Methods for Cell Analysis (MCA)

The course Methods for Cell Analysis has been organised by BioVis since 2007. It is a 3.5 credit point course for 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 and flow cytometry. Electron microscopy and latest technical achievements like super resolution 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. For more information please contact and see a schedule example.

Methods for Cell Analysis Spring (2024 May): click here for application

Methods for Cell Analysis Autumn (2024 October): click here for application

Introduction to Image Analysis Softwares (IAS)

How to make measurements from images – science and journals increasingly want numbers e.g. how many cells, has their size number, size, shape or distribution changed.

The IAS course is suitable for those beginning or wanting to start image analysis and is very hands on. There are two targets, understanding the fundamental of image analysis and learning how to use particular software, which we pursue in parallel. Initially working with ImageJ, the most popular scientific software, and then learning how to create macros to automate analysis. The course ends  with the participants, working in groups, presenting their solution to a problem they are interest in.

Cell Profiler, Imaris and the deconvolution with Huygens are also included in the 5 day course.

For more information contact

IAS Spring (2023 June 1,2 and 7,8,9): click here for application

IAS Autumn (2023 Sept 25-26, 28-29, Oct. 02): click here for application

Image Analysis - monthly courses

Image Analysis

Image acquisition is not the final step in your experiment, journals increasingly want measurements and a full description of image analysis and processing; the number of GFP positive cells, colocalization, the size of cells etc. BioVis offers the following courses. Courses will cost 700 SEK per course day for Uppsala University participants. Different prices apply for non-UU participant. To register email

  • Introduction to Image Analysis (ImageJ)
  • Writing ImageJ Macros
  • Deconvolution using Huygens  

ImageJ 1 and ImageJ2         Macro 1 day course
Room: Rosalind Franklin Room: Rosalind Franklin
January 23 and 30 March 20
April 17 and 25

Course: Introduction to Image Analysis (ImageJ1/2)

ImageJ is the most widely used image analysis software, it is open source and users have developed a huge range of plugins that extend its utility. The course has two aims (A) to understand the potential of image analysis and (B) how to use ImageJ. We offer 2 one day sessions named ImageJ1 and ImageJ2. We recommend taking both - but the two do not have to be taken in the same month. The course is highly interactive, with a worksheet and a set of test images. It is split over two days to gently examine how images can be processed (altered) and measurements made. See table below for dates the course is given.

Course:  Writing ImageJ Macros

A one day course suitable for those familiar with ImageJ - the next step is automating your analysis. You will be able to efficiently use the same protocol on multiple images, get much greater control over the image analysis, and provide a full description of the analysis for the methods section of publications. No experience of writing software needed. See table below for dates the course is given.

2 half days      Tuesday May 3rd & 10th  9am-12.45pm

Course: Image Deconvolution using Huygens   

Deconvolution improves the quality of images (resolution and noise) based on the known optical properties of the microscope and the fluorophores – unlike Photoshop. The gain can be substantial, especially with widefield images when much of the out of focus blur is removed. Deconvolution also substantially improves confocal, multiphoton images and STED images.

Improve your images - legitimately. The lower half is the original widefield image (Mitotracker red, 63x NA 1.4 objective) with the deconvolved version above.

The quality of images can be substantially improved using the known optics of the microscope and the fluorophore’s spectra. The result is an increase in resolution and a reduction in noise, which improves the appearance and improves subsequent quantitation. We use the commercial software Huygens (SVI) running on a powerful computer. After training you can book and use Huygens on our computer.

A course (minimum 2 person) is arranged by contacting

Last modified: 2023-10-11