ACMM MiCroAnAlysis Newsletter - University of Sydneysydney.edu.au/acmm/pdf_doc/news/v32_ACMMnewsletter_12... · 2011-12-15 · MiCroAnAlysis in tHis issue 01 introduCtion to iMod

1

ACMM Newsletter

AustrAliAn Centre for MiCrosCopy & MiCroAnAlysis

in tHis issue

01 introduCtion to iMod

02 ConferenCes in 2012

03 ConferenCe report

04 MeMbers of pArliAMent visit

05 fliM WorksHop

06 inCredible inner spACe

07 Help us to Help you

AustrAliAn Centre for MiCrosCopy & MiCroAnAlysis

feAtured MiCrogrApHs

sHort Course: introduCtion to iMod for biologists: 3-d teMby filip brAet

issue 32 septeMber–deCeMber 2011

Slag sample from a blast furnace, showing variations in the crystalline orientation of two of the phases (colours correspond to crystal lattice orientations). Technique: electron backscatter diffraction. Image by Pat Trimby.

Surface of an ant eye. Technique: scanning electron microscopy. Image by Delfine Cheng and Errin Johnson.

As many of you might be aware, the ACMM is equipped with the latest-generation transmission electron microscopes (TEMs), which allow you to generate 3-D data stacks of whole-mount biomaterials or thick biological sections (typically around 220–320 nm in thickness). These stacks form the basis of biological electron tomography. The process starts with collecting a ‘tilt series’,

a series of transmission images of your sample at known tilt angles over a large range of angles. After using a software program to align the features of interest in the tilt series, you then use the software to apply a back-projection algorithm (essentially a mathematical reversal of the image-forming process) to generate a 3-D, digital image stack of your sample.

10μm

10μm

Increasingly microscopy is becoming tomography, generating structural and/or chemical information about the three-dimensional (3-D) morphologies of samples at the microscale and nanoscale. Here’s an opportunity to learn how to produce basic 3-D models of biological materials from transmission electron micrographs.

2

The main instruments for this technique at the ACMM are the JEOL 2100 and JEOL 1400, which were fully commissioned in mid-2009 and are our primary TEM-platforms for biological investigation. The JEOL 2100 is a high-end cryo-TEM micro-scope that is equipped with tomographic recording capabilities; the JEOL 1400 also was set up recently for recording tilt series on fixed and embedded samples. Dedicated courses, training and user manuals are readily available for our user community to train them in the use of these instruments, and in the recording of transmission electron tomograms.

Despite the fact that we provide extensive training to collect TEM tomograms, some 3D stacks that have been collected recently have just sat on DVDs or portable hard disks without any further use. This is unfortunate, as quality 3-D structural biology data are lost and never reach the scientific community. The major user feedback I have received over the past 18 months is that these data are not being analysed because the available shareware software programs for image analysis are difficult to use, especially for young researchers who often do not have much background in image processing and analysis. For this reason, I have written a concise introduction to IMOD, the most commonly used reconstruction and analysis software in electron tomography (http://bio3d.colorado.edu/imod/).

This manual is entitled “IMOD for Dummies, written by a dummy” and will be made available to users as part of a half-day work-shop that the ACMM is going to start running early next year.

The workshop will guide you through the process of successful-ly installing IMOD, and then explore some basic 3-D rendering concepts such as 3-D view, XYZ slicing, image calibration and basic ‘object modelling’ functions. I will introduce these pro-cesses on an example raw “.mrc” file to illustrate the different data processing steps from beginning to end. This workshop is not aimed to be a fully comprehensive training in 3-D TEM modelling, but rather will be a solid introduction to the ABC of IMOD to help you overcome the activation energy of getting started with IMOD when you want to generate and analyse 3-D TEM tomograms. To solidify the principles demonstrated and provide a handy reference for users after the course, I will provide participants with my short IMOD manual.

To allow time to clearly address questions and undertake the practical demonstrations, I aim to run this workshop in small groups – a maximum of four people at a time – on an ad hoc basis as the need arises. If you would like to attend the IMOD introductory course, please email your request to me: [email protected]

ConferenCes in 201222nd AustrAliAn

MiCrosCopy And MiCroAnAlysis ConferenCe

Wun-spin 2012 At tHe ACMM

From the 5th to 9th of February 2012, the Australian Conference on Microscopy

and Microanalysis will be held in Perth, Western Australia.

