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Learning Microscopy for Research

Training Flowchart

Learning how to use microscopy for your research requires at least four steps:

  1. Conceptual: classwork to learn fundamental concepts for all microscopes
  2. Concrete: supervised, hands-on training to operate a particular microscope or instrument; experienced users can skip the training.
  3. Safety Test: pass an individual certification test to show that you can safely use the instrument on your own.
  4. Practice: for your initial period of unsupervised use, you'll be on probation, restricted to business hours, thus allowing you to ask us for immediate help
  5. Specialized Techniques: one-on-one training for specialized and advanced techniques

We only charge users for hands-on or one-on-one training and certification (see fee schedule). All other troubleshooting help is provided free as a part of membership.

Before you commit to a microscopy strategy, we strongly encourage you to make an appointment to discuss your research needs. It's a free service, and it can save a lot of anguish.


  1. Conceptual Learning (Formal Classes)
  2. Modern microscopy naturally splits into two modalities: electron microscopy vs. light and fluorescence microscopy. For each modality, we teach an introductory course that covers both fundamental and some advanced application concepts.

    These courses are intended for researchers that want to use these techniques in their own biomedical projects. We focus on how modern microscopy could have an impact on your research. Because real research applications requires real understanding, we suggest that you take the appropriate course before you enroll for one-on-one training.

    All courses will be taught by Dr. Kuo and the Facility staff, and are described below. for more information.

    ME110.807: Fundamentals of Fluorescence and Confocal Microscopy
    Completely Revised in 2012: New emphasis on computer-based tools for image preparation and analysis with sessions in computer lab almost every week, complementing lectures. An additional lab day for operating a generic fluorescence microscope, learning to avoid common errors that preclude quantitative image interpretation.
    Beyond Photoshop, what is a digital image and how can it be interpreted quantitatively? How does a light and fluorescence microscope form an image? When can the microscope 'see' things better than me? When can people see things better than the computer? What are the different types of confocal microscopy (laser-spot scanning, slit scanning, spinning disk), why are they special, and when is each appropriate? Offered annually in fall.

    Next offering: Fall 2013
    Begins: Tuesday, September 10, 2013
    Ends: Tuesday, November 5, 2013

    Lecture day: Tuesday
    Lecture time: 2:15pm-4:15pm
    Lecture location: PCTB 113-114; Computer lab: PCTB 115

    Lab day: TBA (either Wed 10/10/13 or Thu 10/11/13, 2h slots)

    Comments: Students (all levels, including faculty) must register, even if auditing the course, through the SOM Registrar's Office.

    ME110.722: Principles of Light and Fluorescence Microscopy
    This is an advanced course for students wishing to understand state-of-the-art microscopy, perhaps to customize existing instruments. Students should have completed ME110.807 or have equivalent experience. In addition to a more rigorous presentation of the principles of optical image formation for multiple light and fluorescent microscopes, the theory behind "best-practices" in microscopy (Koehler illumination, infinity optics) are actively considered. Not only reviewing the electromagnetic wave nature of light, advanced topics such as Fourier optics, point-spread functions, and spherical aberration will be considered in the context of modern microscopy. The culmination is considering the instrumentation design choices in assembing a multiphoton fluorescence microscope.

    Next offering (bi-annually): To Be Announced

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  3. Concrete Learning (One-on-one Advising and Training)
  4. Pre-arranged via , the Microscope Facility offers both advising and one-on-one training:

    • Available at no cost, are available to discuss research and microscopy strategy. We have lots of experience, specialty software and accessories that can really help. In addition, discussing strategic feasibility in advance can save a lot of anguish!

    • For a fee, is available to teach people how to use microscopes and preparing specimens for electron microscopy.

    Our goal in one-on-one training is to make sure you can operate equipment with minimal sufficiency and safety, but not necessarily proficiency. Only sustained practice grants proficiency, and ultimately, expertise.

    For training on both microscopy and EM specimen preparation, we will guide you through instrument operation, care and safety, allowing you to practice under our supervision. In particular, we are concerned about safety for you and for the equipment. These form the basis of certification testing.

    For training on the microscopes, we will also teach you the controls that affect the quality of images. In particular, we will emphasize the issues that are relevant for your research goals.

    The more experienced you are, the less time the training will take. Similarly, the more concepts you understand (see coursework), the less time the training will take. More than one person can observe a training session. However, only one person can operate the equipment at a time, particularly during supervised practice and during certification testing.

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  5. Unsupervised Practice and Use (Certification and Probation)
  6. Before we can allow you to practice and use the microscope on your own, we must certify that you've been appropriately trained. Please to schedule time for certification.

    For certification, we will observe you while you operate the instrument from start to finish, completely on your own. All safety and Facility logging procedures must be observed. The whole testing process must be scheduled in advance, and can take 15-30 minutes, depending on the complexity of the instrument.

    If you pass the test by safely operating the equipment and observing all Facility logging procedures, you are "certified" and allowed unsupervised use of the instrument. After certification, we will grant you access unsupervised access to the equipment (reservations via webcalendar).

    Upon certification, novice users are subject to a probationary period. Under probation, the online webCalendar will only allow you to reserve equipment for use during standard business hours (MF 9-5). This restriction ensures that we're available to help you if you encounter any problems or if you have questions (no charge).

    If there is a long lapse (>6 weeks) without using equipment immediately after certification, we reserve the right to withdraw a user's certification. There's just no way to remember a complicated process without practicing! In addition, we reserve the right to revoke a person's certification should they repeatedly damage equipment, flaunt safety issues, or flaunt Facility procedures.

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  7. Specialized Techniques (One-on-one training)
  8. Once you've built confidence that you can do the basics, it's natural to consider specialized or advanced techniques on Facility equipment. These include FRAP (Fluorescence Recovery After Photobleaching), FRET (Forster-fluorescence Resonance Energy Transfer) and TIRF (Total Internal Reflection Fluorescence). Presumably, you've already gotten the concepts and principles elsewhere (particularly from our classes).

    Even if you already understand the concepts, using these techniques and getting results takes a significant amount of time. In addition, we have custom-written sofware that goes beyond the commercial software for the quantitative analysis of these and other experiments. with us and we will walk you through the technique in a one-on-one setting.

    Learning microscopy is an ongoing endeavor. The technical envelope of feasibility is always expanding and improving. Learn how to harness these ever-more powerful techniques in your research!

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