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Mon 20 Apr - Wed 22 Apr 2015
09:30, ...

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Other dates:


Mon 11 Dec 2017


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Image Analysis for Biologists
PrerequisitesNew

Mon 20 Apr - Wed 22 Apr 2015

Description
  • This course will focus on computational methods for analyzing cellular images and extracting quantitative data from them.
  • It is aimed at researchers who are applying or planning to apply image analysis in their research
  • 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 around Fiji, an extensible open source software package.
  • On day 2 we will then use Matlab as an environment for bioimage informatics, covering image segmentation and quantitation, interactive data visualization, basic statistical analysis and machine learning algorithms. OME software and data format standards for the storage and manipulation of biological microscopy data will also be presented.
  • On day 3 we will focus on how to use CellProfiler, an open-source, freely-downloadable software package designed for large-scale, automated phenotypic image analysis.
  • A draft agenda 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
  • 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
Prerequisites

Basic programming knowledge (loops, function, variables etc...) would be an advantage

Sessions

Number of sessions: 3

# Date Time Venue Trainers
1 Mon 20 Apr 2015   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Richard Butler,  Alex Sossick
2 Tue 21 Apr 2015   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr B. Antal,  Dr A. Chessel,  Leila Muresan,  Jason Swedlow
3 Wed 22 Apr 2015   09:30 - 16:30 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Mark Bray
Topics covered
  • Introduction to images and commonly used algorithms
  • Handling, processing and analyzing images in Fiji
  • Statistical analysis in Matlab
  • Analysis of biological phenotypes in CellProfiler
  • The Open Microscopy Environment
Aims

The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitive analysis pipelines.

Format

Presentations, demonstrations and practicals

Duration

Three full day sessions

Frequency

Once a year

Theme
Specialized Training

Booking / availability