Frequently Asked Questions

If you ask questions, they'll end up here!


  1. How do I start using the Electron Microscopy Center's facilities?

    Detailed procedures for starting to work within the EMC can be found here, but the bottom line is that you need to talk to the EMC staff about both new projects and any sort of training needed for projects you want to do.

  2. Is there any sort of overview of the entire EMC website?

    We are in the process of creating an index of all the web pages that we hope will allow users to find some of the information in our website that is not easily accessible from (say) the drop-down menus across the top of each page.

  3. Does the EMC have any sort of concrete plans for the future?

    Yes. The EMC has always had a vision for directions it would like to take, many of which are outlined on another web page. Some of the items listed there have already been accomplished (high pressure freezing, STEM tomograph) or at least partially accomplished (automation of image acquisition using serialEM, creation of web portal for data acquired through the EMC, grant submission for a new 120 kV TEM and a direct electron detecting camera), while others remain thoughts for the future.

  4. I sometimes see an image in the home page's random image collection that I'd like to stare at for a while. Are these images anywhere else in the website?

    The entire collection of random images has a web page all its own.

  5. What sort of outreach does the EMC do, and who can I contact about having the facility do something for me?

    The EMC gives tours of the facility for many on and off campus groups, and is also happy to give guest lectures in various classes and other sort of presentations to anyone who would like to know more about the facility. This sort of outreach (including local, national and international meetings that the EMC staff has attended) is summarized here. Various users of the facility have also shown images and other sorts of data in public exhibitions that can be called "art." Those events are briefly described here. Please contact any member of the staff for further information.

  6. I have seen some really neat 3d models of viruses, cellular organelles and exotic geometric shapes. Are there ways to do that around here?

    Several users of the EMC have had 3d models printed, and here's what you need to know.

  7. Who makes electron microscopes and the bells and whistles that can be used with them?

    Here is a short list of EM manufacturers and companies who make attachements, holders, etc.

  8. Speaking of EM supplies and consumables, does the EMC attempt to provide users with any of the things necessary to do this sort of work?

    The EMC is able to supply users with things like EM grids (with and without support films), SEM stubs, various negative stains and many of the consumables needed for high pressure freezing and freeze substitution. These materials are supplied to users essentially at cost, and a list of available items and their costs can be found here.

  9. What magnification should I use to collect my images?

    That will depend on both the actual sample and what you want to accomplish, but here are some guidelines.

  10. How can I determine the electron dose my specimen receives?

    The easiest way to estimate the dose that a specimen receives is to have a calibration that allows the user to relate the incident electron dose with measurable output from the instrument (e.g., the average counts per pixel in an image recorded using a CCD camera or the reading from some sort of meter that reflects the electron current from the electron beam). In order to have these things, the electron dose in a given electron microscope needs to be measured accurately and other microscope properties calibrated. Here is an example of this procedure for the EMC's JEOL JEM 3200FS. Once the instrument's dose has been calibrated, there are several ways to estimate the electron dose.

  11. What factors influence the strength of the electron beam?

    The power of the electron electron beam can be influenced by both things that happen above the specimen and things that happen below the specimen, and in most instances, the user has the ability to control them. For example, the user can deliberately adjust microscope settings to affect the strength of the beam above the specimen. The user can also adjust microscope settings that affect the electron beam after it passes through the specimen (but bear in mind that all these things can only reduce the strength of the beam as it interacts with microscope detectors and not with the specimen).

  12. What do the objective apertures of a TEM do?

    The effects of both the high contrast apertures (HCA) and objective lens aperatures (OLA) when using the JEOL JEM 3200FS are described here.

  13. Can I do cryoSTEM or cryoSTEM/EDX?

    There are fundamental problems associated with cryoSTEM imaging of biological samples, but if you have a problem that you think can only be answered using these techniques, talk to David Morgan and we can try.

  14. What is free lens control?

    Free lens contrll (FLC) is a way for the user to take control of individual lenses on the EMC's JEOL JEM 3200FS. This can be useful for creating things like spot sizes outside the normal 1 through 5 settings, STEM probes that have properties different from the usual S/M/L settings and a "beam shower" to reduce contamination before STEM imaging. A brief introduction to FLC can be found here.

  15. How accurate are the scale bars on TEM and STEM images?

    The scale bars on TEM and STEM images should be reasonably accurate but are unlikely to represent "absolute truth." Reasons for this and ways around the problems are discussed here.

  16. Where do I save images and spectra when using the JEOL JEM 3200FS?

    Follow these instructions.

  17. How can I examine the images I have recorded and saved?

    Here are some possibilities. We are also working on a web portal interface to the image database from the JEOL JEM 3200FS, and there are frequent updates on this effort. If the portal works well, we will expand its use to include the JEOL JEM 1010 and JEOL JSM 5800LV.

  18. How can I extract frames from movies recorded using an electron microscope?

    Here is one method we have used sucessfully with movies recorded using the FEI Titan S aberration corrected TEM-STEM at ORNL.

  19. What are the CCD pixel sizes associated with the microscopes' different magnifications?

    Calibrated pixel sizes for most magnifications on the JEOL JEM 3200FS can be found here.

  20. How can I prevent my samples and stains from wicking along the tips of my tweezers?

    Here are a couple of ways to prevent this.


Please send your questions to David Morgan.