Image Analysis for Biologists PrerequisitesUpdated
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.
- 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
Basic skills in mathematics and programming are an advantage, but not a requirement.
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 | Richard Butler, Jeremy Pike |
| 2 | Tue 13 Dec 2016 09:30 - 17:30 | 09:30 - 17:30 | Bioinformatics Training Room, Craik-Marshall Building | Alexandre Dufour |
| 3 | Wed 14 Dec 2016 09:30 - 16:00 | 09:30 - 16:00 | Bioinformatics Training Room, Craik-Marshall Building | Richard Butler, Jeremy Pike |
Bioinformatics, Biological imaging, Data handling, Data mining, Data visualisation
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
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
Presentations, demonstrations and practicals
| 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) |
Alexandre Dufour |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 17:00 |
Spot detection and tracking |
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 | |
- 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
3 days
Twice a year
Booking / availability