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 Matyas.Molnar@igp.uu.se 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 (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.

The course will be run twice in 2020

Due to the Corona situation will we run the Spring course (canceled) in August.

Introduction to Image Analysis and Software (IAS August 2020)

Introduction to Image Analysis Software (IAS Nov 2020)

For more information contact Jeremy.adler@igp.uu.se

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 jeremy.adler@igp.uu.se.

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 jeremy.adler@igp.uu.se.