Information For New Users

EMC mailing lists: New users of the EM Center should subscribe to the mailing list for all users of the facility: send an empty e-mail to LIST@LIST.INDIANA.EDU that contains SUBSCRIBE EMC-1010-USERS-L as the subject. A more thorough description of the mailing list system can be found here.


Starting new projects: Before starting a new project with the EMC, please discuss the project details with the EMC staff. Such discussions should include the laboratory PI and all lab personnel who will work on the project. Discussions should include any useful background information (especially references to similar work), the project's specific goals, the state of the sample(s) to be examined, expectations for the project's time-to-completion (including possible benchmarks along the way), involvement of the staff versus lab personnel (e.g., specific roles in providing advice, training, imaging and/or analysis). The EMC will then provide a document that includes an assessment of overall project feasibility, and where possible, timelines and estimates of the amount of effort required by everyone involved in the project. The document will also describe fees associated with various parts of the project. To commence work on the project, the PI will need to provide an account number to be charged.

NOTE: When the staff is asked to perform fee-for-service work, even more attention than usual should be paid to the discussions and documents described above. While some fee-for-service work is quite simple and straight-forward, other projects can be more ill-defined, open-ended and/or at the cutting edge of what is feasible. Everyone involved in such difficult projects needs to have a clear understanding of goals, timelines, feasibility, etc., and that only happens with frequent and detailed communication among the involved parties. Plans for such communication should be part of the initial discussions before beginning a project.

Training with equipment: All new users of EMC equipment will need training, regardless of previous experience with similar (or even identical) equipment. All training starts in the Myers Hall area, under the supervision of Barry Stein. After discussing your project with the EMC staff, please contact Barry to begin training with the necessary equipment.

Some details (including time estimates) about training with EMC equipment can be found below.


New users of the JEOL JEM 1010 should expect to spend 2 or 3 two-hour sessions with Barry Stein when learning to use the transmission electron microscope (TEM). People familiar with the operation of other TEM's can often accomplish this training in one or two 2-hr sessions. Training for the 1010 can be done before a user has a specimen to examine, and new users often learn TEM techniques more quickly using a well-behaved specimen than when they try to learn using their own sample of interest.

Training for the JEOL JEM 1400plus transmission electron microscope (TEM) will start in February (or early March), 2017. Users of the 3200FS can expect to spend 2 two-hour training sessions learning how to operate the new microscope while new users (or existing users of the 1010) should expect to need 3 or 4 two-hours training sessions. Training to use the Oxford Instruments AZtecEnergy EDX system will involve additional training.

Training for simple imaging with the JEOL JEM 3200FS can begin only after training on the 1010 or 1400plus has been completed and after a user can show the required degree of proficiency with either instrument. Actual training on the 3200FS generally requires as many as 4 or 5 two-hour training sessions before a new user is comfortable using the instrument and competent to obtain publication quality images. Initial training is best done using a standard, well-behaved specimen, though most new users can begin to examine their own specimens before training is complete. Contact Barry Stein to initiate the work using the 1010 or 1400plus, and then David Morgan to discuss the work specific to the 3200FS. More details about starting to use the 3200FS can be found here.

Advanced use of the the 3200FS such as low dose work, cryo-imaging, tomography, STEM, STEM/EDX, etc. will require additional training sessions (again in blocks of about 2 hr) followed by practice in order to become comfortable and proficient. All advanced training is at the discretion of the staff and requires that a user be both comfortable and competent while using the 3200FS for routine imaging tasks. Most advanced techniques require one or perhaps two training sessions, but they all require multiple additional sessions in order for a user to be proficient and able to produce useful results. Contact David Morgan for further information about these topics.

Tomographic data collection using serialEM can be performed using either the 1400plus or the 3200FS and training to use serialEM can start as soon as a user is well-trained with either instrument. The initial training involves 2 or 3 four-hour blocks of time. Extension of this training to low dose tomography and eventually to cryo-tomography (cryoET) will require an additional 3 or 4 four-hour blocks. As with other advanced microscopy techniques, learning to perform the steps is different from being able to produce high quality results all the time, and extensive practice is needed in order to become proficient. Contact David Morgan for further information about using serialEM.

Training with the Wohlwend and Leica AFS-2 is relatively simple and should only require one session to learn the mechanics of using either of these machines. However, both high pressure freezing and freeze-substitution are currently a bit more art than science, and productive use of these machines will involve practice and some trial and error while optimizing conditions. The staff encourages users to search the literature for high pressure freezing reports about similar samples. We can also put our users in contact with several experts in the field who can offer invaluable advice and potentially save months of otherwise un-productive effort. We have recently begun a monthly discussion group that deals with issues of high pressure freezing and freeze substitution. This meeting occurs on the first Tuesday of each month, from 11 am until noon in Simon Hall 030.. Interested people should contact David Morgan about this meeting.

Use of the Porter-Blum and LKB ultramicrotomes is also more voodoo than science, and it can be quite difficult to predict how much training a person may require. Initial training usually involves 2 four-hour sessions and generally results in the ability to cut "semi-thin" sections competently using a glass knife. An additional 4-hour session is often all that is needed to graduate from semi-thin to thin sections. Use of EMC diamond knives will be allowed once a user shows proficiency with glass knives, but bear in mind that this is under the supervision and at the discretion of Barry Stein. The EMC strongly suggests that users who plan to cut lots of sections should also plan to invest in a personal (or lab) diamond knife.

The Denton DV502 carbon evaporator can be used for several completely different purposes, and training in its use will depend on what the user needs to do. The most common use of the Denton is to glow discharge carbon coated TEM grids, which involves about an hour of training. The Denton can also be used to deposit thin, amorphous carbon for TEM support films or to metal shadow samples both using a rotary turntable and unidirectionally. This work can only be done under the supervision of Barry Stein. Contact Barry directly if you think you will need to use the Denton for such purposes.

The Vitrobot Mk 3 and EMS manual plunge freezer are both simple to operate, and training with either requires about one hour. However, use of either device to produce high quality plunge-frozen grids on a routine basis is likely to require both some practice and a certain amount of trial and error. The staff of the EMC can offer suggestions when standard freezing conditions do not produce acceptable grids, but bear in mind that most samples behave slightly differently from others, and some of them can be terribly idiosyncratic. Most (but not all) samples can eventually be plunge-frozen adequately, but there are cases where the amount of trial and error does seem excessive.

DISCLAIMERS: The number of sessions and their lengths described above are intended to act as a general guideline and not as a guarantee: while all these time estimates are reasonable based on the staff's previous experiences, there is no promise that a particular new user will be adequtely trained after exactly the listed number of sessions. Also bear in mind that use of all the EMC equipment improves with practice, and especially for devices like the Wohlwend, Leica AFS-2 and the plunge freezers, learning the mechanics of how such equipment works is only the first step in learning to use such equipment well enough to generate useful results routinely.