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Sydney MicroScopy & MicroanalySiS

IN THIS ISSUE

01 A word from THE dIrEcTor

03 mEET yoUr TEAm

04 NEw fEE ScHEdUlE

05 X-rAy ANd 3d dEvElopmENTS

06 fAST, flEXIblE TrAININg wITH myScopE

07 brEAkINg THE opTIcAl dIffrAcTIoN lImIT

08 wHAT’S oN HElp US To HElp yoU

AUSTrAlIAN cENTrE for mIcroScopy & mIcroANAlySIS

fEATUrEd mIcrogrApHS

A word from THE dIrEcTor by SImoN rINgEr

Two scanning electron microscope images of natural nacre (mother of pearl) taken on the Hitachi S4500 FEG-SEM. The layers of overlapping hexagonal plates of aragonite (calcium carbonate) are interspersed with an organic matrix making nacre very tough and resistant to cracking. Images: Xing Huang

orgANISATIoNAl cHANgES

In the context of ensuring transparency and consistency with the University’s governance and economic model, in mid-2012 we went through a change program to delineate different microscopy-related activities at Sydney. We created Sydney Microscopy & Microanalysis (SMM) as a professional service unit (PSU) within the DVCR portfolio. SMM will manage all service activities to our user community, and we have moved the externally funded operations, researchers and research programs such as the AMMRF and our ARC Centre of Excellence, into relevant faculties. That important research-focussed enterprise remains a priority for the University, and will be branded as the Australian Centre for Microscopy & Microanalysis (ACMM). There is a strong, broad consensus that Sydney should retain the kudos of the ACMM brand, serving as the interdisciplinary umbrella that connects the world-class research activities that are undertaken therein. This reflects the way that University academics can ‘leverage’ from the core facilities such as SMM to bring in external funds and generate new research initiatives. Also

In this issue we cover the important changes to our operation that have occurred as part of the change management undertaken by the University, to meet its Strategic Plan 2011- 2015 objectives.

SMM Newsletter

SydNEy mIcroScopy & mIcroANAlySIS

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relevant is our position nationally. Sydney continues to serve as the national headquarters of the Australian Microscopy and Microanalysis Research Facility (AMMRF), which is a joint venture between a number of research intensive universities to link our research capability. Funded through to 2015 by the NCRIS program, this highly successful organisation has much to offer you and details are available at ammrf.org.au

SMM now operates as a University core research facility, providing high quality, value-added services to the University research agenda. Its activities are supported by a combination of cost drivers embedded in the UEM, together with user fees. The unit is overseen by a Management Committee comprising of nominees of the Deans of Engineering, Medicine and Science and Chaired by the DVCR.

fAcIlITy AccESS cHArgES INcrEASE from 1 JUly

Financial sustainability for the operation of SMM as a core research facility will depend critically on striking the right balance between managing costs and generating income from external and internal users. To achieve this balance we must increase our user fees, which have not been adjusted since 2006.

As of 1 July 2013, our Pay-As-You-Go rate and annual Subscription Fees will increase as detailed on page 3. The new fee schedule has been set considering benchmarking data we have for our costs and charges against other microscopy centres nationally and internationally. It is needed to ensure we can continue to provide users with a high quality microscopy service. Together with the Management Committee, my team and I have worked hard to devise a new fee schedule that will deliver value to all levels of users and ensure a sustainable and bright future for microscopy at The University of Sydney.

THE Smm TEAm

Solving complex ‘structure-function’ problems often requires multiple modes of microscopy, coupled with a diverse range of technical expertise. This is what the SMM team comprises. Specifically, we have 11 technical staff and two administration staff in continuing positions at the Centre to deliver our services for you. This highly skilled and dedicated team is overseen by myself and Deputy Directors Associate Professors Filip Braet and Julie Cairney from the school of medical sciences and the school of aerospace, mechanical and mechatronic engineering (AMME), respectively. Incidentally(!) my own teaching and research is also now academically domiciled within AMME and these arrangements are working well.

