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Mon 26 Jun - Wed 28 Jun 2017
09:30, ...

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

Provided by: Bioinformatics


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Image Analysis for Biologists
PrerequisitesUpdated

Mon 26 Jun - Wed 28 Jun 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 describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualisation, 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. In the afternoon, we will present the Image Data Resource, an added-value platform that combines data from multiple independent imaging experiments and imaging modalities and integrates them into a single resource for reanalysis in a convenient, scalable form.

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: 3

# Date Time Venue Trainers
1 Mon 26 Jun 2017   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Richard Butler,  Jeremy Pike
2 Tue 27 Jun 2017   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Alexandre Dufour
3 Wed 28 Jun 2017   09:30 - 16:00 09:30 - 16:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Richard Butler,  Stephanie Owen,  Eleanor Williams
Topics covered

Bioinformatics, Biological imaging, Data handling, Data mining, Data visualisation

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
Aims

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
Format

Presentations, demonstrations and practicals

Timetable

Day 1 Topics Speaker(s)
9:30 - 11:00 Introduction to images

Introduction to image processing

Richard Butler, Jeremy Pike
Processing using Fiji
11:00 - 11:30 Coffee
11:30 - 12:30 Image processing for analysis Richard Butler, Jeremy Pike
Processing using Fiji
12:30 - 13:30 Lunch
13:30 - 15:45 Introduction to image analysis Richard Butler, Jeremy Pike
Analysis using Fiji
Image analysis pipelines
Designing and running pipelines in Fiji
15:45 - 16:15 Coffee
16:15 - 17:30 Introduction to ImageJ macros Richard Butler, Jeremy Pike
Making simple macros
Fiji plugins
17:30 Summary and discussion
Day 2
9:30 - 12:30 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 - 13:30 Lunch
13:30 - 17:00

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 - 12:00 Time series processing and cell tracking using TrackMate Richard Butler, Stephanie Owen
12:00 - 13:00 Lunch
13:00 - 14:30 Time series processing and cell tracking using TrackMate (continued)
14:30 - 16:00 Image data management, visualization and analysis with the Image Data Resource (IDR) Eleanor Williams, Gabriella Rustici
16:00 Wrap up
Registration fees
  • Free for University of Cambridge students
  • £ 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
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 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
Duration

3 days

Frequency

Twice a year

Related courses
Theme
Specialised Training

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