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Thu 15 Dec - Fri 16 Dec 2016
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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Using CellProfiler and CellProfiler Analyst to analyse biological images

Thu 15 Dec - Fri 16 Dec 2016


Microscopy experiments have proven to be a powerful means of generating information-rich data for biological applications. From small-scale microscopy experiments to time-lapse movies and high-throughput screens, automatic image analysis is more objective and quantitative and less tedious than visual inspection.

This course will introduce users to the free open-source image analysis program CellProfiler and its companion data exploration program CellProfiler Analyst. We will show how CellProfiler can be used to analyse a variety of types of imaging experiments. We will also briefly discuss the basic principles of supervised machine learning with CellProfiler Analyst in order to score complex and subtle phenotypes.

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 want to extract quantitative information from microscopy images
  • 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 knowledge of fluorescence microscopy and digital image acquisition assumed.
  • No computational expertise is required.

Number of sessions: 2

# Date Time Venue Trainer
1 Thu 15 Dec 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Beth Cimini
2 Fri 16 Dec 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Beth Cimini
Topics covered

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


After this course you should be able to:

  • Set up a CellProfiler pipeline for image analysis
  • Troubleshoot and optimize a pipeline for a particular data set
  • Analyze CellProfiler data with CellProfiler Analyst

During this course you will learn about:

  • Basics of image analysis
  • Methods of distinguishing objects of interest from the image background
  • Methods of separating clusters of touching objects
  • Identification of subcellular compartments
  • Obtaining measurements from the cell and subcellular compartments
  • Basics of machine learning for phenotype identification

Presentations, demonstrations and practicals


Day 1 Topics Speaker(s)
9:30 – 9:45 Introduction to CellProfiler Beth Cimini
9:45 - 11:00 CellProfiler tutorial- Translocation, part 1
11:00 - 11:30 Tea/Coffee Break
11:30 - 12:30 CellProfiler tutorial- Translocation, part 2
12:30 - 13:30 Lunch
13:30 - 15:00 CellProfiler tutorial- Utilizing pixel classification Beth Cimini
15:00 - 16:30 CellProfiler tutorial- Cell Painting
16:30 - 17:30 Summary and discussion
Day 2
9:30 – 10:00 Introduction to CellProfiler Analyst Beth Cimini
10:00 - 11:00 CellProfiler Analyst tutorial- Translocation, part 3
11:00 - 11:30 Tea/Coffee Break
11:30 - 12:15 CellProfiler/CellProfiler Analyst tutorial- Quality control
12:15 - 12:30 Summary and discussion
12:30 - 13:30 Lunch
13:30 - 17:30 Data clinic (sign up required) Beth Cimini
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

2 days


Once a year


Booking / availability