Course catalogue doctoral education - HT23

  • Ansökan kan ske mellan 2023-04-17 och 2023-05-15
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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 2023-01-30 -- 2023-02-17
Responsible KI department Institutionen för biovetenskaper och näringslära
Specific entry requirements The applicants must have an on-going microscopy project and be able to prepare their own fluorescent sample for that project. In their lab or local facility, they must have been trained on a microscope able to acquire images of fluorescent samples and they must be very familiar with using that microscope (using it at least 3 months prior to the start of the LCI course).
Purpose of the course The purpose of this course is to enable PhD students and researchers who have already and recently used a microscope to acquire images of fluorescent samples, to improve their microscopy skills.
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 about their OWN sample and their OWN microscope, to enable them to 1) prepare their sample and formulate their scientific question in a way that is suitable for data extraction from fluorescence images, 2) properly use the hardware available in their lab/facility and 3) fully understand each parameter they need to set in the software in their lab/facility. The aim is to provide them with the tools to acquire on ANY wide field, confocal or light sheet microscope, images of their samples that reliably answer their scientific question.
Intended learning outcomes At the end of the course, the participants will be able to:
1- Formulate their scientific question in terms of which objects in the image need to be segmented, which parameters need to be measured and what image resolution is needed to enable this measurement.
2- Explain how their microscope works and argue if this is the most suitable type of microscope to answer their scientific question or if (and why) a different type of microscope would be more adequate.
3- Explain how their sample corresponds to/deviates from a perfect sample for light microscopy, justify why they are preparing their sample the way they do and what they can do to improve their preparation.
4- Explain why the objective they use is adequate to answer their scientific question or why another type of objective would work better.
5- Explain what pixel size their images have and which acquisition settings this depends on. Explain if this is appropriate to capture the information delivered by the objective, if this is required by the scientific question, and what they can do to improve their settings.
Contents of the course Aside from the points described in the Learning Outcomes, the participants will be able to learn the following:
- The differences (theory and hardware) between wide field, confocal and light sheet microscopes as well as the different types of confocal microscopes
- How to pick the best combination of fluorophores for their own sample on their own microscope, identify and eliminate bleed-through and cross-excitation problems
- How to find the area of interest in their sample without bleaching it
- How to adjust the condenser for proper transmitted light imaging
- How to set the following microscope parameters: resolution, pixel size, averaging, scan speed, illumination power, detector gain and offset, camera readout rate, exposure time and binning
- Many practical tricks about fixation, mounting and handling of their sample in a way that is optimal for imaging
- How to deal with the challenges of imaging fluorescent volumes
- What hardware or software autofocus, spectral detector, resonance scanner, two-photon or super resolution microscopy are used for
- Many personalized tips on how to improve the preparation and imaging of their own sample on their own microscope (through the workshop where we will image their own sample)
- Where to get help to create an image analysis pipeline for their own images and scientific question
- The ethics of handling scientific images for publication
- How to easily assemble a figure for publications
Teaching and learning activities Lectures, videos, workshops, group discussions, project presentations, quizzes and assignments.
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 the 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 written examination at the end of the course
3) The way the students demonstrate in the weekly reports that they have reached the Intended Learning Outcomes
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 - 20
Selection of students The selection will be based on the applicants' potential to follow the course and fulfil the imaging assignments, and the usefulness of the course to their current research project.
More information The students must a) have an active microscopy project where they acquire digital images of fluorescently labelled samples; b) be able to bring their sample to the course; c) have access to their microscope during the course (some assignments require submitting new images); d) be fully committed to the course for 3 weeks. The applications must contain the following 4 parts: 1) the confirmation that the applicants fulfil the a, b, c and d conditions listed above; 2) a brief description of the scientific aim of their own imaging projects; 3) a brief description of their past microscopy experience, when they started their current microscopy project (should be at least 3 months) and which microscope(s) they currently use; 4) fluorescent images of their sample acquired by them and uploaded in the original format delivered by their microscope (please write to Anna Wallén ( to ask for a link to upload your original images). Applications will only be considered when original images are submitted. Researchers who have not yet used microscopy or do not have an active microscopy project are advised to get trained at their local imaging facility, acquire images for at least 3 months then apply to the LCI course next year.
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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