As new research proposals are developed, I encourage you to contact my team to explore SMM’s superb capabilities for imaging and analysis using light, lasers, X-rays, electrons, and ion-optical systems!

We look forward to playing an enabling role in your future research agenda.

The University has invested strongly in microscopy since 1958 and continues its commitment to excellence and leadership in this critical capability.

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For staff contact details visit sydney.edu.au/acmm/about/staff

mEET yoUr TEAm

mISSIoN

The mission of Sydney Microscopy & Microanalysis (SMM) is “to support high-quality research across the University of Sydney by providing leading academics, researchers and students with access to world-class instruments and expertise in microscopy and microanalysis.”

vISIoN

Our Vision is to be “a leading core facility of the University of Sydney, and the partner of choice for the best research and research training via our provision of a world-class research capacity.”

THE TEAm

A critical part of SMM’s research capacity is the knowledge base of our academic, administrative and technical staff and their core areas of responsibility are set out below. This interdisciplinary team has the skills to translate the capabili-ties of our instruments into research outcomes across a wide range of disciplines in the life and physical sciences, and engineering.

Job opporTUNITIES

We are presently recruiting for a professional officer with key responsibilities in our outstanding light optical microscopy section. Please monitor the University website for more details or contact eleanor.kable@sydney.edu.au

Our technical staff has a mix of expertise to enable a wide range of research. We love solving problems and finding solutions for researchers.

SMM Management Committee

Simon ringer Director

lisa Abraham / linda cassimatis Admin Manager rebecca potter

Front Desk

filip braet Deputy Director (Bioscience)

Toshi ArakawaEngineering & maintenance

Steve moodySEM (FIB)

Takanori SatoAtom Probe

Julie cairney Deputy Director (Materials)

matthew foleyX-Ray & image analysis

Sherin chikhaniBiological Techniques

Ellie kableLab Manager

pat TrimbySEM (EBSD)

Naveena gokoolparsadhBiological Specimen Prep

vacancyLight Microscopy

Hongwei liuTEM

Adam SikorskiMaterials Specimen Prep

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NEw fEE ScHEdUlE

The new fee schedule reflects our operating costs more accurately, while maintaining discounts for academic users and offering competitive rates for commercial customers. Experienced users will also benefit from new off-peak rates. Any subscription purchased before 30 June 2013 will continue to be charged at the current rates until it expires.

The new fees are comparable with other leading national and international microscopy facilities. They also reflect the instrument and technical staff time required to deliver quality outcomes for our diverse range of users.

To help you make this transition smoothly and to get the best advice for your circumstances, we encourage you to contact us to discuss your current and future requirements.

Please feel free to contact Lisa Abraham, Subscription & Administration Manager on (02) 9351 4499 or at lisa.abraham@sydney.edu.au

We are introducing a new fee schedule effective 1 July 2013.

fees for University of Sydney users

Registration & training

$250 flat fee per new user

category peak: 9am–5pm Hours per annum

off-peak: 5pm-9am

Pay-As-You-Go $65 per hour Unlimited $44 per hour

Level 1 $3,600 per annum

60 ƛ 50% time bonus applies: 1.5hrs for the price of 1 hr, 3 hrs for the price of 2 hrs, etc.

ƛ Off-peak rates apply to experienced users only (Category 3).

ƛ Technical support staff not available off-peak.

ƛ Off-peak rates may also apply for some overnight/longer experiments that do not require continuous operator support.

Level 2 $9,000 per annum

200

Level 3 $17,500 per annum

500

Level 4 $25,000 per annum

1000

Level 5 $50,000 per annum

3000

fees for external users (excluding gST)

Registration & training $250 flat fee per new user

category Instruments per hour

Technical staff per hour

Total per hour

Publicly funded research organisations $120 $180 $300

Commercial $320 $180 $500

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X-rAy ANd 3d dEvElopmENTS

A new computer workstation for visualisation and software for XRD data mining/analysis have also been purchased. These will be used to obtain advanced qualitative and quantitative information from material structures imaged using our 3D data collection systems such as the Auriga and the Xradia MicroCT.

