CT@IMBL-2017

20 Mar 2017, 09:30 → 21 Mar 2017, 16:00 Australia/Melbourne

Andrew Stevenson (Australian Synchrotron/ CSIRO), Anton Maksimenko (Australian Synchrotron), Chris Hall (Australian Synchrotron), Robbie Clarken (Australian Synchrotron), Sherry Mayo (CSIRO)

The second Imaging and Medical Beamline CT workshop: CT@IMBL-2017.

Thanks your interest in attending. Please use the link below to register your interest in receiving the course material, and for news of further events.

The purpose of the workshop is to increase familiarity with the techniques for collecting and processing data from the IMBL.

During this two day workshop we will run tutorial sessions covering all operations, from setting up the beam line, collecting data, to reconstructing and visualising CT data on IMBL.

In the mornings a series of presentations will explain the principles. Hands-on practical sessions in the afternoons will allow you to practice IMBL CT work-flows using your own, or demonstration data sets. Sessions will be run by CSIRO and Synchrotron staff.

On the first day there will be an opportunity to visit the beamline, for those who are not familiar with it.

Day 1: Takes you through the components of the beam line and the principles of computed tomography. This will be followed by descriptions of the interfaces, and how we run CT on IMBL. Once data has been collected the management of data will be explained including remote access and transfer. First level processing including reconstruction of 3-D volume data cubes from raw data will be demonstrated. The new ASCI compute cluster will be used and demonstrated. A practical session in the afternoon will allow delegates to practice using their own, or our provided training data.

Day 2: Once simple reconstruction is finished, visualisation is the next step in the process.Processing of large amounts of data using scripts will be described. 3-D visualisation will be explained, using the tools available on the ASCI Compute Desktop. A new session will be introduced, where experienced Users will describe their experiments and experiences on IMBL.  A second practical session after lunch will allow for practice and questions.

Workshop topics will include:

• Practical considerations for mounting and moving samples
• How to choose the best x-ray energy
• Avoiding artefacts in the reconstructed data
• Presenting CT data through segmentation and animation

Registration

• Includes a light lunch, morning and afternoon teas.
• Access to all workshop materials

​Accomodation and travel assistance

• Accomodation will be made available at the AS guest house. This will be at no cost, for registered interstate and country Victoria participants only.
• Other participants may book guest house accomodation at their own expense.

What you will need to provide

Bring along your own laptop. If for some reason you are not able to do this we will have a limited number of PCs/laptops available. Please let us know during registration if you would like to make use of them.

We look forward to seeing you at the Australian Synchrotron...

Chris Hall, Anton Maksimenko, Andrew Stevenson, Sherry Mayo...Workshop Organisers

---

 

more information

• AS-Ancillary_movies.zip
• SM-Batch_scripts.zip
• XLI_prac.pdf
• XTRACTCheatSheet_ASCI.pdf

Slides

• AM-Ways_to_collect_CT_data_sets_on_IMBL.pdf
• AS-CT@IMBL_Phase_contrast.pdf
• AS-CT@IMBL_X-ray_Characteristics_and_General_Imaging.pdf
• CJH-Considerations_for_2D_Image_Quality.pdf
• CJH-Data_visualisation_with_ImageJ_and_FIJI.pdf
• CJH-IMBL_detectors.pdf
• GenevieveBuckley_CT@IMBL.pdf
• RBC_-_ASCI.pdf
• RBC_-_Data_Management.pdf
• SM-CT_at_IMBL_X-TRACT_intro.pdf

Monday, 20 March

09:30 → 10:00 Coffee

Coffee and biscuits available

10:00 → 10:15 Welcome and introduction

A welcome to all workshop delegates to the Australian Synchrotron.
Some housekeeping announcements and an overview of the program.

Convener: Dr Chris Hall (Australian Synchrotron)

10:15 → 10:45 IMBL characteristics: X-ray characteristics and general imaging

A short review of x-ray imaging followed by details of how imaging is achieved on IMBL.
The talk will include a description of the source, filtration, slits, monochromator, shutters, and monitoring systems. Our detector systems will be introduced along with a short introduction to the data storage.

Convener: Dr Andrew Stevenson (Australian Synchrotron/ CSIRO)

10:50 → 11:10 IMBL detectors: What they are and their characteristics

The best CT reconstructions come from the best quality projection images. In this session we will discuss the effect imaging parameters like photon energy and exposure time, have on the data quality.

Convener: Dr Chris Hall (Australian Synchrotron)

11:15 → 11:35 IMBL User interfaces: Our Graphical User Interfaces

In this session we will introduce the various ways that CT data sets are collected. These include:
Stop and shoot, Asynchronous continuous rotation, Triggered continuous rotation, Multi-segment, and Multi-patch protocols.