However, this is no ordinary microscopy conference (not that they

are ordinary, anyway) as the conference will be integrated with the 10th Asia-Pacific Microscopy Conference (APMC 10), the 2012 International Conference on Nanoscience and Nanotechnology (ICONN 2012). It will be a chance not just to learn about the latest developments in, and applications, of advanced microscopy, but also to keep abreast of the latest work in nanotechnology, with an expected turn out of more than 2000 delegates from over 30 countries.

Of course, the ACMM will be actively participating in the conference—from giving presentations and posters to chair-ing sessions—but will also be actively involved in some of the short courses and workshops. On the morning of Sunday the 4th, Assoc. Prof. Allan Jones will co-convene a workshop on Micro-CT experiences and Dr Michael Moody will co-convene a workshop on LEAP – atom probe. There will be plenty of other workshops on the Saturday and Sunday, along with short courses on the preceding Thursday and Friday, so check out the website (apmc-10.org) for details about these or for more information about attending this integrated conference.

From the 23rd to 25th of July 2012, the Australian Centre for Microscopy & Microanalysis will host WUN-SPIN 2012, the Worldwide Universities Network’s 4th International Conference on Spintronics, here at the University of Sydney.

WUN-SPIN 2012 will feature an innovative program designed to show off the best of spintronics’ multidisciplinary nature, a program that will be attractive to materials scientists, physicists, engineers and students alike. Our own Prof. Simon Ringer and Dr Rongkun Zheng are co-chairing the confer-ence, which will further explore this rapidly growing field and its ability to transform the future of information technologies.

Keep an eye on the conference website for more details about the program (wired.ivvy.com/event/WUN12S). Early-bird registrations close on 1st February 2012 and abstracts are due by 31st March 2012.

APM

C10

ICO

NN2012 ACMM

22

ICON

N2012

AP

MC10

5-9 Febru

ary 2

012

Perth, WA A

ustra

lia

www.apmc-10.org | www.iconn-2012.org | www.acmm-22.org

Sponsorship & Exhibition Prospectus

3

ConferenCe report: MiCro sCopy & MiCroAnAlysis 2011by errin JoHnson

Like electrons to an Everhart-Thornley detector, hundreds of beaming microscopists were attracted, from across the whole spectrum of science, to this annual conference and were all charged up by the prospect of immersing themselves in the latest microscopy techniques, applications and technological advances. This year we converged on Nashville for an illuminating week of talks, posters, vendor schmoozing, country music (from which there was unfortunately no escape, even in the convention centre’s toilets) and deep-fried food (especially for breakfast). I wouldn’t be telling a FIB if I said that it was the biggest meeting yet, although it’s hard to be objective when so many great talks and exhibitions are condensed into one week.

The meeting opened on the Sunday night with welcome drinks and the conference dinner (an old-fashioned Southern buffet), during which del-egates were treated to a microscopy-themed country song, live on stage. It was indeed as corny as it sounds. Over the next four days, up to 16 concurrent sessions were held throughout the morning and early afternoon, with the mid-to-late afternoon session devoted to a new set of posters each day. The main themes of the conference were: EBSD, FIB, imaging of nano-materials, atom probe, super-resolution optical microscopy and bio-medical imaging. The full program (EXPO Issue, Vol 17, Supplement 1) can be downloaded from the Microscopy & Microanalysis journal website. The complete pro-ceedings are on DVD, which is available to borrow.

The ACMM was strongly represented by a diverse mix of staff and students, all of whom gave aberration-corrected talks (except Guy Cox, who was there on a Press Pass!). Needless to say, we were all ‘Stoke-ed’ at the opportunity to present the following talks:

ƛ Dr Michael Moody (invited talk) – “A lattice-rectified and detection-efficiency-compensated APT reconstruction” in Advancing Data Collection and Analysis for Atom Probe Tomography.

ƛ Dr Patrick Trimby (invited talk) – “Exploring innovative and challenging applications of EBSD in the geologi-cal and biological sciences” in EBSD Data Collection and Analysis on Challenging Materials and Applica-tions.

ƛ Dr Patrick Trimby (talk) – “Using EBSD to aid identification of fossil-ized dinosaur eggshells” in Micro-analysis at 60 Years: A Symposium Dedicated to Raimond Castaing.

