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Image analysis for biologists (2-day)

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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

 

Trainers

Richard Butler, University of Cambridge

Jeremy Pike, CRUK

Stephanie Owen, CRUK

 

Audience and Prerequisites

  • 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

 

Syllabus, Tools and Resources

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

 

Learning 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

 

Links

Book Here

 

Timetable

Day 1

Topics

Speaker(s)

9.30

Introduction to images

Richard Butler, Jeremy Pike

Introduction to image processing

Richard Butler, Jeremy Pike

10.30

Processing using Fiji

Richard Butler, Jeremy Pike

11.00

Coffee

11.30

Image processing for analysis

Richard Butler, Jeremy Pike

12.00

Processing using Fiji

Richard Butler, Jeremy Pike

12.30

Lunch

13.30

Introduction to image analysis

Richard Butler, Jeremy Pike

14.00

Analysis using Fiji

Richard Butler, Jeremy Pike

14.30

Image analysis pipelines

Richard Butler, Jeremy Pike

14.45

Designing and running pipelines in Fiji

Richard Butler, Jeremy Pike

15.45

Coffee

16.15

Introduction to ImageJ macros

Richard Butler, Jeremy Pike

16.45

Making simple macros

Richard Butler, Jeremy Pike

17.15

Fiji plugins

Richard Butler, Jeremy Pike

17.30

Summary and discussion

 

Day 2

 

 

9:30

Time series processing and cell tracking using TrackMate

Richard Butler, Jeremy Pike

12:00

Lunch

 

13:00

Deconvolution

Stephanie Owen

13:30

Deconvolution exercises

 Stephanie Owen

15:00

 Coffee

 

15:30

Colocalisation

 Stephanie Owen

16:00

Colocalisation exercises

 Stephaine Owen

 16:00

 Wrap up

 

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