Quest for the South Magnetic Pole

Mark Pharoah, South Australian Museum

South Australian Maritime Museum

Dr. Paddy McGee, eResearch SA

During the 1908-1909 expedition to find the location of the South Magnetic Pole, stereographic photography was used to record various aspects of the expedition.

As part of the "Quest for the South Magnetic Pole" exhibition at the South Australian Maritime Museum, some of these stereo images are in display as red/cyan anaglyphs, allowing them to be viewed by groups of people at a time. The processing to convert the digitised copies of the original prints to anaglyph format was undertaken at eRSA, using the following steps:

• cut the left- and right-hand-side images from the digitised original
• clean / repair the images as necessary to reduce the appearance of spots, scratches and other faults
• adjust black and white levels, and gamma to improve the dynamic range of the images
• align the two images to provide a good sense of depth, suitable zero parallax, and acceptable ghosting in the final anaglyph image
• crop to suit a 4:3 landscape aspect ratio whilst maintaining the important sections of the image
• render as a single red/cyan image.

Using the anaglyph format for the displayed stereo images allows for flexibility (works with standard monitors and projectors), simplicity (only one standard projector or monitor is required), and robustness (allowing for touring the exhibition).

        

       

Flinders Ranges in stereo

Tim Baier, VFXgang
Rae Grierson, SA Great

Tim Baier works in the visual effects industry and is committed to the use of stereographic visuals in both an entertaining and intellectually satisfying way.

He has produced a stereo "documentary" covering the Flinders Ranges and the Arkaroola region in particular. A self-funded project, this work brings the geology of the Ranges to life in a way that is not possible via monoscopic (or two-dimensional) imagery.

Using single and paired cameras, the regimes range from macrophotography through to landscape photography from a microlight aircraft, all in stereo. Both single and time-lapse sequences were captured.

The many images thus obtained were developed into a cohesive presentation, in collaboration with Doug Sprigg (Arkaroola Wilderness Sanctuary), Professor Ian Plimer (Professor of Mining Geology at the University of Adelaide) and Dr. Jim Gehling (SA Museum), who all contributed to the accompanying text. The result is a work that describes in detail the unique geology of the Flinders Ranges via stereo imagery and informed comment.

The intent is to provide an audio-visual documentary, with stereo visuals, that can be shown at venues capable of screening stereo images. It is hoped that this project will generate an interest for visually and intellectually stimulating stereographic content that will be accessible to the public.

In association with SA Great, eResearch SA, and the Art Gallery of SA, this project was launched at a breakfast event on December 12th, 2007. The venue was the Radford Auditorium at the Gallery, where a portable (passive polarised) stereo projection rig was set up for the event.

After introductions by Judy Potter (CEO of SA Great), Christopher Menz (Director of AGSA), and Tim Baier, a screening of the work was given.

This event took place during the "A Century in Focus" exhibition at the Gallery, in which a number of antique stereo images were displayed as anaglyphs on computers monitors. The full range of stereo photography was on show, from early examples in that exhibition, to current state-of-the-art imagery at the launch.

As the original imagery for this project was taken at very high resolution (well above HD), the content is suitable for viewing at venues which have sufficiently large projectors to take advantage of the resolution inherent in these images.

A century in focus: Stereo images at the Art Gallery of SA

Julie Robinson, Senior Curator of Prints, Drawings and Photographs, Art Gallery of SA
Maria Zagala, Associate Curator of Prints, Drawings and Photographs, Art Gallery of SA
Dr. Paddy McGee, eResearch SA

A Century in Focus was an exhibition at the Art Gallery of South Australia (9/11/07 – 28/1/08), covering a century of South Australian photography from the 1840s to the 1940s.

Part of the exhibition covered stereo photography taken by George Burnell and H. H. Tilbrook. Burnell's images document a trip along the Murray River in the 1860s, whilst Tilbrook's images are from a few decades later, and were taken in a variety of locations.

A selection of original card-mounted stereo pairs from the Gallery's collection was digitised for conversion to a format suitable for viewing on computer monitors in the exhibition space. Red/cyan anaglyph presentation was selected as the method for most convenient display in this context.