ƛ Dr Errin Johnson (talk) – “Specimen preparation for X-ray micro-computed tomography of plants and fungi” in Advanced Technology in Biological Microscopy.

ƛ Peter Felfer (talk) – “Atom probe tomography of interfaces at the near-lattice level” in Advancing Data Collection and Analysis for Atom Probe Tomography.

And now to the tradeshow. With 118 booths, boasting fully operational spec-imen preparation equipment, confocals and even SEMs and TEMs, the exhibi-tor’s hall at this year’s M&M was every microscopist’s Graceland (well, we were in Tennessee). ACMM delegates enjoyed demonstration sessions on a variety of shiny instruments, including a Tousimis automated critical point dryer, an SPI Supplies osmium sputter coater, a 5 kV bench-top TEM (interesting, but sections needed to be 30 nm thin!), a bench-top FESEM, a Tescan Vega FESEM and an ASPEX analytical SEM. Pat Trimby and I attended a range of lunchtime tutorials run by Zeiss on the Tuesday and Wednesday. I enjoyed the ESEM and Super-Resolution Optical Microscopy sessions, while Pat took advantage of the Merlin FESEM (the next-generation Ultra) and Auriga FIB/SEM sessions, which were a great op-portunity to get up close and personal with the latest microscopes.

Unfortunately, the ACMM was unlucky in the tradeshow ‘passport’ competition, although Karen Privat, from the AMMRF node at UNSW, did win a Kindle eReader. Hopefully, we will have better luck at next year’s confer-ence, which will be held in Phoenix, Arizona, from July 29th and, judging by the cacti-decorated flyer, should be prickling with more great talks and microscopy experiences!

M&M 2011 was held at the Nashville Conference Centre, Tennessee, from the 7th to 11th of August. Warning: bad micro scopy

puns ahead!

4

MeMbers of pArliAMent visit tHe ACMMFriday 7 October was all action as the Hon. Tanya Plibersek, MP, and the Hon. Carmel Tebbutt, MP, were given the tour of key research infrastructure.

Two ministerial visits occurred on the same day entirely by coincidence, in response to invitations from the Australian Microscopy & Microanalysis Research Facility (AMMRF). In the case of Tanya Plibersek, Federal Member for Sydney and Minister for Human Services, and Carmel Tebbutt, Member for Marrickville and Shadow Minister for Education and Train-ing, the University of Sydney was in their electorates. So the ACMM was the node that they visited to learn more about the impact of high-end research infrastructure.

Ms Plibersek, who was on a tight schedule was treated, in a roundtable format, to a brief overview of the ACMM, the AMMRF and the importance of national investment in re-search infrastructure. This introduction was followed by two rapid-fire case studies of the impacts of such investments; one case study was presented by the ACMM’s Prof. Si-mon Ringer on design of advanced al-loys, and one by Prof. Tony Weiss, from the School of Molecular Bioscience, on the structure and applications of elastin and its fundamental protein tro-poelastin. After being joined by Prof. Jill Trewhella, DVC(R), Ms Plibersek was given the Cook’s tour of the ACMM, taking in some of the more impressive instruments such as the JEOL 3000F transmission electron microscope and the Imago atom probes. This quick tour, with the smoothest of segues, ended in the centre’s new focused ion beam (FIB) suite, where the minister was to officially open the Zeiss Auriga® Cross-beam®, the combined high-end FIB and field-emission scanning electron microscope that was installed recently thanks, in part, to an Australian Research Council LIEF grant. After receiving an introduction to what the Auriga could do, the minister said a few words to open the instrument and then spent a moment exploring the intricacies inside a computer’s CPU as exposed by a the precision cutting of the ion beam. Prof. Ringer then gave Ms Plibersek a perspex-embedded micrograph as a reminder of her visit, before she had zip off, just before 11am, for her next meeting.

Some 30 minutes later, Ms Tebbutt arrived and, having a tad more time available, was taken on a tour of the cell-culture facilities and associated microscopes, the X-ray microtomography instruments, and the FIB platforms and atom probes. The roundtable that followed gave the minister an introduction to the ACMM and AMMRF – focusing on the outcomes from previous New South Wales Govern-ment investments in microscopy and the need for future investments in research infrastructure – and the two case studies on alloy design and elastin. After an informal discussion around the table with the minister, Prof. Ringer also presented Ms Tebbutt, before her departure, with an embedded micrograph to adorn the ministerial desk.

