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Thu 19 May - Fri 20 May 2016
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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Image Analysis for Biologists

Thu 19 May - Fri 20 May 2016


This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines.

On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based on Fiji, an extensible open source software package.

On day 2, we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualization, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager).

The timetable can be found here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

Target audience
  • Researchers who are applying or planning to apply image analysis in their research
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Further details regarding eligibility criteria are available here
  • Further details regarding the charging policy are available here

Basic skills in mathematics and programming are an advantage, but not a requirement.


Number of sessions: 2

# Date Time Venue Trainers
1 Thu 19 May 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Richard Butler,  Jeremy Pike
2 Fri 20 May 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Alexandre Dufour

After this course you should be able to:

  • Perform routine image analysis with ImageJ/FIJI/Icy
  • Apply workflows for the analysis of High Content Screening data

During this course you will learn about:

  • commonly used algorithms for image analysis
  • handling, processing and analyzing images in Fiji and Icy
  • cellular phenotyping and analysis of High Content Screening data
  • focus on live cell imaging data

Presentations, demonstrations and practicals




Twice a year


Booking / availability