At eResearch SA, the image files were processed as follows:

• The left and right-hand side images were cut from the digitised originals, and saved separately.
• These images pairs were rotated and translated as necessary for good alignment, and to give an acceptable level of ghosting when viewed with anaglyph glasses. Some edge-of-field depth conflict was on occasion necessary in order to achieve this.
• Image pairs were saved as single red/cyan anaglyph images.
• Black, gamma and white levels were adjusted so as to improve the dynamic range of the images.
• Scratches, blemishes, etc, were removed in order to improve the quality of the images, in particular to reduce their presence in either just the right- or left-side image, which can have a significant detrimental effect on stereopsis.

For the exhibition, the final anaglyphs were assembled into a cycling PowerPoint presentation, and displayed on LCD monitors. Red/cyan anaglyph glasses were available at each monitor for viewing.

The siting of the displays within the exhibition space is in accordance with the progression of the original photography in its historical context. Thus, the display of Burnell's work is early in the exhibition, as he flourished early in the era under consideration; Tilbrook worked later, and that display is positioned accordingly.

Experimentia: An Inter-Arts project

Director/Choreographer: Amanda Phillips
Composer: Alexander Waite Mitchell
Software Design: Jonathon Mah, Damian West
Performers: Gala Moody, Lisa Griffiths, Deon Hastie
Live Technology Performance: Alex Mitchell & Damian West
Filming: Alex Waite Mitchell, Damian West & Amanda Phillips

3xperimentia is a series of investigations at the interface of 3D stereoscopics and the visual and performing arts that has resulted from a successful arts-business partnership between eResearch SA and the team of interarts collaborators headed by Amanda Phillips and Alexander Waite Mitchell. 

3xperimentia is an ongoing public art and performance project that will evolve over time. Since 2007, this research has resulted in several outcomes including rendered versions of film and dance film creation, computer generated imagery and the development of custom software that facilitates live cinema and interactive installation versions of the work.

The flagship production 3xperimentia: Live Cut, Australia’s first 3D-stereo live edit performance, grew from this significant partnership. 3xperimentia: Live Cut, is a performed 3D stereoscopic cinema work fusing contemporary dance, computer generated imagery and real-time interactive effects.

Collaborating across performance and technology and continuing the artistic repertoire of Amanda Phillips and Alexander Waite Mitchell, the 3xperimentia creative team includes visual programming by Jonathon Mah and pre-filmed dance footage of stellar Australian performers Gala Moody, Lisa Griffiths & Deon Hastie.

3xperimentia: Live Cut was named ‘Best of The Fringe’ in The Advertiser for the 2009 Adelaide Fringe, and the production received a 2009 Ruby Award for Innovation; the Rubies are South Australia’s premier arts and cultural awards. This recognition confirms the value of the in-house research that the team conducts at eResearch SA through the use of the Visualisation Laboratory, camera systems and visualisation consultancy. 

Noted at the 2008 World Dance Alliance Global Summit as a ‘work with a high level of social and artistic currency,’ 3xperimentia integrates and develops both technology and performance.

The work is potently live as the dual un-rendered video streams are triggered through touch activation, operator manipulation and audio-reactive environments.

The continuing support of eResearch SA is vital to the research that this team of collaborators is conducting, and is an exciting example of a South Australian cross-industry partnership.

3D visualisation of protein modelling

Associate Professor Maria Hrmova, Australian Centre for Plant Functional Genomics

Protein modelling provides techniques whereby the three-dimensional structure and biological function of protein molecules can be identified.

Associate Professor Maria Hrmova from the Australian Centre for Plant Functional Genomics and the University of Adelaide researches the structures of agriculturally significant grass proteins for research into improving crop resistance to abiotic stresses such as temperature, drought, and salinity.

Results from X-ray crystallography studies of the proteins are processed using eResearch SA supercomputers. This processing allows the atomic structure of the proteins to be modelled.

Other software is used to display these models, so that they may be studied and interpreted visually. A stereo three-dimensional visualisation workstation, with specifications developed by eResearch SA, allows researchers to perceive the protein model in three-dimensional space; that is, as a natural, solid body, the shape and structures of which may be seen and interpreted intuitively by visual means.

