If you have any questions about the Electron Microscopy Center (EMC) or our equipment and processes, please send them to David Morgan at dagmorga@indiana.edu, and they'll be answered below!
Frequently Asked Questions of the Electron Microscopy Center
We offer detailed procedures for starting to work within the EMC, 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.
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.
Yes. The EMC has always has a vision for directions it would like to take. Many of these future directions for the EMC are gathered elsewhere. 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.
The entire collection of random images has a web page all its own.
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.
Several users of the EMC have had 3D models printed, and here's our collected information on 3D model making.
Here is a short list of EM manufacturers and companies who make attachments, holders, etc.
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 we offer a list of available items and their costs.
That will depend on both the actual sample and what you want to accomplish, but we do offer some guidelines on magnifications.
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.
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).
We offer information on the effects of different apertures when using the JEOL JEM 3200FS, specifically the use of high contrast apertures (HCA) and objective lens aperatures (OLA).
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 at dagmorga@indiana.edu and we can try.
Free lens control (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. We offer a brief introduction to free lens control (FLC).
The scale bars on TEM and STEM images should be reasonably accurate but are unlikely to represent "absolute truth." We offer additional information on scales bars, including proof supporting this statement, as well as some ways around this issue.
We offer a set of instructions on saving images and spectra.
We offer some some information on how to directly display dm3 files. We are also working on a web portal interface to the image database from the JEOL JEM 3200FS, and there are frequent updates on the Scalable Computer Archive (EMC-SCA) project. If the portal works well, we will expand its use to include the JEOL JEM 1010 and JEOL JSM 5800LV.
We have detailed one method of extracting movie frames, successfully recorded using the FEI Titan S aberration corrected TEM-STEM at Oak Ridge National Laboratory (ORNL).
We offer calibrated pixel sizes for most magnifications on the JEOL JEM 3200FS.
We have detailed a few methods to prevent samples and stains from wicking on tweezer tips.