It was a hectic morning, but proved really enjoyable and fruitful for the ministers. Both of them expressed just how impressed they were with the facilities and how worthwhile they had found the visits; and both were emphatic that this exercise should be repeated with other MPs to increase political awareness of Australian science and research, and the impact it is having, nationally and internationally.

5

A sHort lifetiMe spent leArning About MeAsuring lifetiMesby ellie kAble

Here’s a quick rundown on recent training and workshops in fluorescent and optical microscopy that were held in the ACMM.

On 5 and 6 September, nine personnel from around the nodes of the Australian Microscopy & Microanalysis Research Facility (AMMRF) came together in the ACMM to enhance their skills in fluorescence-lifetime imaging microscopy, or FLIM. As its (full) name implies, FLIM involves mapping differences in the fluorescent lifetime of fluorophores in biological samples to gain insights into the localised environment. Given that lifetimes are independent of concentration and that each fluorophore has a unique lifetime, FLIM can be used in multi-labelled experiments to separate dyes with similar emissions, to measure ion concentrations or cell chemistry, and to measure quantitative fluorescence resonance energy transfer (FRET).

The FLIM workshop comprised two days of lectures, data collection and analyses under the expert guidance of Dr Dylan Owen, from the Centre for Vascular Research at UNSW, and the ACMM’s own Assoc. Prof. Guy Cox. The group examined, discussed and dissected different techniques for collecting fluorescence-lifetime data and images, and was able to examine first-hand the advantages and disadvantages of each different method. Most importantly, and as is often difficult in today’s busy world, the two-day workshop gave the attendees

the uninterrupted time to immerse themselves in these advanced techniques, thereby facilitating a greater awareness of and confidence in the technology. Everyone felt this oppor-tunity to work and gather data with a group of colleagues was invaluable. Another workshop is planned for 2012; watch this space for details. This very productive workshop concluded with a memorable dinner at a local restaurant.

The attendees from the FLIM workshop who were able to stay on until the afternoon of 7 September got to participate in the revival of the Sydney Light and Optical Users Group, with 47 researchers from all over Sydney. The focus of the group is to give short technical talks, which are balanced with discussion and question time. This time, the topics ranged from correct use of objectives to problems in live-cell imaging and from setting up experiments to dealing with large datasets. The meeting and light refreshments were sponsored by Leica.

If you are not on the mailing list for the Sydney Light and Optical Users Group and would like to be included, please contact Ellie Kable on [email protected]

6

sCienCe And beAuty Meet in inner spACe

The AMMRF’s Incredible Inner Space exhibition of micrographs officially opened on Friday 18 November at Questacon, the National Science and Technology Centre, in Canberra.

The images for this memorable exhibition have been brought together from all around the AMMRF and serve to highlight just how much microscopy matters, not only in providing fundamental data to researchers, but also in communicating the wonders of science to a wide audience of Australians. Many of the images were created at the ACMM and demonstrate the wide range of techniques we offer and the diversity of research being done. There is an atom probe image, two beautiful electron backscatter diffraction images, an X-ray microtomography image, several scanning electron micrographs and a few confocal micrographs.

At the launch event, surrounded by the assembled guests, Patricia Kelly, Deputy Secretary of the Department of Innovation, Industry, Science and Research, spoke enthusiastically about the exhibition and the AMMRF, emphasising that the images are not merely beautiful, but also the result of real scientific enquiry made possible by the strategic investment in national research infrastructure. Dr Paul Willis, director of RiAus and former presenter on the ABC’s Catalyst program, then opened the exhibition with an insightful and entertaining talk about the nature of science and the role of the unseen in shaping our vision of the world.

By all accounts, the exhibition is being extremely well re-ceived by visitors to Questacon. I experienced this firsthand at the launch, when a member of the public, after viewing the images, excitedly said to me, “aren’t they just fabulous!”

Incredible Inner Space has also inspired the media, with excellent coverage received in the Sydney Morning Herald, The Age in Melbourne and various other major and regional

newspapers and their websites. The exhibition has also been profile internationally on the New Scientist website and many BBC sites from Brazil to Russia.

