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Mon 2 Jul 2018
12:30 - 17:00

Venue: Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

Provided by: Bioinformatics


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CRUK: Image Analysis with Cellprofiler

Mon 2 Jul 2018


CellProfiler is a free, open-source image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

This course will introduce you the basic usage, and several application examples to help you understand and build up image processing and analysis workflows within CellProfiler. It will also cover a brief introduction to the usage of its companion package CellProfiler Analyst, which allows interactive exploration and analysis of image data. Some related theoretical topics in image processing will also be covered.

This course is run by the CRUK CI Light microscopy core facility.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

Target audience
  • The course is recommended for staff scientists and students who need to routinely analyse image data, or need to process large amount of image data 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
  • This course is designed for those who have already performed some image processing and analysis on their own.
  • It is recommended to take the Image Analysis with Fiji course first, although not obligatory.

Number of sessions: 1

# Date Time Venue Trainers
1 Mon 2 Jul 2018   12:30 - 17:00 12:30 - 17:00 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE map Z. Huang,  Dr Stefanie Reichelt,  Mark Fernandes
Topics covered

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


After this course you should be able to:

  • Load and group your image data properly in CellProfiler.
  • Build image processing project for simple tasks such as counting ISH spot per cell in CellProfiler.
  • Automatically process and analyse all image files acquired and organized in the same way with previously built CellProfiler processing pipeline.
  • Use CellProfiler Analyst to perform simple image classification with supervised machine learning tool.

During this course you will learn about:

  • What is image data, image metadata and how to load and parse them
  • Methods of distinguishing objects of interest from the image background
  • Methods of generate ROI surrounding objects and separating clusters of touching objects
  • Obtaining masks of cells from image data
  • Obtaining measurements from the cell and subcellular compartments
  • Basics of machine learning for phenotype identification and image quality control

Presentations and practicals


Time Topics
12:30 - 13:15 Introduction to CellProfiler
13:15 - 14:00 CellProfiler demo
14:00 - 14:30 Practice session 1
14:30 - 15:00 Tea/Coffee Break
15:00 - 15:45 Practice session 2
15:45 - 16:15 Introduction to advanced image processing
16:15 - 17:00 Practice session 3
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
  • 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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