Trainers

Jeremy Pike, Image Analyst for COMPARE

Alessandro Di Maio, Microscopy lead for the Microscopy Facilities

Summary

Fiji/ImageJ is a leading open-source image analysis 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.

Target Audience

• The course is recommended for all researchers who use light microscopy.
• This is an introductory course, designed for those with no, or limited experience, in bioimage analysis.
• Graduate students, postdocs and staff members from the Universities of Birmingham and Nottingham, affiliated institutions and other external institutions or individuals.

Aims and Objectives

After this course participants should be able to:

• Perform basic image handling, manipulation and visualisation using Fiji. This will include working with multi-channel, z-stack and time-lapse data.
• Understand and use meta-data, for example adding scale bars to images.
• Load common microscopy formats using Bio-formats.
• Perform volume rendering using ClearVolume.
• Use simple image analysis and processing techniques. To include automated thresholding, de-noising, spot detection and background subtraction.
• Design and construct routine analysis workflows.
• Perform batch processing using the ImageJ macro language (if time allows).
• Find information online for further study. For example learning resources and forums.

Course Materials

Note, this material was adapted from a course run at the Cancer Research UK Cambridge institute.

• Lecture Slides
• Exercises
• Sample Data Zip file (~ 59Mb)
• Batch processing macro
• Batch macro with user interface
• Slice labelling macro

Course Software

In this course participants will use Fiji and some of its plugins.

• Fiji download
• ClearVolume documentation
• PureDenoise documentation