The exhibition is at Questacon until the end of January and will then go to the Australian Conference on Microscopy & Microanalysis in Perth after which it will tour the country. It can be seen online at ammrf.org.au/innerspace.

by Jenny WHiting

7

AustrAliAn Centre for MiCrosCopy & MiCroAnAlysis

for More inforMAtion ContACt

t +61 2 9351 2351f +61 2 9351 7682e [email protected]/acmm

Help us to Help youWhen you are writing up your research, please remember to acknowledge the use you have made of ACMM facilities and expertise.

Now you might be asking yourself, “Why should I bother?” Good question. Probably the main reason is that acknowledg-ment of the ACMM’s past support helps us to continue to provide a high-quality service that can support your future research activities. Now I hear you asking, “How does it help?” Well, direct acknowledgments make it much easier for us to confirm that you have made use of the ACMM facilities and/or staff expertise in specific work. And those confirmed publica-tions are a key metric that help to justify the continued funding of the ACMM, by the University of Sydney and by government sources, to support your ongoing research.

For your reference, the suggested form of the acknowledge-ment is: “The authors acknowledge the facilities, and the sci-entific and technical assistance, of the Australian Microscopy & Microanalysis Research Facility at the Australian Centre for Microscopy & Microanalysis, The University of Sydney.”

That bit about the Australian Microscopy & Microanalysis Research Facility, or AMMRF (see ammrf.org.au), is particularly relevant when it comes to securing government funding for major research infrastructure. Of course, you can be more fulsome in

mentioning help from specific staff, if you feel it is warranted. And don’t forget to acknowledge the facilities in presentations and posters too. Follow the Acknowledge Us “Quick Link” on the ACMM homepage for more details.

To wrap up, here is a sampling of recent publications from us-ers of the ACMM. Not only did these publications acknowledge the use of, or support from, the ACMM, which meant we could find the publications readily enough, but they also illustrate the breadth of research being done by the user community. Keep up the good work, and don’t forget to help us to help you.

reCent publiCAtions froM tHe user CoMMunity

J. Rnjak-Kovacina, S.G. Wise, Z. Li, P.K.M. Maitz, C.J. Young, Y. Wang, A.S. Weiss, “Tailoring the porosity and pore size of electrospun synthetic human elastin scaffolds for dermal tissue engineering,” Biomaterials, 32 (2011) 6729–6673.

M.J. Hanus, K.J. MacKenzie, A.A.K. King, O.M. Dunens, A.T. Harris, “Parametric study of coiled carbon fibre synthesis on an in situ generated H2

S-modified Ni/Al2O

3 catalyst”, Carbon

(2011) 4159–4169.

H. Henneicke, M. Herrmann, R. Kalak, T.C. Brennan-Speranza, U. Heinevetter, N. Bertollo, R.E. Day, D. Huscher, F. Butt-gereit, C.R. Dunstan, M.J. Seibel, H. Zhou, “Corticosterone selectively targets endo-cortical surfaces by an osteoblast-dependent mechanism”, Bone, 49 (2011) 733–742.

S. Wang, P. Sharp, L. Copeland, “Structural and functional properties of starches from field peas”, Food Chemistry, 126 (2011) 1546–1552.

I. Bibi, B. Singh, E. Silvester, “Akaganéite (beta-FeOOH) precipitation in inland acid sulfate soils of south-western New South Wales (NSW), Australia”, Geochimica et Cosmochimica Acta, 75 (2011) 6429–6438.

G.E. Schröder-Turk, S. Wickham, H. Averdunk, F. Brink, J.D. Fitz Gerald, L. Poladian, M.C.J. Large, S.T. Hyde, “The chiral structure of porous chitin within the wing-scales of Calloph-rys rubi”, Journal of Structural Biology, 174 (2011) 290–295.

N. Amanat, A.F. Nicoll, A.J. Ruys, D.R. McKenzie, N.L. James, “Gas permeability reduction in PEEK film: Comparison of tet-rahedral amorphous carbon and titanium nanofilm coatings”, Journal of Membrane Science, 378 (2011) 265–271.

A.I. Lukman, B. Gong, C.E. Marjo, U. Roessner, A.T. Harris, “Facile synthesis, stabilization, and anti-bacterial performance of discrete Ag nanoparticles using Medicago sativa seed exudates”, Journal of Colloid and Interface Science, 353 (2011) 433–444.