CRUK: Intermediate Image Analysis

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This course will cover common image analysis problems including colocalization, segmentation and tracking. We will also cover the handling of large data including registration, fusion and visualization. We will use Fiji and Icy; two leading open source image analysis software applications.

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.

• The course is recommended for all staff and students who regularly use image analysis in their research and would like to develop more advanced skills.
• This is an intermediate course, designed for those with some basic experience of image analysis.
• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals

You should have already attended one of our introductory courses or have equivalent experience.

Number of sessions: 2

After this course you should be able to:

• Implement unbiased colocalization workflows to quantify and identify statistically significant changes.
• Use plugins to segment and track objects in timelapse data. For example cell tracking or microtubule plus ends.
• Work with large datasets and visualize them in Fiji.
• Perform 3D reconstruction and deconvolution of multi-view image data for further analysis.

During this course you will learn about:

• ImageJ macros and Icy protocols for workflow implementation.
• Good practice for colocalization analysis. Workflows for both pixel and object based analysis will be covered.
• The use of advanced segmentation algorithms including deformable model (active contours and level set).
• Tracking in time-lapse data.
• Introduction to 6D light sheet microscopy datasets
• Registration of images and 3D stacks acquired from multiple sides for multi-view fusion (based on fiduciary markers and sample features)
• Visualization of large datasets using Bigdata viewer and Mamut viewer in Fiji

Presentations and practicals

• 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

Two half day sessions

Once a year

• CRUK: Image Analysis with Fiji
• Image Analysis for Biologists