Microscopy: improve your imaging skills – from sample preparation to image analysis, 17 Jan – 09 Feb 2017, Karolinska Institute, Stockholm, Sweden

course webpage


Target audience:

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.

Two courses run in parallel: the full course contains lectures and workshops while the short course contains only lectures.

Aim of the course:

The focus is 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 available hardware 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 microscope, images that exactly match their samples and answer their scientific questions in a reliable way.

Participants will learn the theory and many practical tricks about the parameters and hardware used in confocal imaging, how to identify and avoid imaging artifacts, 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 techniques like two-photon microscopy, super resolution and spectral imaging.

They will get personalized expert feedback as well as a full analysis of their sample preparation and imaging strategy, using their own sample.

Learning outcomes for the full course:

At the end of the course, students will be able to:

  • 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 which application
  • Evaluate fluorophores by matching their spectra with the microscope light source and filters, identify and avoid bleed-through and cross-excitation and pick the best combination of fluorophores for their own microscope
  • Explain objective specifications and limitations and describe the appropriate objective for their own application
  • Describe how to fix, mount and handle their sample in a way that is optimal for imaging
  • Find their sample and the area of interest without bleaching it
  • Adjust the condenser for proper DIC imaging (Koehlering)
  • Explain the theory behind resolution, pixel density, averaging, scan speed, which laser power, detector gain and offset to use and describe which settings are best suited to their application
  • 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
  • Run a simple image analysis on freeware (Cell Profiler) and describe the imaging requirements for automated image analysis
  • Critically comment on their peers’ imaging settings and troubleshoot their images

 Registration fee:

Registration is free

Number of participants:

Theory and workshops: max. 16
Theory only: unlimited


Lectures and workshops: 9-17 every day
Lectures only: 10-15 every day

Contact and venue:

Sylvie Le Guyader
Live Cell Imaging facility, Nikon Center of Excellence
Karolinska Institutet
Hälsövägen 7
14157 Huddinge, Sweden
Facility website

course webpage