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Mon 11 Dec - Tue 12 Dec 2017
09:30 - 17:30

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

Provided by: Bioinformatics


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Image Analysis for Biologists
PrerequisitesUpdated

Mon 11 Dec - Tue 12 Dec 2017

Description

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 cover time series processing and cell tracking using TrackMate. The afternoon of day two will focus on understanding the basics of deconvolution and colocalisation, using tools in Fiji to look at basic examples of how to apply deconvolution and how to carry out colocalisation analysis in fluorescence microscopy.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your 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
  • Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Prerequisites

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

Sessions

Number of sessions: 2

# Date Time Venue Trainers
1 Mon 11 Dec   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Richard Butler,  Jeremy Pike
2 Tue 12 Dec   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Richard Butler,  Jeremy Pike,  Stephanie Owen
Objectives

After this course you should be able to:

  • Perform routine image analysis with ImageJ/Fiji
  • Design custom workflows to analyse bio-image data
  • Apply time series processing and cell tracking using TrackMate
  • Perform deconvolution and colocalisation analysis with Fiji
Aims

During this course you will learn about:

  • commonly used algorithms for image analysis
  • handling, processing and analyzing images in Fiji
  • batch process data using ImageJ macros
  • time series processing and cell tracking
  • applying deconvolution methods to remove blur from images
  • basics of colocalisation analysis
Format

Presentations, demonstrations and practicals

Registration fees
  • Free for University of Cambridge students
  • Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Timetable

Day 1 Topics Speaker(s)
9:30-10:30 Introduction to images and image processing Richard Butler, Jeremy Pike
10:30-11:00 Processing using Fiji Richard Butler, Jeremy Pike
11:00-11:30 Tea/Coffee Break
11:30-12:30 Image processing for analysis, Processing using Fiji Richard Butler, Jeremy Pike
12:30-13:30 Lunch (not provided)
13:30-14:00 Introduction to image analysis Richard Butler, Jeremy Pike
14:00-15:45 Analysis using Fiji, Image Analysis Pipelines, Designing and running pipelines in Fiji Richard Butler, Jeremy Pike
15:45-16:15 Tea/Coffee Break
16:15-17:30 Introduction to ImageJ macros, Making simple macros, Fiji plugins Richard Butler, Jeremy Pike
17:30 Summary and discussion
Day 2
09:30-12:00 Time series processing and cell tracking using TrackMate Richard Butler, Jeremy Pike
12:00-13:00 Lunch (not provided)
13:00-15:00 Deconvolution and Deconvolution exercises Stephanie Owen
15:00 Tea/Coffee Break
15:30-17:30 Colocalisation and Colocalisation exercises Stephanie Owen
17:30 Wrap up
Duration

2 days

Frequency

Twice a year

Related courses
Theme
Specialized Training

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