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Image analysis for biologists

 

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 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).

On day 3, we will cover time series processing and cell tracking using TrackMate. Additionally, in the afternoon we will run a study design and data clinic (sign up will be required) for participants that wish to discuss their experiments.

 

Trainers

Alexandre Dufour, Institut Pasteur

Richard Butler, University of Cambridge

Jeremy Pike, 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 and Icy
  • Cellular phenotyping and analysis of High Content Screening data
  • Focus on live cell imaging data
  • Time series processing and cell tracking

 

Learning Objectives

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
  • Apply time series processing and cell tracking using TrackMate

 

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

Icy Website

Graphical User Interface

Image loading, visualisation (2D/3D)

ImageJ interaction

Plug-in installation

Image annotation, simple measurement

Basic analysis (intensity-based)

Alexandre Dufour

12:30

Lunch

13:30

Spot detection and tracking

Cell segmentation and tracking

Colocalisation

Task automation via graphical programming

Task automation via scripting

Alexandre Dufour

17:00

Summary and discussion

Alexandre Dufour

Day 3

 

 

9:30

Time series processing and cell tracking using TrackMate

Richard Butler, Jeremy Pike

12:00

Lunch

 

13:00

Study Design and Data clinic (sign up required)

 

16:00

Wrap up

 

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