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Optics and the Basics of Microscopy

Proper use of standard microscopy techniques, such as widefield and confocal fluorescence microscopy, is dependent on the understanding of how light interacts with both the microscope and the sample. Therefore, the fundamental principles of optics and the theory behind microscopy will be covered by introductory lectures to provide students with the knowledge necessary for the remainder of the workshop. Similarly, sample preparation considerations and basic microscopy operation will be discussed.

Advanced Microscopy Techniques

Following an overview of optics and how fluorescent microscopes work, we will explore the wide variety of advanced microscopy techniques available. Learning opportunities include lectures on 3-dimensional and dynamic imaging techniques, such as lightsheet microscopy, as well as lectures on super-resolution microscopy. These lectures will coincide with hands-on laboratory sessions that provide opportunities to see first-hand the application and function of enhanced and super-resolution techniques.


Fluorescent Probes and Reporters

In parallel to the lectures and practical sessions on microscopy techniques, we will discuss optimal fluorophore choice and introduce advanced biosensor design and application. The workshop will cover photomanipulation techniques, such as FRAP, FLIP, optogenetics, and how photoconversion, photoactivation, as well as FRET-based biosensors, can be used to reveal various biological phenomena.

Image Processing and Quantitative Analysis

Image processing and analysis are fundamental requirements for the appropriate and meaningful extraction of information from digital images. Hands-on tutorials in computer labs will provide a comprehensive introduction to quantitative image analysis using FIJI. Assisted by the faculty, students will be provided with the knowledge of how best to approach a variety of questions typically encountered in life sciences. This will cover the workflow from image processing to image analysis. Students will apply this knowledge during the final class project.


Portable Microscopes in the Field

An important aspect of microscopy, especially in Africa, is its use in diagnosing infectious diseases. These diagnoses are most effective when conducted in the field or at a point-of-care such as clinics or a mobile healthcare units. Together with simple analytical methods, cellphone-based portable microscopes can provide efficient diagnoses and can be used to monitor treatment response. During the course, students will have the opportunity to assemble and use their own cellphone-based microscopes for image acquisition and analysis.

Scientific Communication of Microscopy Data

Effective communication of microscopy data is vital for successful grant application and publications. With this in mind, we will conduct a unique scientific writing workshop that will guide students in writing accurate and effective research reports for the class project. Students of this workshop will also be encouraged to participate in an optional proposal writing competition based on their research. The competition winner will be awarded an all-expenses paid research visit to the Advanced Imaging Center at the HHMI Janelia Research Campus. The workshop faculty will facilitate the preparation of these proposals.

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