Course catalogue doctoral education - VT24

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Title Microscopy: Improve Your Imaging Skills - From Sample Preparation to Image Analysis
Course number 2870
Programme Utveckling och regeneration (DevReg)
Language English
Credits 6.0
Date 2021-01-26 -- 2021-02-12
Responsible KI department Institutionen för biovetenskaper och näringslära
Specific entry requirements
Purpose of the course The aim for this course is to improve the microscopy skills of students and researchers who have already and recently used a microscope to acquire digital images of fluorescent samples and want to improve their skills. This is not a course for researchers who have not yet started to use microscopy.
Intended learning outcomes At the end of the course, the participants will be able to:
1- Describe the difference between wide field, confocal and light sheet 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 wide field, a confocal or a light sheet 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, 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- Describe the imaging requirements for automated image analysis
12- Run an image analysis pipeline on freeware (ImageJ/FIJI, Cell Profiler) designed for their own images and scientific question.
Contents of the course The course is NOT aimed at training people to use the LCI facility 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, confocal or light sheet microscope, images that exactly match their samples and answer their scientific questions in a reliable way.
The participants will learn theory and practice about the parameters and hardware used in wide field, confocal and light sheet 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 practical 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. They will also get help to build a pipeline to analyse their images.
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 at each workshop
3. The written examination at the end of the course.
The student must 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 (PDF file available at the KI library)
Number of students 12 - 16
Selection of students All students must have an active microscopy project where they acquire images of fluorescently labelled samples. They will need to bring their samples to one workshop and submit new images during the course. The selection will be made based on the usefulness of the course to the research project, judged from the application. The application must describe the student’s microscopy project and past microscopy experience, as well as some images of the sample (sent to
More information The detailed program of the course can be found on the LCI website ( Presence at the course is mandatory 3 days/week (Tue-Thu) during 3 consecutive weeks, from 09:00 to 17:00 as well as for the examination (Friday of 3rd week). The course counts for 4 weeks because some time before, during and after these 3 weeks is used in preparing samples and completing assignments. The venue is the Live Cell Imaging facility at KI Flemingsberg campus in the Neo building. The students will get marks for each workshop, for each assignment and for the final examination.
COVID-19 information: We are aiming at running lectures, discussions and workshops online. In cases when this is not possible, lectures and discussions will be held in a large room (capacity: 80 persons) in such a way that distancing is achieved. For workshops that cannot be held online and must be run in a small space near the microscopes, students and teachers will be requested to wear a face mask.
Additional course leader In case of problem with the application process, please contact Anna Wallén
Latest course evaluation Course evaluation report
Course responsible Sylvie Le Guyader
Institutionen för biovetenskaper och näringslära
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