The software purchased includes the latest powder diffrac-tion file for the identification of samples from XRD scans. This is a significant update to our older PDF database from the late 90’s and we can now identify over 300,000 different samples from experimental and theo-retical sources. Coupling this with the TOPAS software that we have also purchased has given us the ability to perform Rietveld analysis (quantitative analysis of multiphase mixtures) in a far more accessible manner, extending our XRD capabilities significantly.

The big software story however, is Avizo Fire. This software extends our 3D visualisation capacity to include analysis of large datasets in both two and three dimensions. We were fortunate enough to have representatives from VSG (the company behind Avizo) demonstrate the software earlier in the year and the response from users was overwhelmingly positive. It is hoped that we will be able to build a working rela-tionship with the VSG team in further developing our data presentation and analysis opportunities.

In terms of hardware updates, we have had a few small changes along with a very exciting one. The Skyscan 1172 micro-CT has had its camera upgraded and source replaced, cutting scan times down to 25%–30% of their previous times. This, coupled with the latest reconstruction software, has reduced the time between starting the scan and having it reconstructed down to as little as 30 minutes. The XRDs are both being considered for an upgrade to their operating PCs which will ensure their stability going forward. This will include updating main board and software on the Shimadzu while maintaining the use of its in-situ heating stage (temperatures up to 1000°C).

We are pleased to announce the Xradia NanoXCT is operational. We now have a fully functional CT system that gets down to 50nm feature resolution. The system can

operate in two modes - absorption and phase contrast – and at two resolutions

– 16µm or 64µm field of view. We are now seeking expressions of interest from potential users who might be interested in trialing their samples at this scale.

The area that will benefit the most from the X-ray overhaul is image analysis. Matt is planning to work closely with other sections in the ACMM to develop and support more comprehensive analysis opportunities to ensure that

users leave with not just incredible images, but relevant and useful data

as well. If you have any ideas or questions about image analysis opportunities, please feel free to get in touch with Matt directly.

matthew.foley@sydney.edu.au

Further information on software packages mentioned above can be found at:www.vsg3d.com/avizo/firewww.icdd.com/products/pdf4.htmgoo.gl/M1dQr

Images by Matt Foley: concrete dust imaged on the NanoCT operating in Large Field of View Absorption mode and presented using Avizo Fire. Coloured features indicate high-density inclusions within the dust particle. Scan represents a volume of approximately 43 x 40 x 57µm.

The area that will benefit the most from the X-ray overhaul is image analysis.

Matt Foley was appointed the X-ray section manager at the end of 2012 and is already making a positive impact, with new X-ray sources and camera upgrades already installed and operational.

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fAST, flEXIblE TrAININg wITH myScopEIn 2012 we launched a new e-learning platform, MyScope – a training tool to enable advanced microscopy research. This online resource is now integrated into our user training.

Six learning modules cover: scanning electron microscopy (SEM); transmission electron microscopy (TEM); X-ray Diffraction (XRD); scanning probe microscopy (SPM) / atomic force microscopy (AFM); confocal and microanalysis.

Driven by the AMMRF program, an enormous amount of work has gone into these, with contributions from many of the staff in that facility’s nodes around Australia. We at Sydney have played a key role in developing the confocal microscopy module.

So how does this work for you? Our training now includes a requirement that users complete relevant modules of MyScope so that the efficiency of the beam-time of our instruments and that of our staff is maximised. The initial feedback from all involved is that this is working! There is a vast amount of content under each of the modules and we work with you to customise the components that are most relevant for your experiments.

New users are asked to work through a number of the most important concepts relevant to the technique that they are learning, and to then complete a short test. Successful completion of this will earn the user a personalised certificate which progresses their training to the next phase: hands-on with our staff at the instrument.

