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Mon 12 Dec - Wed 14 Dec 2016
09:30, ...

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

Provided by: Bioinformatics


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Image Analysis for Biologists
PrerequisitesUpdated

Mon 12 Dec - Wed 14 Dec 2016

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.

A timetable is available here.

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
  • 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 12 Dec 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Richard Butler,  Jeremy Pike
2 Tue 13 Dec 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Alexandre Dufour
3 Wed 14 Dec 2016   09:30 - 16:00 09:30 - 16:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Richard Butler,  Jeremy Pike
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, Jeremy Pike
12:00 - 13:00 Lunch
13:00 - 16:00 Study Design and Data clinic (sign up required)
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
  • £ 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

Theme
Specialized Training

Booking / availability