Our Training Courses

The Micron short course curriculum provides an in-depth study of microscopy, from the basic principles to advanced super-resolution methods. These theoretical courses are intended to complement the practical and experimental training provided during your practical microscopy training session at Micron. Participation in these courses is strongly encouraged for anyone utilising microscopy in their research. 

Micron users can book a place on each course via PPMS.

These courses are small group sessions with a max of 6 to 12 attendees per session. 

This introductory course is designed to give you a foundational understanding of fluorescence microscopy. The following key topics will be covered:

• Using fluorescence microscopy to understand the inner workings of biology.
• Specificity and contrast in microscopy. 
• Techniques in quantitative fluorescence microscopy.
• Overview of various types of fluorescence microscopes. 
• Tags: small molecules, antibodies, nanobodies, GFP, Halo, FISH.  
•  Core principles of fluorescence and Jablonski diagrams. 
• Understanding fluorescent spectra, fluorophores, and autofluorescence.
• Addressing challenges in fluorescence microscopy: photobleaching and phototoxicity.

No prior experience with fluorescence microscopy is required for this course.

This course is designed to provide you with an in-depth understanding of the two fundamental microscopy techniques: widefield and confocal microscopy. The following subjects will be covered:

Anatomy of a Fluorescence Microscope: Explore the key components of a fluorescence microscope, including objectives, illumination sources, dichroic mirrors, and detectors.

Widefield vs. Confocal Microscopy: Understand the differences between Widefield and Confocal microscopy and learn how to choose the appropriate technique for your research project.

Magnification and Resolution Concepts: Magnification and resolution, with an introduction to Abbe’s resolution limit, the Rayleigh Criterion, and Nyquist sampling.

Ideal vs. Real Microscopy: the differences between ideal and real microscopy, covering topics such as spherical and chromatic aberrations, scattering, background noise, and the importance of deconvolution in image processing.

 This beginner-friendly course provides a foundation in the principles of optics as applied to microscopy. Participants will explore the nature of light, the role of lenses in image formation, and the fundamentals of diffraction. Through examples and simple demonstrations, students will learn how these core concepts influence resolution, contrast, and image quality in microscopy. Designed for newcomers, the course emphasizes clear explanations and hands-on understanding to build confidence in applying optical principles to real-world microscopy.

Sample preparation has a major impact on microscopy and good sample preparation is a prerequisite to ensure high quality data is captured. In this course we will cover the multiple steps of sample preparation for fluorescence microscopy, including the imaging workflow, fixation, permeabilisation, fluorescence labelling and staining, and choosing fluorophores. Understanding the impact of each step in the sample preparation process is essential for achieving optimal imaging results

This course delves into the theory and application of super-resolution microscopy. It is designed for participants who have an immediate need to implement these advanced techniques in their biological research. The course will cover the following topics: STED, SIM, localization microscopy (including PALM, dSTORM, and PAINT), pixel-reassignment, and super-resolution imaging of living samples. All these super-resolution techniques are available to access in Micron. 

Participants should have a solid understanding of basic microscopy techniques and some experience in fluorescence microscopy. Familiarity with biological imaging and prior exposure to advanced imaging methods will be beneficial, as the course is geared towards those who plan to apply super-resolution to their research.

This course delivers tips and tricks for those starting out in SMLM. The course covers the applications of SMLM,  sample preparation, types of hardware, image acquisition and an introduction the FIJI Plug-in ThunderSTORM. 

 This course provides researchers with essential skills to ensure accuracy, transparency, and reproducibility in microscopy-based experiments. Participants will learn best practices for data acquisition, documentation, and reporting in line with community standards. As leading publishers now require detailed reporting guidelines for microscopy data, the course provides practical strategies to meet these standards.

This course provides a foundation in image analysis tailored to microscopy. Participants will learn the principles of digital imaging, common analysis techniques, and best practices for extracting meaningful biological information from microscopy data. Topics include image preprocessing, segmentation, quantification, and visualization using widely adopted open-source tools. 

This is an interactive course to introduce attendees to the principles and practical methods of co-localisation experiments. The session provides a comprehensive overview of how to do spatial analysis between fluorescent signals using FIJI, covering key quantitative approaches such as correlation, co- distributions and co-occurrence. Attendees will learn how to design robust co-localisation experiments including selection of appropriate controls and fluorophores, and how to interpret results effectively. The workshop includes hands-on exercises using test datasets, with the option for attendees to analyse their own data if they wish. You are encouraged to bring their own laptop, and FIJI will be installed as part of the course.

The registration fee is £75 per course and this will be charged at month end for University of 

Oxford staff and students. Course cancellations within 48 hours will be charged at the full rate. These courses run a waiting list, therefore if you can no longer attend a course please contact us as soon as possible.  Substitutions may made be please inform us.