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Fri 11 Nov 2016
12:30 - 17:00

Venue: Room 313, 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 Fiji
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Fri 11 Nov 2016

Description

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.

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
  • 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
Prerequisites

No previous experience required

Sessions

Number of sessions: 1

# Date Time Venue Trainers
1 Fri 11 Nov 2016   12:30 - 17:00 12:30 - 17:00 Room 313, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE Jeremy Pike,  Gopi Shah
Objectives

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).
Aims

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).
Format

Presentations and practicals

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
Duration

0.5 days

Frequency

Once a month

Related courses
Theme
Bioinformatics

Booking / availability