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Tue 30 Apr 2019
11:00 - 17:00
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Provided by: Bioinformatics


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CRUK: Processing, Visualization and Analysis of multi-dimensional biological microscopy images using arivis Vision 4D software

Tue 30 Apr 2019

Description

This course has the following objectives:

  • To provide an overview on the importance of microscopy image analysis and tools in Arivis Vision4D software for the quantification of various biological problems: cell analysis, time-lapse, colocalization, stitching, handle large images etc
  • Practical session with computers during which participants will be introduced to image analysis and visualization using Vision4D
  • Demonstration on how virtual reality can help with image visualization and quantification

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
  • This course is suitable for students (graduate and PhD students) and researchers (staff, Post-Docs) doing imaging in any modality, but especially light microscopy who are interested in learning about image visualization and quantification.
  • No previous knowledge in image analysis or Vision4D software is required
  • 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
Prerequisites

No previous knowledge in image analysis or Vision4D software is required

Sessions

Number of sessions: 2

# Date Time Venue Trainers
1 Tue 30 Apr   11:00 - 12:00 11:00 - 12:00 Cancer Research UK Cambridge Research Institute, Lecture Hall map Fadwa Joud,  David Wiles
2 Tue 30 Apr   13:00 - 17:00 13:00 - 17:00 Clinical School, E-learning 1, 2, 3 (Level 2) map Fadwa Joud,  David Wiles
Topics covered

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

Objectives

After this course you should be able to:

  • Open an image in Vision 4D
  • Visualize your image in 2D and 3D modes
  • Set up an image analysis pipeline to quantify parameters such: cell count and cell properties such intensity, volume and morphological parameters
  • Set up a pipeline for time-lapse analysis track quantification: trajectory length, cell speed, and cell properties changes over time
  • Stitch multiple volumes using mosaic tiling and multiview fusion
  • Generate high-resolution movies and animations
Aims

During this course you will learn about:

  • How to get started using Vision4D
  • Image Visualization and 3D Rendering
  • How to get started with image analysis
  • How to set up an image analysis pipeline
Format

Presentations and practicals

Timetable

Day 1 Topics
11:00 - 12:00 General talk

12:00 - 13:00 Lunch (not provided)
13:00 - 14:00 3D image segmentation and quantification (number or cells, cell intensity, volume, etc)

14:00 - 15:00 Time-lapse image analysis (tracking etc)

15:00 - 15:15 Coffee break
15:15 - 16:15 Stitching, Multi-volume fusion and creation of animations

16:15 - 17:00 Demonstration of Immersion visualisation via Virtual Reality

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
Duration

1

Frequency

Once a year

Theme
Specialized Training

Booking / availability