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Infrared Beamline Data Analysis Workshop; PhD Scholarships in Biomedical Imaging

Infrared Beamline Data Analysis Workshop

The Australian Synchrotron is pleased to announce the 2012 Infrared Beamline Data Analysis Workshop.

This workshop will focus on data analysis and in particular on resonant Mie scattering (RMieS) correction. A RMieS correction algorithm based on extended multiplicative signal correction (EMSC) has been developed by Paul Bassan and Peter Gardner of Manchester University, UK and Achim Kohler of Nofima Mat, Norway in order to remove the baseline distortion in FTIR spectra, particularly in biological single cell spectra. This correction is now being increasingly used on spectra from both single cells and tissue sections. Paul Bassan will join the IR beamline team as workshop instructors.

The workshop will feature a series of lectures on the first day, providing background on aspects on data analysis for FTIR as well as data analysis using the new version of OPUS 7 software (which is now being commissioned and will be available to users for data analysis on our offline beamline PC). The second day of the workshop will be hands-on, working through tutorials on RMieS correction. We are pleased to announce that the tutorials will involve use of our high performance computing cluster, MASSIVE. MASSIVE has been found to reduce the computation time for RMieS by 60-100 times when compared to a high-end desktop PC. The workshop will also serve as the launching platform for the use of MASSIVE as a remote resource for users and collaborators.

This workshop is aimed at current users of the IR beamline who have data to analyse and are concerned with sloping baselines in the spectra and/or would like to learn more about the best pre-processing routines to achieve optimal results. Students and early researches are particularly encouraged to apply. Prospective attendees will be advised if their registration has been accepted in mid May.

There will be no charge for registered attendees and lunch, coffee breaks and a workshop dinner will be catered for. Some travel and accommodation support will be available to interstate visitors and in particular students. There will be limited number of places available based on various selection criteria . Attendees are expected to bring their own laptop to the workshop.

For more information and registration, please see:

Monash / NICTA Scholarships (including scholarships in Biomedical Imaging)

Starting from this scholarship round, Monash and NICTA will jointly offer scholarships for exceptional PhD students who want to work in the following flagship programs at Monash:

Biomedical Imaging (Leader: Gary Egan)

  • Novel algorithms for computational imaging and analysis - Novel algorithms including compressed sensing and iterative reconstruction are being applied to improve and accelerate image acquisition and reconstruction, to enable studies with special characteristics such as very high time or sub-voxel spatial resolution. Morphological techniques (e.g. 3-d shapelets) are being applied for segmentation and classification of images, and non-parametric techniques such as manifold analysis for dimension reduction in large, multi-subject studies. Our current biomedical imaging projects require the development of advanced automatic feature segmentation techniques.
  • Accelerating computational imaging and analysis - Graphical processing units (GPUs) such as those powering the Multi-modal Australian ScienceS Imaging and Visualisation Environment (MASSIVE) are being used to accelerate computational imaging and image analysis. Reductions in processing time up to 100 times make very large, multi-subject, multi-modal imaging studies feasible, open up new approaches to algorithm choice and application, and can assist in translating computationally-challenging algorithms to real time clinical use. Specific areas of application include linear and non-linear image registration, cortical surface extraction and microstructural tractography.
  • Visualisation-led discovery and communication - The two great challenges of contemporary visualization are (i) managing very large, multi-dimensional datasets yet still delivering useable, interactive visualisations; and (ii) reducing the extensive filtering and censoring of data that is commonplace in published graphs and data projections, while retain meaning and context. Volume rendering of large datasets has recently been achieved using 2.5 teravoxel-per-second rendering on an intermediate-size GPU cluster. With collaborators from several disciplines we are developing non-commercial technologies for embedding 3-d scientific figures in PDF files, for application in the academic publishing industry, together with new visualisation paradigms for improving the comprehension and communication of neuroimaging data.

Computational Biology (Leader: Geoff Webb)

  • Integrated computational technologies for determining the structure and dynamics of very large macromolecules: While techniques for determining the structures of small and medium sized proteins are well developed, they do not scale effectively to large proteins. As the determination of novel protein structures has high impact (eg many Nobel prizes have been awarded for it), this is an area of high impact. This flagship program seeks to create novel computational technologies for constructing models for large protein molecules from X-ray crystallography, small-angle x-ray scattering (SAXS), circular dichroism (CD), Cryo-electron Microscopy (Cryo-EM), molecular modelling and simulation data.
  • System Biology and biological processes: Holistic understanding of biological processes and systems (abstracted as multi-layered interacting networks) plays a vital role in unravelling Natures choreography of life. This program aims to develop methodologies for modelling such processes (e.g. Bayesian network), their graphical representation (e.g. SBGN) and analysis to study environment, epidemiology or systemic diseases (e.g. malaria, tuberculosis, cancer) for drug design.
  • Computational Genomics - We develop novel computational solutions to distinguish mutations identified in cancer genome sequencing projects as drivers of pathogenesis from functionally inconsequential ones (i.e. the so called passenger mutations).
  • Computational Proteomics - We aim to model and understand the structure and function of proteins and protein-protein interactions.

Optimisation (Leader - Mark Wallace)

  • Transport this flagship program will conduct research relating to transport and transport systems and using optimisation techniques identify how transport can be improved.
  • Sustainability this program explores how organisation might better exploit and manage assets to maximise performance and minimise life cycle costs.

Monash University has up to two Monash/NICTA stipend scholarships (APA rate) and a few top-up scholarships ($7,000 supplementary stipend) to be awarded to eligible students in the second half of 2012 (Top-ups are available to students who are already recipients of stipends such as Monash Graduate Scholarships, or who are successful in the upcoming Monash mid-year round)

Please encourage prospective students to submit a PhD application to Monash and then complete the NICTA application by Thursday, 31 May. Current students who are applying for top-ups, will only need to submit a NICTA application. After this time, a panel will be convened to look at eligible applications. Recommendations of the panel will be forwarded to NICTA, and then the proposed project must be endorsed by NICTA before an offer can be made to a student.

Applications submitted after this date will be considered later in the year in September.

Application forms:

Applications to Monash are via MRGS:

NICTA application forms are available directly from the NICTA website:

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