The addition of the extra dimension of depth when it is perceived directly by stereopsis, rather than only indirectly by other clues such as occlusion or shading, greatly improves the ability to interpret structure and relationships within complex shapes.

Stereo visualisation makes it possible to precisely interpret the electron density map with respect to structural features such as backbone or ligands and how these features relate to each other. Interactions between these and other components, such as those between protein and DNA, or protein and carbohydrate, can then be modelled to help determine the precise biological role of the protein in the organism.

The eResearch SA visualisation workstation is supplied as a complete, integrated and ready-to-go system. For 3D display use, it incorporates a workstation graphics card, high-end cathod ray tube monitor, infra-red emitter with shutter glasses, and is pre-installed with Linux and appropriate open-source visualisation software.

Interactive stereo visualisation of modelled molecular structures

Dr. Grant Booker, School of Molecular and Biomedical Science, University Of Adelaide

Using molecular visualisation software such as Chimera, eResearch SA's VisLab and the SAVRC allow researchers to view molecules with full stereoscopic vision. This allows their three-dimensional structures to be interpreted much more readily than is the case with non-stereo imagery. This is particularly important when the interaction between molecules is of concern, since this is related to how closely the different molecules' surfaces can come into contact.

The ability to see directly this level of contact allows researchers to classify and rank molecular models very rapidly, thus greatly enhancing the efficiency of the molecular modelling process.

From Dr. Booker: "We have been using the VisLab to review protein structures that have been determined either locally or with colleagues from interstate and overseas. The ability to discuss the details of the three-dimensional structures with others helps to make sense of the molecular mechanisms associated with the functions of these proteins.

"Using the Vis Lab, we review the results of molecular docking experiments. We screen a target protein structure with the 3D coordinates of structures of up to 500,000 organic compounds using Dock 5.0 from the UCSF. A consensus-scoring algorithm is then used to select candidate structures that may act as ligands for the target. As a group, we are able to decide which of the top 50 candidates meet a range of criteria such as how well the shape of the molecule complements the binding site.

"We then purchase those compounds that meet our criteria for testing in biochemical or biological assays. Using this process we have been able to find high-affinity enzyme inhibitors.

"We have also been using SAVRC for Biochemistry III tutorials in order better to explain the intricacies of protein structure to students."

Visualisation of quantum chromodynamics

Professor Derek Leinweber, Discipline of Physics, University of Adelaide

Quantum chromodynamics (QCD) is a theory used to describe the interactions of quarks and gluons, fundamental sub-atomic particles which comprise more-familiar particles such as protons and neutrons.

Converting the mathematics of QCD theory into computer code, researchers are able to model the behaviour of these fundamental fields and particles. Such simulations are run on powerful supercomputers, such as those operated by eResearch SA, where their high computational speed and data-handling ability allow the vast number of calculations required to be performed in reasonable time frames.

Visualisation packages, such as Advanced Visual Systems (AVS) Express, are used to convert the large amount of data which are generated by such simulations into images. In many cases, various parameters of the model are calculated on a regular (x,y,z) grid, and AVS Express will be used to display these data as a three-dimensional plot.

Such graphical representation allows the researcher to see the variation in the data values across the simulated space in a simple and intuitively understood way. If the data are generated for different values of time, the evolution of these quantum-scaled fields and particles may be shown in a way that greatly assists their understanding.

Furthermore, with the appropriate display hardware (such as eResearch SA's VisLab, SAVRC, or desktop visualisation workstations), the images can viewed in real-time in stereo. As in many other fields of study, such stereoscopic viewing allows one much more readily to interpret complex three-dimensional structure than does monoscopic viewing. Indeed, the use of general visualisation software such as AVS Express, coupled with stereoscopic display, is of benefit to many areas of research.

Some of Professor Leinweber's animation work (see here for several examples), produced using AVS Express, was used in Professor Frank Wilczek's 2004 Nobel Prize Lecture.

South Australian Museum: Icthyosaur modelling project

Dr Ben Kear, SA Museum and School of Environmental and Earth Sciences, University of Adelaide

The South Australian Museum enjoys a globally significant collection of palaeontology specimens including unique and well-preserved fossil remains of ichthyosaurs, marine reptiles from the Mesozoic period.

