Methods for Cell Analysis

The course Methods for Cell Analysis has been organised by BioVis since 2007. It is aimed at postgraduate students, post-docs and research engineers who wants to learn more about Light Microscopy, Flow Cytometry and Electron Microscopy. The course is based on a lecture series and practical hands on sessions. Lectures will cover e.g. theory of fluorescence, its application in various light microscopy techniques as well as flow cytometry and image analysis. Electron microscopy and latest technical achievements like super resolution - and lightsheet microscopy are covered as well. The practical hands-on sessions include resources found at BioVis like laser scanning and two photon microscopy, flow cytometry and cell sorting, electron microscopy, image analysis with Cell Profiler and IMARIS. For more information please contact and see a schedule example.

MCA SPRING: 6-15 May 2020. ! Cancelled due to Covid-19 !

MCA AUTUMN: 7-16 October 2020. For application, click here

Introduction to Image Analysis Softwares

The Introduction to Image Analysis Software course provides an introduction to image analysis in general and to common image analysis software. Students will learn to use and compare the merits of ImageJ, Imaris, Cell Profiler and Huygens. The course is very hands on and the participants will initially use ImageJ and, in groups, and progress to more complex sequences of operations by creating ImageJ macros. The students will emerge with enough skills and confidence to apply image analysis to their own images. For more information, and to apply, please contact and see a schedule example from the previous year.

Application: IAS 1st-7th April

First steps in image analysis

First Steps in Image Analysis - An introduction to image analysis using ImageJ.

Journals increasingly ask for measurements, how many, how big, how colocalized.

The course has two aims: (i) to understand what is possible with image and (ii) how to actually use ImageJ, a popular, powerful and free package.

The course will be very hands on: open images, manipulate them and make measurements while examining the underlying ideas. We have expanded the course has been from one to two days, to provide more time to work with ImageJ and to include time for examine the participant’s own images or any particular area of interest. The gap between the two days allows time to test and digest the earlier material before moving onto more detailed examination of the topic.

  • Displaying data
  • Processing – changing images to display when more clearly or make them easier to analyse
  • Segmentation – identifying areas of interest
  • Measurements – what and how, in 2D and 3D

Please be aware that we will charge 500 SEK  for each application.

February: Day 1 Friday 14th Feb 2020, Day 2 Tuesday 25th Feb

May: Day1 Wednesday 20th May 2020, Day 2 Friday 29th May 2020

For more information, please contact

Writing Image J Macros

Create new protocols and automating existing methods. Macros are text files holding a sequences of actions that allow the repeated and rapid use of a standard analysis. We can also create new protocols that are not available in commercial software. Macros can be reused, shared and included in the methods section of publications.
This one day course is intended for those familiar with ImageJ (First Steps course) and focuses on automating image analysis.

! We will charge for the course 500 SEK per application !

BioVis Macro course Monday 27th Jan 2020

BioVis Macro course Friday March 13 2020

BioVis Macro course Friday 12th June 2020

For more information, please contact