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Mon 24 Jun - Wed 26 Jun 2019
09:30, ...

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

Provided by: Bioinformatics


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Image Analysis for Biologists

Mon 24 Jun - Wed 26 Jun 2019

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 and advanced image segmentation using Ilastik. 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.

On day 3, 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).

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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 registered 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 24 Jun   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Jeremy Pike,  Z. Huang
2 Tue 25 Jun   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Jeremy Pike,  Z. Huang
3 Wed 26 Jun   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map David Gaboriau
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
  • Perform image segmentation with Ilastik
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
9:30 - 11:00 Introduction to images

Introduction to image processing
Processing using Fiji

11:00 - 11:30 Tea/Coffee break
11:30 - 12:30 Image processing for analysis

Processing using Fiji

12:30 - 13:30 Lunch (not provided)
13:30 - 15:45 Introduction to image analysis

Analysis using Fiji
Image analysis pipelines
Designing and running pipelines in Fiji

15:45 - 16:15 Tea/Coffee break
16:15 - 17:30 Introduction to ImageJ macros

Making simple macros

17:30 Summary and discussion
Day 2
9:30 - 11:30 Time series processing and cell tracking using TrackMate
11:30 - 12:30 Advanced segmentation
12:30 - 13:30 Lunch (not provided)
13:30 - 14:30 Macros, segmentation and tracking (continued)
14:30 - 17:00 Study design and data clinic (sign up required)
Day 3
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)

12:30 - 13:30 Lunch (not provided)
13:30 - 17:00

Spot detection and tracking
Cell segmentation and tracking
Task automation via graphical programming

17:00 Summary and discussion
Registration fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) 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

Frequency

Twice a year

Theme
Specialized Training

Booking / availability