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Mon 10 Dec - Tue 11 Dec 2018
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

Mon 10 Dec - Tue 11 Dec 2018


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.

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 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
  • 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
  • Basic knowledge of fluorescence microscopy and digital image acquisition assumed.
  • No computational expertise is required.

Number of sessions: 2

# Date Time Venue Trainers
1 Mon 10 Dec 2018   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Beth Cimini,  Z. Huang
2 Tue 11 Dec 2018   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Beth Cimini,  Z. Huang
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 and image quality control
  • Utilization of pixel classification tools to help in object detection and measurement

Presentations, demonstrations and practicals


Day 1 Topics
Session 1 Introduction to CellProfiler
Session 2 CellProfiler tutorial - Translocation, part 1
Session 3 CellProfiler tutorial - Translocation, part 2
Session 4 CellProfiler tutorial - Utilizing pixel classification
Session 5 CellProfiler tutorial- Cell Painting
Day 2
Session 1 Introduction to CellProfiler Analyst
Session 2 CellProfiler Analyst tutorial - Translocation, part 3
Session 3 CellProfiler/CellProfiler Analyst tutorial- Quality control
Session 4 Data clinic
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



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