Microscopy 13 half days course

Improve your imaging skills

– learn the theory behind all settings

January 2017

Foto: Tomas McKenna

This course is designed for you who already have a little

experience of fluorescence microscopy but feel that you

need to improve your microscopy skills in order not to limit

your performance.

About the course

The aim for this course is to improve your microscopy skills for acquiring

digital images of fluorescent samples .

At the end of the course, you will be able to: -

• Describe the difference between wide field and confocal microscopes

as well as the different types of confocal microscopes

• Evaluate fluorophores by matching their spectra with the microscope

light source and filters, identify and avoid bleed-through and cross-

excitation

• Explain objective specifications and limitations

• Explain the theory behind resolution, pixel density, averaging, scan

speed, which laser power, detector gain and offset to use

• Explain which applications require a hardware or a software

autofocus, a spectral detector, a resonance scanner, two-photon

microscopy or super resolution

• Explain the advantages in using the automation of a microscope

system to collect multidimensional data

• Explain how to deal with images before publication in scientific

journals

Course Content

The course includes the theory of the parameters and hardware used in

confocal imaging, how to identify and avoid imaging artifacts, deal with

the challenges of imaging fluorescent volumes, as well as how to handle

scientific images for publication. You will learn about more advanced

techniques like two-photon microscopy, super resolution and spectral

imaging.

Throughout the course you will also improve your critical thinking skills

through peer review and discussions.

COURSE LEADER

Sylvie Le Guyader

Course leader and Microscopy Facility

Manager

Department of Biosciences and Nutrition

Karolinska Institutet

“A lot can go really wrong with

microscopy. It is really important to

acquire a solid education to be able to

troubleshoot and move forward!”

Microscopy 13 half days course Improve your imaging skills – learn the theory behind all settings

WHO IS THIS FOR?

Researchers, technicians, group

leaders or others who wants to improve

their microscopy skills.

Participants should preferably have a

little experience from microscopy

imaging, to be able to follow the tuition.

COURSE STRUCTURE

The course will run 3 half days per week

during 4 weeks and consists of lectures,

videos, peer review and image

troubleshooting in groups.

Study outline

Week 1 : 17 jan, 18 jan, 19 jan

• Microscope types, Fluorescence

• Fluorophores, filters and spectra

• Objectives, cameras/detector

Lectures, Quiz and assignments

Week 2: 23 jan, 24 jan, 25 jan

• Resolution and contrast

• Confocal and wide field settings

• Visualizing protein-protein interactions and colocalization

Lectures , Quiz and assignment discussion

Week 3: 30 jan, 31 jan, 1 feb

• Scaling up: xyz automation, autofocus, fast imaging, high throughput imaging

• Volume imaging, light sheet and multiphoton microscopy, Super resolution

• Statistics in imaging

Lectures, Quiz and assignment discussion

Week 4: 6 feb, 7 jan, 8 jan, 9 feb

• Data handling, processing and management

• ImageJ/Fiji

• Image processing and quantitative analysis- Cell Profiler and Cell Profiler Analyst

Lectures, Quiz and assignment discussion

• Examination (9 feb)

TIME

2017-01-16 - 2017-02-09

3 half days/week during 4 weeks.

All scheduled days between 10:00-15:00.

VENUE:

Karolinska Institutet, Huddinge,

Live Cell Imaging facility

PRICE: 20 000 SEK (exkl VAT)

HOW TO APPLY

www.ki.se/uppdragsutbildning

Last day to apply: Dec 10th 2016

For questions on the course content:

Sylvie Le Guyader

Course leader, Microscopy Facility

Manager

Live Cell Imaging facility

Department of Biosciences and Nutrition

Karolinska Institutet

Email: Sylvie.Le.Guyader@ki.se

For questions on how to apply:

Nadja Saltell,

Project coordinator

Karolinska Institutet Executive Education

E-mail: nadja.saltell@ki.se

TIME AND ADMISSION

MORE INFORMATION

Course teachers

Sylvie Le Guyader

Sylvie started the Live Cell Imaging

facility at KI in 2008 after 10 years of

research using microscopy. Her

experience was enriched by training

hundreds of users with a wide panel

of samples. She now runs the facility

as well as the intensive microscopy

course.

Arne Lindqvinst

Arne is a group leader at the KI

department of Cell and Molecular

Biology. His group focuses on the

regulation of cell division that they

study using fluorescence microscopy

and FRET sensors. He will give a

lecture about how to quantify protein-

protein interaction using the FRET

technique.

Carolina Wälhby

Dept. of Information Technology and

SciLifeLab at Uppsala University.

Her lab develops advanced methods

and software tools to quantify and

mine the rich information present in

microscopy images. She will run a

one day workshop in Image Analysis.

Jan Mulder

Jan is the group leader of

the Fluorescence Tissue Profiling

facility at KI/ScilLife. The aim of the

group is to identify proteins involved

in brain development, normal brain

physiology and pathophysiology of

brain disorders.

For this they use a vast antibody

collection and perform multiplex

fluorescence imaging. Jan will give a

lecture on how to prepare tissue

before imaging.

Jeremy Adler

Jeremy works mainly at the core

imaging facility (BioVis) at Uppsala U

on microscopy & image analysis and

also at the BMC in Ingela Parmryd’s

group on live imaging and

colocalization measurements. He will

tell the students how to avoid the

potential dangers associated with

colocalization.

Kjell Carlsson Kjell is a Professor at the KTH School of

engineering sciences where he teaches

Applied Physics including microscopy and

photography. He will help students

understand the physics behind imaging.

Tessma Mesfin Kassaye

Messfin is a Lecturer and

Statistical Consultant at the KI Department of

Learning, Informatics, Management and

Ethics and that you are involved in

teaching, assignments and research in the

field of medical statistics. He will teach the

students about statistics applied to

microscopy images.

Gabriela Imreh

Gabriela used microscopy a lot in her

research at KI. She now works full time at the

Live Cell Imaging facility. She will run several

workshops on sample preparation, spectral

unmixing and give loads of tips and tricks.

Vladana Vukojević

Vladana is a group leader at the KI

Department of Clinical Neuroscience. Her lab

studies how opioid receptor-mediated

signaling is perturbed by abuse of drugs and

alcohol. For this they use functional

Fluorescence Microscopy Imaging (fFMI), a

multiplexed approach combining high-

resolution fluorescence microscopy imaging

and fluorescence correlation spectroscopy.

Vladana will give a lecture on fluorophores.

Victoria Menendez-Benito

Victoria is a group leader at the Department

of Biosciences and Medical Nutrition at KI.

Her group focusses on the role of

centrosomes in asymmetric cell division. For

this they screen yeast libraries using

fluorescence imaging and image analysis.

She will share with students many tips about

high throughput image-based screens.

Edward Verwayen

Edward is a Key Account Manager for Cell

Signaling Technology, a company that

specializes in antibody production and testing

especially in the domain of cancer research.

Karolinska Institutet Executive Education

171 77 Stockholm

E-mail epe@ki.se | Fax: 08-508 846 20

ki.se/epe