Two Day Course: Large Data Image Reconstruction and Visualisation - Turing Summer School

The CCPi is pleased to announce the two-day training course based at RAL, Didcot is now Open for Registration that is collocated with the Advances in XCT Workshop. We thank specific sponsorship from the Alan Turing Institute and CCPi.

Thu 11- Fri 12, June 2020 Training and hand-holding sessions
. First Training Day focussing on the Core imaging Library software framework https://www.ccpi.ac.uk/CIL
. Second Training Day focussing on post-processing and visualisation with the Avizo and Tomviz frameworks

Course Title: Large Data Image Reconstruction and Visualisation

Course Aims and Outcomes:

The two day course will describe, through different software frameworks, the image reconstruction process, focussing on tomography, but includes the generic image processing pipeline including data loading, preprocessing, reconstruction, postprocessing and visualisation.

The Core Imaging Library (CIL), is a open source python framework for complete tomographic reconstruction from image capture to volume processing and two alternative dataflow visualisation systems; Kitware's Tomviz and Thermo Fisher's Avizo are exploited by the steering team and invited attendees. There will be a series of best practice talks by invited speakers, with hands-on sessions where we would expect the attendees to become :
1. familiar with modular methods that may be appropriate for their imaging needs;
2. be able to use the modular design of CIL integrating customised algorithms especially in tomography;
3. be confident to build new simple and fast prototyping of optimisation-based reconstruction algorithms;
4. and use visualisation techniques within a scientific framework.

Aim is to "understand a versatile software framework for tomographic image processing".

Course Registration

Open NOW and link here: http://www.cvent.com/d/0nqqyl

Training Schedule

First Training Day: 11 June 2020, RAL Visitors Centre

1. Image reconstruction techniques with CCPi framework (1 day)

Introduction to XCT Imaging session and use of advanced iterative reconstruction methods to extract improved information content from your data. This course comprises of five interactive jupyter notebooks:

. https://github.com/vais-ral/CIL-Demos/tree/master/Notebooks
. Framework documentation http://edosil.net/stfc/cil1910/html/index.html

. Reconstruction Introduction
. Tikhonov Block Framework Reconstruction
. Diamond Light Source 3D Imaging
. PDHG Tomographic Reconstruction
. Multi-Channel Reconstruction

Keynote talk on Astra Toolkit roadmap and exemplars by Sophia Coban

Evening networking even proposed at Ridgeway House.

Second Training Day: 12 June 2020, RAL Conference Room CR16/17

2. Post-processing and visualisation with Avizo framework (1/2 day)

Although the direct benefit of X-ray tomography is the 3D visualisation of the internal structure of specimens, which is very valuable to understand the structure/function relationships, the technique has however a lot more to offer. The information is hidden in the data and robust methods and workflows are needed to extract it in a relevant and accurate way, and make it readily available for decision making. The speakers will provide guidelines and computer-based sessions on designing a workflow and visualising the dataset in a sophisticated way within Avizo framework:

. Lean how to develop a workflow to quantify the particle size distribution of a nodular cast iron material
. Assess the impact of noise/artefacts on the pore size distribution from two repeat scans
. Introduction to the powerful technique of digital volume correlation at the end of the session (demo) to extract mechanical information from CT time series of the same material (tensile test)”

3. Process manipulation with Tomviz (Kitware Inc) framework (1/2 day)

The Tomviz project is a cross platform, open source application for the processing, visualization, and analysis of 3D tomographic data. Here with hands-on examples the full pipeline of data processing steps from reconstruction to visualization to analysis of 3D data can be presented, saved, and restored. A suite of Python tools for 3D analysis is packaged to accommodate custom algorithms. Tomviz is tested on Windows, macOS, and Linux:

. Documentation site at https://tomviz.readthedocs.io/
. Updated course details will be at: https://openchemistry.github.io/tomviztutorial/

Descriptions of Core Imaging Library

“I am absolutely blown away by the results of today. I don’t think anyone is even close to do this type of reconstruction” DP

"Intelligent choices of image reconstruction lead to improved quantification" MT

Confirmed List and CCPi sponsored speakers:

Prior to this training event is the Advances in XCT Imaging Workshop, where we have cross-related speakers and encourage delegates to register for this event as well:

Speakers attending the Training sessions and the Advances workshop include:

. Marcus Hanwell, Kitware - https://tomviz.org/downloads/
. Stephen Dann and Ceri Brenner- EPAC
. Suren Chilingaryan - Karlsruhe Institute of Technology
. Simon Stute - CASToR; Customizable and Advanced Software for Tomographic Reconstruction http://www.castor-project.org/
. Evangelos Papoutsellis - CIL Core Imaging Library https://ccpi.ac.uk
. Sophia Bethany Coban - ASTRA toolkit

Accommodation and Logistics

Suggestion for overnight accommodation should you need it if taking part in both activities is available at Ridgeway House.

Venue RAL Visitors Centre, first day, and RAL Conference Room CR16/17, second day.

Delegates will be expected to bring their own laptop.

Scientific Committee and Trainers

. Martin Turner
. Gemma Fardell
. Edoardo Pasca
. Kamel Madi
. Tristan Lowe
. Evangelos Papoutsellis
. Marcus Hanwell
. Jakob Jorgensen

Date: 
Thursday, 11 June, 2020 - 10:00 to Friday, 12 June, 2020 - 17:00