Essentials I – Essentials of Widefield-Microscopy (online)

Organizer: Stefan Terjung, Sabine Reither, Marko Lampe and Christian Tischer

Registration for EMBL staff only

The course is a beginners course with focus on teaching the essential knowledge needed to conduct a widefield microscopy-based experiment, to generate reliable data and to inspect and handle the acquired images. It will take place online and consists of a practical session on Thursday February 3rd (10 am – 5 pm) and an image handling and inspection session on Monday February 7th (2 – 5 pm).
Knowledge of this course will be the basis for the Essentials in Microscopy II (Confocal Microscopy) course.

Please be aware that the first part of this course will be mainly an interactive demonstration at the microscope with only a limited amount of theory. The necessary theory for the course is covered in below mentioned online tutorials. Therefore, it is required to watch the following tutorials in advance.

Transmission light path and its alignment
https://www.ibiology.org/talks/microscope-imaging-koehler-illumination/
Fluorescence Microscopy
https://www.ibiology.org/talks/fluorescence-microscopy/
Bit depth and resolution in an image
https://www.ibiology.org/talks/digital-image-analysis/
Resolution in Microscopy
https://www.ibiology.org/talks/resolution-of-a-microscope/
Objectives and optical aberrations
Objectives and Eyepieces
Point spread function
https://www.youtube.com/watch?v=Tkc_GOCjx7E&list=PL7Y2NBzyw8AhVl5iJZIACsq-Rk8fmB5f9&index=2

Course dates and program outline (additional breaks will be included on demand):

Practical session February 3rd:

Estimated Time	Topic
10:00 am – 10:15 am	Welcome and introduction round
10:15 am – 11:00 am	Transmission light path and Köhler illumination
11:00 am – 12:30 pm	Fluorescence microscopy, filters and how to find good filter fluorophore combinations
12:30 pm – 2:00 pm	Lunch break
2:00 pm – 4:30 pm	Open discussion round (including spontaneous brakes): ‘What is a good image?’ We’ll cover the following topics (not exclusively): Light sources, Microscope objectives, magnification, resolution, brightness, exposure time, bit depth and LUT, background level, cover slips, remarks on sample preparation
4:30 pm – 5:00 pm	Discussion / Q&A and closing remarks

Image handling and inspection session February 7th:
2 – 5 pm: Using ImageJ, we will cover the following topics related to image data handling and inspection:

Opening images
-Image content and inspection
-Image calibration
-Image data types
-Image file formats

Further teaching material:

In case you are interested in learning the theory of widefield microscopy in more detail, please check out the following links:

Olympus interactive Java tutorial https://www.olympus-lifescience.com/en/microscope-resource/primer/java/
iBiology microscopy courses https://www.ibiology.org/online-biology-courses/microscopy-series/
Microcourse done by Jennifer Waters https://www.youtube.com/channel/UC4cOKa0TZK8CQhzSQqfwuMQ/

Bookings

This event is fully booked.