais through version 3 and possibly on older Titans, this is available through the Start menu under Programs - Tecnai. For Tecnai version 4 and newer Titan software, it is under Programs - FEI Company - TEM Software.
  2. Select the "Projection" tab after the program starts.
  3. Press the arrow next to "Magnification". If a magnification appears, you have the adapter; if not, there will be an error message in the status bar at the bottom of the window.

Although SerialEM itself is open source, the microscope plugins and some camera plugins in this software are provided free for non-commercial purposes. By downloading the distributed 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.

The program has been installed on over 200 FEI and 130 JEOL microscopes.

Setting Up SerialEM

Program and configuration files are available on the download site. Follow the instructions in the README file to get started. As a first step, it is highly recommended that you fill out the questionnaire and send it to David Mastronarde, who will prepare an initial configuration file.

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).

Guenter Resch from Nexperion offers SerialEM installation and training for both FEI and JEOL microscopes. This service is available worldwide, but visa arrangements for the the United States may need extra attention. Chen Xu at the University of Massachusetts Medical School may also be willing to help with installation; email David Mastronarde for contact information.

SerialEM Discussion Group

The SerialEM discussion group 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. Digests and posting via email (i.e. list server functionality) are provided. Additional capabilities, including browsable / searchable archives are available through a web interface. Access to the web interface requires a Google login profile, which must be associated with the email address at which you wish to be contacted. (Non Gmail addresses can be used with a Google login, with or without a Gmail address. See the Email section of your Google Account settings). The postings are not moderated, but joining requires approval.

To subscribe or visit the group via the web interface please visit SerialEM. If you do not have and are not willing to create a Google login and are satisfied with email only access, you can also request membership by sending an email to

asking to be added to the SerialEM list, and you will be added manually. Be sure that this email is sent from the same address as you would use to post to the list.

After your request is approved, you will be added to the group and will receive a confirmation email with additional instructions. Once subscribed, we request that you edit your membership settings for this group so that your display name is your real name. To post to the forum you can either use the web interface or simply email your posting to serialem@colorado.edu

To cancel your subscription, use the web interface or send an email to serialem+unsubscribe@g.colorado.edu.

When replying to a previous posting via email, you will have the option to reply to the sender or to the list.

Other Helpful Materials

A standalone 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.

A repository for contributed scripts (macros) was developed by Guenter Resch from Nexperion and is hosted on the Nexperion site. If you have scripts that may be useful to others, please consider adding them to the repository.

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. The videos are also available right here; if you sort on the "Last modified" column they will be in a good order for viewing.

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:

Source Code for SerialEM and SerialEMCCD Plugin

Both SerialEM and the SerialEMCCD plugin to DigitalMicrograph are open source; SerialEM under an MIT license, and SerialEMCCD under the GPL version 2. You can browse the SerialEM source here and SerialEMCCD source here, or you can download either repository with Mercurial. See the IMOD source instructions for setting up Mercurial and updating a repository. This SerialEM repository has been pruned of all changes before Feb. 17, 2017 so as not to disclose calls to proprietary microscope and camera interfaces. However, it is updated nightly from the main development repository, with changes committed with the original comments.

To clone the open-source SerialEM repository, run

    hg clone http://bio3d.colorado.edu/SerialEM/OpenSerialEM

To clone the SerialEMCCD source, run

    hg clone http://bio3d.colorado.edu/SerialEM/SerialEMCCD

If you are going to try to compile either of these projects, you will also need the collection of libraries, which is now in a separate SerialEMLibs repository. You can download this with:

    hg clone http://bio3d.colorado.edu/SerialEM/SerialEMLibs