Microscopy Basic Training

This is the textbook for the microscopy basic training course that is provided to new members of the Laboratory of Experimental Biophysics at the École Polytechnique Fédérale de Lausanne (EPFL), Switzerland.

The course grew out of a yearly survey of lab members asking about problems and inefficiencies in their research. Participants indicated that they felt underprepared to address unexpected technical problems that arise during imaging experiments. These problems are further compounded by the fact that the lab uses a mixture of custom and commercial microscopes and software. In addition, we are a multidisciplinary lab with a range of backgrounds and experience, so our communal knowledge tends to be dispersed among our members. As a result it is often difficult to find the right person to help.

The EPFL BioImaging and Optics Platform (BIOP) provides a yearly course in advanced microscopy. At the time of this basic training's conception, those students who had attended the BIOP course felt that it was useful, but too focused on theoretical aspects of microscopy to address the problems identified in the survey. We therefore collectively decided to create our own basic training course that would complement the material covered by the BIOP, focusing on hands-on learning and problem solving.

Focus Areas

In a follow-up discussion we decided upon a list of areas that the course should emphasize:

• Microscope customization to better fit the needs of an experiment
• How to adjust microscope settings for optimal imaging
• Relationships between microscope parameters and tradeoffs
• Micro-Manager
• How to identify points of failure (software, sample, camera, etc.)
• How to describe imaging problems clearly and demonstrate a train of thought
• Asking for help effectively

Many of these skills cannot be directly taught. We hope that the problem solving scenarios that one naturally encounters when building and operating a custom-built microscope will instead serve as a sufficient environment for learning practical skills.

Structure and Duration

The course is intended to last at most two weeks with students spending a few hours per day on the material. It is divided into modules so that

• a set of modules may be chosen according to each student's background and needs
• a module can be studied independently and as needed throughout the course of a student's or post-doc's time in the lab

An experienced member of the lab will provide help and feedback during the course, though free time for play is encouraged.

Corrections and Suggestions

Any corrections or suggestions may be made by opening a pull request or issue at this book's GitHub repository: https://github.com/LEB-EPFL/basic_training