Kurskatalog forskarutbildning - VT19

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Titel Microscopy: improve your imaging skills - from sample preparation to image analysis
Kursnummer 2870
Program Utveckling och regeneration (DevReg)
Språk Engelska
Antal högskolepoäng 6.0
Datum 2019-01-22 -- 2019-02-08
Kursansvarig institution Institutionen för biovetenskaper och näringslära
Särskild behörighet 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.
Kursens syfte 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.
Kursens lärandemål 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
Kursens innehåll 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.
Arbetsformer Lectures, videos, workshops, peer review, image troubleshooting in groups, project presentations.
Obligatoriska moment 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.
Kurslitteratur och övriga läromedel Reference literature: Handbook of Biological confocal microscopy, James Pawley Springer Editions 2006
Antal studenter 10 - 16
Urval av studenter The participants will be selected based on the usefulness of the course to their research project. The students must have been acquiring images on a microscope in the past 1 year. Their microscopy research project, as well as their previous microscopy experience must be described in writing in the application.
Övrig information The detailed program can be found on the LCI website (https://ki.se/en/bionut/welcome-to-the-lci-facility) under Learning microscopy. Presence at the course is mandatory 3 days/week during 3 consecutive weeks, from 09:00 to 17:00. The course counts for 4 weeks because some time before, during and after these 3 weeks is used in preparing samples and for 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 the assignments and for the final examination (on 08/02).
Ytterligare kursledare
Tidigare omdöme av kursen omdöme
Kursansvarig Sylvie Le Guyader
Institutionen för biovetenskaper och näringslära

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