In collaboration with Dr Ben Kear, a vertebrate palaeontologist from the SA Museum and the University of Adelaide, and Ben Hill, a student from the University of South Australia, eResearch SA provided advanced computing and visualisation support for a project to reconstruct the head of one such ichthyosaur.

With Dr Kear's advice, Ben Hill created a three-part computer model of the skull of an ichthyosaur. The model is as anatomically accurate as possible, including the size and position of the muscles controlling the jaw, the position of the eye and possible location and shape of the "nose".

The base of the model is a scan of a well-preserved ichthyosaur skull; on this were built several major muscles (from scars left on the skull) and then the external surface of the ichthyosaur.

The skull was scanned at the Queen Elizabeth Hospital. The DICOM images were then converted to .stl format (using Osirix) and imported into Rhino for the reconstruction and eventual animation using Quicktime Pro.

A number of marine fossils have been found in areas of Australia that are now well inland; studies of the geological history of Australia show that it once had a major inland sea.

 

 

 

 

 

Impossible images project

Professor Chris Mortenson, Discipline of Philosophy, School of Humanities, University of Adelaide

The term 'impossible images' refers to images depicting objects which cannot exist in normal 3-D Euclidean space.

Impossible images have a long history, stretching back to the walls of Pompeii. However, the major work was done in the twentieth century, beginning with Oscar Reutersvaard 1934, then following him some twenty years later by M.C.Escher and Roger Penrose, then later many others including Bruno Ernst.

Work has tended to focus on producing new sorts of images, while little work has been done on their mathematical description. However, the most fruitful approach to the latter would seem to be to define geometrical objects existing in an inconsistent 3-D space, with projections to the 2-D images.

This project aims to investigate impossible images on several levels.

1. to continue the work of producing new sorts of images
2. to classify those already found: so far, it seems that four main types have been discovered
3. to animate these images
4. to apply the techniques of stereoscopic images and virtual reality to produce 3-D effects
5. to provide mathematical descriptions of the inconsistent 3-D spaces, utilising the techniques of inconsistent mathematics.

For an example of the animation work being done, watch 'Escher Meets Ernst', by Peter Quigley, Chris Mortensen and Steve Leishman.

For more information, see Inconsistent Images.

eResearch SA's role in this project was the provision of stereo stills and video of real-life scenes which were edited in an attempt to convert real objects to impossible objects within the real-world framework, as well as advising on convenient viewing methods for such stereo content.

eResearch SA can advise on, and assist with, the capture, processing and display of stereographic stills and video imagery. We also have experience processing archival stereograms for display with contemporary equipment.

 

 

 

Bragg about Adelaide

Mark Pharoah, SA Museum

Craig Hill / Dr. Paddy McGee (eResearch SA)

When a beam of X-rays is passed through a regular, crystalline substance, the X-rays are diffracted, and will form a pattern on a suitable recording surface. The actual structure of the crystalline substance may be determined by the correct interpretation of this diffraction pattern. The discovery of this technique was of extreme importance in the many fields of research which involve chemical and molecular structure.

William Henry Bragg and his son William Lawrence Bragg won a Nobel Prize in 1915 for their definitive work in X-ray crystallography. In 1886, W.H. was appointed the Elder Chair of Mathematics and Experimental Physics at the University of Adelaide, and in 1908, W. L. graduated from the same institution with a B.A. with First-Class Honours in Mathematics.

As part of an exhibition at the State Museum of South Australia, eResearch SA developed a short presentation that covered the Braggs' use of X-ray diffraction in crystallography, its relevance to the deduction of the structure of DNA, and future prospects for crystallography in Australia.

This involved the creation of stereo computer-generated animations to represent X-ray diffraction by salt crystals and the crystalline form of DNA, and the processing of archival stereographic images for display in our VisLab. Scripting and presentation were done by eResearch SA staff.

As part of the opening of the Bragg exhibition, a presentation of the show was attended by the Premier Mike Rann, the Hon. Dr. Jane Lomax-Smith, and Professor Baroness Susan Greenfield (SA Thinker-in-Residence at the time).

This show ran once daily on week-days, for six weeks during August–September 2005, and was held in the eResearch SA VisLab.

