Course catalogue doctoral education - HT21

  • Application can be done between 2021-04-15 and 2021-05-17
Application closed
Title Microscopy: improve your imaging skills - from sample preparation to image analysis
Course number 2870
Programme Development and regeneration (DevReg)
Language English
Credits 6.0
Date 2020-01-21 -- 2020-02-07
Responsible KI department Department of Biosciences and Nutrition
Specific entry requirements Participants must have used a microscope to acquire digital images of fluorescently labelled samples during the past 1 year and be able to prepare their own samples at own department at the start of the course.
Purpose of the course The aim for this course is to improve the microscopy skills of students and researchers who have already used a microscope to acquire digital images of fluorescent samples and want to improve their skills.
Intended learning outcomes At the end of the course, the participants will be able to:
1- Describe the difference between wide field and confocal microscopes as well as the different types of confocal microscopes and choose which system is most suited to their experiments
2- Pick the best combination of fluorophores for their experiment by matching their spectra with the microscope light source and filters, identify and eliminate bleed-through and cross-excitation problems
3- Explain objective specifications and limitations and choose the appropriate objective for their own experiments
4- Describe how to fix, mount and handle their sample in a way that is optimal for imaging
5- Find their sample and the area of interest without bleaching it
6- Adjust the condenser for proper DIC imaging (Koehlering)
7- Explain how to set the following parameters on a confocal or a wide field system to best match the requirements of their sample and reliably answer their scientific question: resolution, pixel size, averaging, scan speed, illumination power, detector gain and offset, camera readout rate, exposure time and camera binning
8- Explain which applications require a hardware or a software autofocus, a spectral detector, a resonance scanner, light sheet, two-photon or super resolution microscopy
9- Explain the advantages in using the automation of a microscope system to collect multidimensional data
10- Explain how to deal with images before publication in scientific journals
11- Run a simple image analysis on freeware (ImageJ/FIJI, Cell Profiler) and describe the imaging requirements for automated image analysis
12- Critically comment on their peers' imaging settings and troubleshoot their images
Contents of the course The course is NOT aimed at training people to use the LCI unit microscopes. The focus is instead on providing the students with enough theoretical and practical knowledge so that, when they go back to their lab, they are able to properly use the hardware available there and so that they fully understand each parameter they need to set in the software. The aim is to provide them with the tools to acquire on ANY wide field or confocal microscope, images that exactly match their samples and answer their scientific questions in a reliable way.
The participants will learn the theory and many practical tricks about the parameters and hardware used in wide field and confocal imaging, how to identify and avoid imaging artefacts, deal with the challenges of imaging fluorescent volumes, get started with automated image analysis, as well as how to handle scientific images for publication. They will also hear many tricks about fixation, mounting and handling of their sample in a way that is optimal for imaging and they will learn about more advanced microscopy techniques. Through the workshop where we will image their own sample, they will get tons of personalized tips on how to improve the preparation and imaging of their own sample.
Teaching and learning activities Lectures, videos, workshops, peer review, image troubleshooting in groups, project presentations.
Compulsory elements Attendance to all sessions is compulsory. Any absence must be reported to the course leader in advance by e-mail. Absence from any part of the course (lectures, laboratory sessions, discussion sessions and exam) is generally not accepted but could in exceptional cases be compensated by a written additional assignment to ensure the learning outcomes of the day have been reached. If it is not possible to compensate, the student will be given a chance to complete the course by attending the missing sessions the following year.
Examination The final mark (pass or fail) will depend on the results of:
1. The weekly assignments
2. The skills shown in each workshop
3. The written examination at the end of the course.
The student has to show that all intended learning outcomes of the course have been reached.
Literature and other teaching material Reference literature: Handbook of Biological confocal microscopy, James Pawley
Springer Editions 2006
Number of students 10 - 16
Selection of students The selection will be made based on the wwritten motivation in the application. The application must describe the student's research project, their past experience using fluorescence microscopy and how useful this technique is to their research project. The participants will be selected based on the usefulness of the course to their research project.
More information The detailed program of the course can be found on the LCI website ( Presence at the course is mandatory 3 days/week during 3 consecutive weeks, from 09:00 to 17:00 as well as for the examination, on the last day of the 3rd week. The course counts for 4 weeks because some time before, during and after these 3 weeks is used in preparing samples and to complete assignments. The venue is the Live Cell Imaging facility at KI Flemingsberg campus in the Neo building. This course is run in parallel with course 2871 ”Microscopy: improve your imaging skills”.
Additional course leader
Latest course evaluation Course evaluation report
Course responsible Sylvie Le Guyader
Department of Biosciences and Nutrition
Contact person -