CT@IMBL-2018A

Australia/Melbourne
NCSS Seminar room (Australian Synchrotron)

NCSS Seminar room

Australian Synchrotron

800 Blackburn Road Clayton Victoria 3168
Andrew Stevenson (Australian Synchrotron/ CSIRO) , Anton Maksimenko (Australian Synchrotron) , Chris Hall (Australian Synchrotron) , Hausermann Daniel (Australian Synchrotron) , John Marcou (Australian Synchrotron) , Ron Bosworth (Australian Synchrotron) , Sherry Mayo (CSIRO)
Description

Imaging and Medical Beamline CT workshop: CT@IMBL-2018A

Thanks for you interest in the CT workshop.

The registration limit has been reached. If you would like to be put on the reserve list for the next workshop please email Chris Hall (chris.hall@synchrotron.org.au)

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

During these two days we will make presentations and 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 talks 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 Synchrotron and CSIRO staff.

On the first day there will be an opportunity to visit the beamline.

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 a CT scan 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 its use for processing IMBL data 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 complete, 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. Supper on Monday evening.
  • 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 accommodation at their own expense.
  • To book a room please click on the Guesthouse link.

What you will need to provide

Access to the IMBL filestore and ASCI computer is through a web page interface, Please bring along your own laptop/tablet for this. 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


 

    • 09:00 09:30
      Coffee and Tea NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      Coffee and tea available

    • 09:30 09:45
      Welcome and introduction NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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)
    • 09:50 10:20
      IMBL characteristics: X-ray characteristics and general imaging NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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)
    • 10:20 10:45
      Phase Contrast: Phase contrast CT NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      One of the great benefits of using a synchrotron x-ray beam for imaging is its inherent coherence. In this session the idea of utilising this for x-ray phase contrast imaging is explained.

      Convener: Dr. Andrew Stevenson (Australian Synchrotron/ CSIRO)
    • 10:45 11:15
      Coffee and tea break NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168
    • 11:20 11:45
      IMBL User interfaces: Our Graphical User Interfaces NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

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

      Convener: Dr. Anton Maksimenko (Australian Synchrotron)
    • 11:45 12:10
      CT data collection: Sample alignment and ways to run a CT NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      Careful setting up of the CT collection is important to obtain the best quality images. Although the alignment is usually done for you the process will be explained.

      Convener: Dr. Anton Maksimenko (Australian Synchrotron)
    • 12:15 12:35
      Data management: Where your data is stored, and how to access it NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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: Mr. John Marcou (Australian Synchrotron)
    • 12:35 13:15
      Lunch break 40m NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      Lunch and Poster viewing

    • 13:15 14:00
      Visit to the IMBL IMBL

      IMBL

      Australian Synchrotron

    • 14:00 14:25
      An introduction to ASCI Desktop: The User Interface to the AS cluster NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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: Ron Bosworth (Australian Synchrotron)
    • 14:30 14:50
      Data visualisation with Fiji NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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)
    • 14:55 15:20
      The basics of CT reconstruction: Going from a projection set to a clean volume set NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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)
    • 15:20 16:00
      Tea break 40m NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168
    • 16:00 16:40
      Remote access: Practical session with ASCI Desktop NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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)
    • 16:40 17:30
      CT artefacts: How to avoid/handle them: Practical session using the ASCI Desktop NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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)
    • 17:30 19:55
      Supper Kitchen Synch

      Kitchen Synch

      Australian Synchrotron

      Join us for a banquet supper in the Kitchen Synch. Bring your best singing voice for some karaoke enterntainment!

    • 09:00 09:10
      Recap NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

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

      Convener: Dr. Chris Hall (Australian Synchrotron)
    • 09:10 09:30
      Optimising the quality of your raw data NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      Just like in cooking, if you start with great ingredients you get great results. The ingredients for CT reconstructions are the set of 2D x-ray projection images. So it’s useful to understand how to get the best quality projection set from the iMBL instrumentation. In this presentation we will explore some of the things that degrade an otherwise ideal 2-D projection image.

      Convener: Dr. Chris Hall (Australian Synchrotron)
    • 09:30 09:50
      IMBL detectors: What they are and their characteristics NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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.

    • 09:50 10:00
      Introducing HDF5: A new data storage format NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      The IMBL standard imaging file format is currently TIFF (Tagged Image File Format). Although this is a common and highly supported format, it is not ideal for collecting computed tomography data. Other facilities have moved to a more compact and database-like format called HDF5. IMBL will introduce this format next year. This session will give a brief introduction.

    • 10:05 10:25
      Scripting your workflow: Batch processing many images NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168
      Conveners: Dr. Anton Maksimenko (Australian Synchrotron) , Dr. Sherry Mayo (CSIRO)
    • 10:25 11:05
      Coffee break 40m NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168
    • 11:05 11:45
      3D data visualisation: Rendering with Drishti NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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)
    • 11:50 12:30
      User Experiences: Learn how others use IMBL NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      This session is reserved for anyone who would like to give the workshop the benefit of their IMBL experience.

    • 12:30 13:15
      Lunch break 45m NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      Lunch and poster vieweing

    • 13:15 14:15
      Animation for presentations: Creating movies to show off your data NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      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)
    • 14:15 15:30
      Practical session - Rendering and animation NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      This 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)
    • 15:30 16:00
      Coffee break NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168
    • 16:00 17:00
      Practical session: Rendering and animation (contd.) NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      This session continues after the break.

    • 17:00 17:10
      Closing session- Round up NCSS Seminar room

      NCSS Seminar room

      Australian Synchrotron

      800 Blackburn Road Clayton Victoria 3168

      A final chance to ask questions or clarify what you've learned, before we say goodbye.

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