 

 

 

 

'Harmony of the Spheres' concerts

Syntony vocal ensemble

Dr. Paddy McGee (eResearch SA)

Computer-generated animations developed by eResearch SA were used as a visual backdrop for concerts presented by Adelaide-based vocal group Syntony.

The animations consisted of a tour of our solar system, visiting all the major planets, including (as it was at that time) Pluto. Presentation was monoscopic, as a portable stereoscopic projection rig was not available, and most importantly, the visuals were intended as an accompaniment to the music, and not the other way around.

Rendering software was used to generate the imagery, with the virtual camera path set so as to display the main aesthetic qualities of the various planets.The animations were not timed to the pieces performed; during performance, a filler animation of a starry background was used between planet fly-bys, and was run until it was felt that the next fly-by should begin.

The two concerts were held in the Art Gallery of SA Auditorium, and at Veritas Winery in the Barossa Valley, in September and October 2004.

Christine Garnaut – Director Architecture Museum, University of South Australia

 

“Working with e-research has been a really positive experience – the staff have been incredibly enthusiastic and supportive of our vision.” – Christine Garnaut, Senior Research Fellow, Director Architecture Museum.

Filed away in the Architecture Museum at the University of South Australia are over 200,000 documents, books and publications, donated by private practitioners, which represent the diverse aspects of South Australia’s architectural history.

Looking for technical expertise and fresh ideas about how to utilise and present items in this extensive collection, Christine Garnaut, Senior Research Fellow and Director of the Museum at the School of Art Architecture and Design at the University of South Australia, reached out to eResearch SA.

Working in conjunction with one of the Museum’s research collaborators, History SA, Christine and her colleagues came up with the idea of putting together a 3D representation of a historical South Australian property.

They chose Joseph Elliot’s cottage built in 1856 in Jeffcott Street, North Adelaide.

“Joseph had described the cottage and its furniture and contents as well as its garden in a highly detailed letter which he wrote in 1860 to his mother in England,” Christine says.

“The letter is published in a book called Our Home in Australia. The book includes a commentary and sketches by architect and academic Stefan Pikusa and a foreword by Joseph Elliott’s grandson, Brian.

“Through the letter and significant interpretative material from these two authors, we were able to get a real understanding of the cottage and how it might look in 3D form.”

Christine submitted a proposal for the project to eResearch SA.

“In no time at all they had organised for Lyndon Warren, a communications student from Flinders University to assist us, through the eResearch SA scholarship program,” she says.

The eResearch SA scholarship program is designed to match university students with researchers and supervisors, to assist with research projects that use eResearch techniques and facilities.

Lyndon Warren applied for a summer scholarship with e-Research and was matched with Christine and the Architecture Museum because of his knowledge of the 3D graphics program Maya.

With Christine’s and Julie Collins’ (Collections Manager) help, Lyndon began delving into the architecture of Joseph Elliot’s cottage, documenting every detail from the windowsills to the veranda.

“Lyndon was very keen to learn more about architecture and quite happy and capable to work independently with the sources we had given him, just coming back to us with questions when he needed to,” Christine says.

After coming to a good understanding of the layout of the cottage, Lyndon used the Maya program, (which is also used to create special effects in films) to build an interactive, photo image model of the home – transforming simple sketches and floor plans into an interactive 3D experience.

“What we have now is a computerised model that allows us to experience the Elliott house beyond just words on paper – it’s also given us a better understanding of that particular era of architecture,” Christine says.

“You can walk through the door and around the rooms and really get a sense of the layout and the scale of the house.

“Not only do we now have a means to help promote visual understanding of 19^th century cottages, we now have a practical example of how we can use digital technologies to bring to life items in our collection – it’s been a great outcome.”

 

 

 

 

 

 

Greg Ruthenbeck - Haptic simulations for surgical training

 

“Our experience with e-Research SA has been very positive –
 they have provided access to cutting edge technology and
 support for our simulation research.”

– Dr Greg Ruthenbeck: Senior Research Associate, Medical Simulation, Flinders Medical Devices and Technologies, Flinders University

Just like a scene from a science fiction movie, Greg Ruthenbeck has spent the past four years of his life developing cut-able soft-tissue simulation effects for virtual reality surgical simulations using haptics technologies.

