Information For New Users

iLab: Reservations and billing for the EMC are handled by a web-based system called iLab. Users and their PI's must have iLab accounts before starting to use the facility. A description of how to interact with iLab can be found here.

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 FirstName LastName" as the subject. A more thorough description of the mailing list system can be found here.


Starting new projects: Please initiate all new projects by requesting a consultation through iLab. The consultation request can be made by anyone with an iLab account but should always be done with the approval of the PI involved in the proposed work. There is no fee for staff time spent on consultations. The offical request through iLab helps the EMC track both new projects and the staff response to them. The iLab consultation request page asks for a brief description of the project and allows the requesting person to upload any additional files (literature references, images recorded in other EM facilities, etc.) and to suggest a time and date for the official consultation.

Once a request has been sent to the EMC, the staff will respond (also using iLab). In most cases, the response from the EMC staff will simply be an invitation to meet face-to-face with the person who made the request. This meeting should involve the PI and all lab personnel who will be involved in the project. The purpose of such a meeting is to review and expand the project described in the iLab consultation request. The meeting can also cover the state of the sample(s) to be examined, expectations for the project's time-to-completion (including possible benchmarks along the way) and involvement of the staff versus lab personnel (for example, specific roles of the staff with regard to providing advice, training, imaging and/or analysis).

After such a meeting, the EMC will 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. This document and an estimate of the fees associated with various parts of the project will be entered into iLab. Before work on the project can begin, the PI will need to authorize the EMC to use a specific account.

NOTE: When the staff is asked to perform fee-for-service work, even more attention than usual should be paid to the discussion 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 make a training request using the iLab Service Request page.

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 this transmission electron microscope (TEM). People familiar with the operation of other TEM's can often accomplish this training in 1 or 2 two-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. After completing these training sessions, a new user will normally be able to use the instrument without any staff supervision and will be authorized to make reservations for the 1010 using iLab. However, the EMC staff can request that a person use the instrument only during the hours when staff is available for help and oversight. More information for new users of the 1010 can be found here.

Training for the JEOL JEM 1400plus can be started after a user shows a required degree of proficiency with the 1010 (described here). New users should expect to need 3 or 4 two-hour training sessions with either Barry Stein or Joe Wang. After completing these training sessions, a new user should be able to demonstrate basic microscope alignment, to start the instrument in the morning, to bake the ACD as the last user of the day and to use the Gatan OneView camera. After completing training with the 1400plus, new users will normally be able to use the instrument without staff supervision and will be authorized to make reservations for the 1400plus using iLab. As with all EMC equipment, the EMC staff can request that a person use the instrument only during hours when staff is available for help and oversight. Additional information for new users of the 1400 can be found here.

Advanced use of the the 1400plus such as low dose or cryo imaging or use of the Oxford Instruments AZtecEnergy EDX system and any of the non-standard holders (e.g., the cryo-holders, the single or dual tilt beryllium holders or the Poseidon liquid cell holder) will involve additional training (and requests for training should be made through iLab). Advanced use training is at the discretion of the staff and will only begin after a user has developed enough proficiency with the 1400plus that the use of the TEM itself is effectively effortless. Contact Joe Wang or David Morgan for further information about these topics.

Training for simple imaging with the JEOL JEM 3200FS can begin only after training on the 1400plus has been completed and after a user can show both a degree of proficiency with the 1400plus and a need for the 3200FS. Actual training on the 3200FS generally requires as many as 4 or 5 two-hour training sessions with David Morgan 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, but most new users can begin to examine their own specimens before training is complete. More details about starting to use the 3200FS can be found here.

Advanced use of the the 3200FS such as low dose or cryo-imaging, tomography, EDX, 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 should be requested using iLab and is at the discretion of the staff. Such additional training 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 2 or 3 four-hour blocks, and will only be done once a user shows competency with room temperature, high dose tomography. As with the 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 with Barry Stein 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. In the past, we have held a monthly discussion group that deals with issues of high pressure freezing and freeze substitution. Interested users should contact David Morgan about restarting such a meeting.

Use of the Porter-Blum and LKB ultramicrotomes is also somewhat more voodoo than science, and it can be quite difficult to predict how much training a person will require. Initial training with Barry Stein 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.

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.