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Tue 10 Dec 2019
09:00 - 16:00

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: Advanced Image Analysis with Fiji

Tue 10 Dec 2019


Fiji/ImageJ is a popular open-source image analysis software application. This course will build on top of the Fiji basic course, to continue explore advanced image processing: segmentation, tracking, and with a specific focus on scripting/programming using Fiji scripting environment. We will use python programming language, and aim to give a tutorial on both image processing and python programming.

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 students or researchers who will systematically doing image processing as part of their project or research.
  • This is an advanced course, designed for life scientist who previously accomplished Fiji basic course, or had used Fiji to perform some image processing and analysis tasks.
  • 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
  • Familiar with image processing in Fiji/ImageJ, basic knowledge in programming (C++, MATLAB, R, or python);
  • Or completed basic ImageJ course, such as CRUK: Image Analysis with Fiji

Number of sessions: 1

# Date Time Venue Trainer
1 Tue 10 Dec 2019   09:00 - 16:00 09:00 - 16:00 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE map Z. Huang
Topics covered
  • Image Data handling
  • ImageJ API and programming basics, python(jython) scripting
  • Segmentation
  • Tracking

After this course you should be able to:

  • Design, create and complete a whole image processing workflow.
  • Automate mostly if not all steps in a given image processing workflow.
  • Good knowledge of image segmentation and object tracking tools and solutions.

During this course you will learn about:

  • Image data representation. Image data import, export visualization, manipulation using Fiji programming interface.
  • Python programming language. Python scripting to solve certain image processing task in Fiji.
  • ImageJ API.
  • Tracking object with TrackMate plugin. Scripting TrackMate.
  • Advanced image segmentation with ilastik.

Presentations and practicals

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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