Working with Professors Karen Reynolds and Simon Carney on the Flinders Endoscopic Sinus Surgery Simulator, Greg is working on technology specifically designed to assist trainee surgeons, garnering attention from surgeons and medical personnel around the world.

Discovering that tissue simulation can effectively use programmable graphics processing units (GPUs), providing hundreds of cores and far greater processing power than CPUs, Greg says this new technology has enabled him to simulate tissue dynamics in real-time.

A critical component lacking from the toolbox of medical simulation developers, these GPUs have formed the basis of interactive tissue simulation at the core of the Flinders Endoscopic Sinus Surgery Simulator.

Having worked as a software developer in the simulation industry since 2002, Greg’s body of work includes the development of medical and defense simulators including ISim: A VR Haptic Endotracheal Intubation Simulation, a tonsillectomy simulation, haptic games for high-school students, and a haptic VR skull jigsaw for learning the complex anatomy of the human skull.

Greg’s work to date on the Sinus Surgery Simulator won him the award for Best Student Presentation in 2009 at the IEEE/CSIRO Science Symposium, and has received positive feedback from surgeons and medical personnel nationally and internationally.

Currently working on integrating tissue models, haptic and visual rendering systems, Greg intends for the project to be finalised early next year for use in surgery training.

Once complete, the software will be trialed in Australia’s five major ENT surgery-training centres, where Professor Karen Reynolds’ team will collect feedback about the practical effectiveness of their simulation technology. Greg also believes it will equally benefit experts by providing them with a risk free environment to practice new techniques.

Kicking off his involvement in haptic technology, eResearch SA provided Greg with his first access to haptic hardware in 2005 when he borrowed a Phantom Desktop haptic device, complete with haptic workbench.

eResearch SA was also responsible for providing access to a VR 3D laptop, introducing the hardware required for delivering portable VR medical training systems to the VR medical simulation research team at Flinders University well before 3D went mainstream.

“In addition to eResearch SA’s technical support, we have also been able to engage high-calibre students for our research through their summer scholarship program,” says Greg.

“This type of funding has afforded us the freedom to better engage students from other disciplines (e.g. Humanities) with the skills needed to open up new directions for our simulation research.

“Our experience with eResearch SA has been very positive – they have provided access to cutting edge technology and support for our simulation research,” he continues.

“Through the scholarship program they’ve also enabled our research group to grow and explore new directions, strengthening and expanding our capabilities.”

 

Heritage visualisation

eResearch SA’s summer scholarship students act as ‘eResearch ambassadors,’ arriving with a skill set their supervisors can use to further their research projects.
 
Jason Haylock was offered a scholarship to work with Theodor Wyeld, director of digital media studies at Flinders University, on his ‘Escape from Adelaide Gaol’ project.

The project is a digital heritage visualisation study, in the form of an educational game. In the game, the Old Adelaide Gaol is depicted as it appeared throughout its history. Players are able to walk around the Gaol, see how it has changed over the years, and re-enact escape attempts.

Jason’s work builds on two theses, that provide detailed reports of attempted escapes from the Gaol, prepared by final year Flinders University Tourism students.

Jason used his 3D animation and computer programming experience to create a prototype of the game.

To ensure the prototype’s historical accuracy, Jason used a set of architectural drawings of the Gaol and its buildings as they appeared in 1841. He imported the drawings into the prototype and used them as a guide in modelling the Gaol’s buildings and walls.

An important part of the project was to visit the Gaol to photograph the building and walls and other surfaces. This meant that realistic and authentic textures could be applied to the model. The photographs were also used as reference for modelling areas and angles of the buildings that didn’t appear in the architectural drawings.

To ensure historical accuracy extended to the playable characters of the prototype, Jason created a texture for one of the basic avatars, basing it on the uniform that convicts wore around 1841, informed by a period character from an 1850 watercolour.

By the end of this project Jason had created a game environment featuring a recreation of the Old Adelaide Gaol as it appeared in 1841, including a detailed Governor’s House and guard tower. Using Jason’s prototype, gamers can control the Governor and walk around the Gaol environment and watch a group of convicts milling about inside.