As many of you will already know, users at SMM progress through various levels of access. Category 1 users are learning their technique and work under direct staff

supervision. Category 2 users have access to the relevant instrument(s) in business hours and Category 3 users have 24 hour unsupervised access. We look forward to accelerating your passage through these categories as appropriate via MyScope.

Our data analytics indicate that the popularity of this e-learning resource is rapidly growing. We encourage you to engage with MyScope and welcome your feedback.

Ammrf.org.AU/myScopE

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brEAkINg THE opTIcAl dIffrAcTIoN lImIT

Various approaches have been devised to achieve optical super-resolution to break the optical diffraction limit.

Stimulated Emission Depletion (STED) uses beam-scanning technology. Structured Illumination Microscopy (SIM) engi-neers illumination into patterns based on a wide-field setup. Another cluster of technologies namely localisation microscopy, including GSDIM, PALM and STORM utilise physics/chemistry methods to switch on and off fluorescent probes so that resolution is in theory pushed down to the molecule size.

GSDIM stands for Ground State Depletion Individual Molecule returns, and is often abbreviated as GSD. In a typical wide-field or confocal fluorescent setup, fluorophore molecules can freely be excited from ground state and return spontaneously via emission of a photon. In GSD the majority of the fluores-cent molecules are pumped optically into a long-lived dark state, e.g. a triplet state. As long as the molecule is in the dark state, it cannot be excited from the ground state and hence is ground state depleted. GSD requires specific fluorophores that can cycle through the processes without being bleached.

Technically, our system is based on the Leica AM TIRF MC system and the Leica DMI6000 B inverted microscope. Users can do super-resolution imaging in Epi Fluorescence and

Total Internal Reflection modes. A wide range of standard fluorochromes have been proven to work including Alexa Fluor 647 Phalloidin and Alexa Fluor 488 IgG.

The Leica GSD SR was added to the optical section of the ACMM in August 2012. Since then users from various faculties, institutes and schools have shown great interest in the novel type of ‘nanoscopy’ and generated results beyond our expectations. GSD intracellular imaging on cultured HUVEC endothelial cells, Microtubules (labelled red) and SENEX (labelled green, a very small protein that plays multiple roles in endothelial cells) colocalised; microtubule filaments measure 50–80nm in diameter. Image courtesy Dr Michael Lovelace, postdoctoral researcher from the Centenary Medical Research Institute, University of Sydney.

1μm

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wHAT’S oN

mATErIAlS prEpArATIoN workSHop, SEmESTEr 2, 30 SEp–1 ocT 2013 (2 dAyS)

This workshop gives practical training in the preparation of a wide range of materials for electron microscopy, including metals, semiconductors, powders, ceramics and thin films. It trains users in the preparation of plain and cross-view sections for studying the microstructure of materials, using a wide range of preparation techniques including sectioning, grinding and polishing epoxy blocks, electropolishing, ion milling and FIB techniques.

Convener: Adam Sikorskiadam.sikorski@sydney.edu.au

HElp US To HElp yoUWhen you are writing up your research, please remember to acknowledge the role of our facilities and expertise.

Acknowledgements demonstrate that investments in equipment and people have led to important outcomes. Your publications, presentations and posters are a vital part of the business case for ongoing funding of the ACMM.

Where microscopy enables your research endeavours, we are counting on you to acknowledge us in your work. Here is a sample of correct acknowledgement.

“The authors acknowledge the facilities and the scientific and technical assistance of the Australian Microscopy & Microanalysis Research Facility node (Sydney Microscopy & Microanalysis) at the University of Sydney.”

You can easily access this text anytime on this link:ammrf.org.au/access/acknowledge-us

SydNEy mIcroScopy & mIcroANAlySIS

for morE INformATIoN coNTAcT

T +61 2 9351 2351f +61 2 9351 7682E acmm.info@sydney.edu.ausydney.edu.au/acmm