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, 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.

• 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

Basic skills in mathematics and programming are an advantage, but not a requirement.

Number of sessions: 3

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

• 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

3 days

Twice a year

• Using CellProfiler and CellProfiler Analyst to analyse biological images
• Biological Imaging Data Management for Life Scientists
• Biological Imaging Data Management for Facility Managers
• CRUK: Image Analysis with Fiji
• CRUK: Processing, Visualization and Analysis of multi-dimensional biological microscopy images using arivis Vision 4D software