Convener: Dr Anton Maksimenko (Australian Synchrotron)

11:40 → 12:00 CT data collection: Sample alignment and ways to run a CT

The beauty of using a synchrotron beam is the ability to collected high quality data quickly. Management of that data can become a major task though when large amounts of data are involved. We will describe the way that raw and processed data is handled in the IMBL system.

Convener: Dr Anton Maksimenko (Australian Synchrotron)

12:05 → 12:25 Data management: Where your data is stored, and how to access it

Convener: Robbie Clarken (Australian Synchrotron)

12:30 → 13:00 Lunch break

Lunch and Poster viewing

13:00 → 13:45 Visit to the IMBL

13:45 → 14:05 An introduction to ASCI Desktop: The User Interface to the AS cluster

ASCI Desktop is a very important tool for IMBL data processing. It provides a simple interface to the power of the Australian Synchrotron cluster computer. In this session one of the team members from our Scientific Computing and IT group will introduce the Desktop and how to choose options which allow the best use of it remotely.

Convener: Robbie Clarken (Australian Synchrotron)

14:10 → 14:30 Data visualisation with Fiji

From when the data is collected to after it has been reconstructed, the ability to visualise the image is essential. Fiji is a very useful tool for displaying and measuring images and image stacks. Fiji is derived from ImageJ. Over the years many additions have been made to ImageJ which are now incorporated into Fiji. The essentials of using these tools for looking at your data is covered in this session.

Convener: Dr Chris Hall (Australian Synchrotron)

14:35 → 15:00 The basics of CT reconstruction: Going from a projection set to a clean volume set

The fundamentals of creating a 3-D array (volume) from a series of projection images is the topic of this session. Understanding the principles is a good way to optimise the collection and reconstruction strategy for the experiment.

Convener: Dr Sherry Mayo (CSIRO)

15:05 → 15:30 Remote access: Practical session with ASCI Desktop

In this session we will practice the data access, and reconstruction methods which were the topics in the morning. We will provide test storage areas with data sets to trial. If you would like to work with your own data that is good too.

Conveners: Dr Andrew Stevenson (Australian Synchrotron/ CSIRO), Dr Anton Maksimenko (Australian Synchrotron), Dr Chris Hall (Australian Synchrotron), Dr Sherry Mayo (CSIRO)

15:30 → 16:15 Tea break

16:15 → 17:00 CT artefacts: How to avoid/handle them: Practical session using the ASCI Desktop

Even with the best raw data and reconstruction algorithms there are features in the reconstruction which are due to processing, rather than the object. In this session we will discuss these and how best to minimise them in your reconstructed data.

Conveners: Dr Andrew Stevenson (Australian Synchrotron/ CSIRO), Dr Anton Maksimenko (Australian Synchrotron), Dr Chris Hall (Australian Synchrotron), Dr Sherry Mayo (CSIRO)

18:00 → 21:00 Supper

Tuesday, 21 March

09:00 → 09:15 Recap

A brief review of yesterday and an opportunity for questions and clarifications.

Convener: Dr Chris Hall (Australian Synchrotron)

09:15 → 09:35 Image quality: Optimising your images

Convener: Dr Chris Hall (Australian Synchrotron)

09:40 → 10:00 Phase retrieval: Phase contrast CT, and alternative reconstructors

Using a synchrotron beam as your x-ray source for a CT brings several advantages. One that is very popular is the ability to make phase contrast CTs. In this session methods for reconstructing which exploit phase contrast are introduced and discussed.

Convener: Dr Andrew Stevenson (Australian Synchrotron/ CSIRO)

10:05 → 10:25 Scripting your workflow: Batch processing many images

Conveners: Dr Anton Maksimenko (Australian Synchrotron), Dr Sherry Mayo (CSIRO)

10:25 → 10:55 Coffee break

10:55 → 11:20 3D data visualisation: Rendering with Drishti

Good visualisation of a volume data set can make a big difference when interpreting the tomograph. The IMBL recommended tool for doing this is Drishti, from the ANU visualisation laboratory (VizLab). In this session we will present the basics of using Drishti to view a volume data cube.

Convener: Dr Anton Maksimenko (Australian Synchrotron)

11:25 → 11:55 Animation for presentations: Creating movies to show off your data

Showing an audience aspects of volume data is often best done using an animation. In this session the way to achieve this is shown, again using Dristhi.

Convener: Dr Anton Maksimenko (Australian Synchrotron)

12:00 → 13:00 User Experiences: Learn how others use IMBL

13:00 → 13:45 Lunch break

Lunch and poster vieweing

13:45 → 15:00 Practical session - Rendering and animation

This final afternoon session will allow delegates to trial the CT data rendering process with members of the team available to help.

Conveners: Dr Andrew Stevenson (Australian Synchrotron/ CSIRO), Dr Anton Maksimenko (Australian Synchrotron), Dr Chris Hall (Australian Synchrotron), Dr Sherry Mayo (CSIRO)

15:00 → 15:20 Closing session- Round up