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Wed 22 Jan 2020
12:30 - 17:00

Venue: eLearning 1 - School of Clinical Medicine

Provided by: Bioinformatics


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CRUK: Image Analysis with Fiji

Wed 22 Jan 2020


Fiji/ImageJ is a popular open-source image analysis software application. This course will briefly cover introductory aspects of image processing and analysis theory, but will focus on practical sessions where participants will gain hands on experience with Fiji.

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 all staff and students who use light microscopy in their research.
  • This is an introductory course, designed for those with little or limited experience in bioimage analysis
  • 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

No previous experience required


Number of sessions: 1

# Date Time Venue Trainer
1 Wed 22 Jan 2020   12:30 - 17:00 12:30 - 17:00 eLearning 1 - School of Clinical Medicine map Z. Huang
Topics covered

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


After this course you should be able to:

  • Load and visualise light microscopy datasets. Add scale-bars and produce images for publication.
  • Construct and implement image analysis workflows for simple tasks such as cell counting.
  • Batch process all image files in a given directory with the same sequence of tasks (if time allows).

During this course you will learn about:

  • Basic image handling, manipulation and visualisation using Fiji. This will include working with multi-channel, z-stack and time-lapse data. Loading of common microscopy file formats will also be demonstrated.
  • Common image analysis and processing techniques. This will include automated thresholding, de-noising, spot detection and background subtraction.
  • The design of simple analysis workflows.
  • Batch processing using the ImageJ macro language (if time allows).

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



Once a month

Specialized Training

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