Microscopy: improve your imaging skills – from sample preparation to image analysis, 22 Jan – 08 Feb 2019, Karolinska Institute, Stockholm, Sweden

Microscopy: improve your imaging skills – from sample preparation to image analysis

22 Jan – 08 Feb 2019, Karolinska Institute, Stockholm, Sweden


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 (#2870) contains lectures, demos and workshops while the short course (#2871) contains mostly 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.

The 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.

They will get personalized expert feedback about their sample preparation and imaging strategy, using their own sample. 

Learning outcomes for the full course:

  • At the end of the course, the participants 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 their experiments
  • 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
  • Explain objective specifications and limitations and choose the appropriate objective for their own experiments
  • 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 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
  • Explain which applications require a hardware or a software autofocus, a spectral detector, a resonance scanner, light sheet, two-photon or super resolution microscopy
  • 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 (ImageJ/FIJI, 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 7C

14157 Huddinge, Sweden


Facility website