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3D and 4D imaging: Automation of data analysis
Convener: Jose Godinho 
Tue, 25 Apr, 08:30–12:00

Tuesday, 25 April between 8:30-12:00

Motivation: 3D imaging techniques such as X-ray micro-tomography and electron tomography are well established to study geological materials, and time-lapse (4D) experiments are increasingly popular to study transformations inside rocks. However, data segmentation is traditionally done manually by the user, which is time consuming and adds subjectivity to the analysis, specially when comparing different datasets.
Aim: to provide the basic tools for automating the segmentation of 3D datasets of geological materials with reduced input from the user.

Plan: 1) Introduction to 3D imaging, analysis and automation (20 min.); 2) Overview of available software and typical automation functions (10 min.); 3) How to construct a workflow strategy to segment objects inside a sample (15 min.); 4) Automatic thresholding techniques (10 min.); 5) Application of workflows to a sequence of datasets, e.g. using ImageJ (15 min.); 6) Visualization strategies for time-lapse studies (4D imaging) (15 min.); 7) Interactive session with questions (30 min.).

The second part of the course will have the format of a workshop where the audience can bring a dataset to work on applying what they learn in the first part.

There are limited number of places, first registered, first served.

PLEASE REGISTER by sending an email to:

Ideally the attendees should bring a fully charged laptop (not necessary for the first part of the course), with ImageJ and/or Avizo installed (even if only free demo).

At the end of the course the attendees should be able to create a workflow specific to their own data.