1
Prof. Simon P. Ringer
The University of Sydney,
Executive Director & CEO, AMMRF
Microscopy & Microanalysis:Challenges & Opportunities in eResearch
2
Outline
• Science drivers for this Facility: about the AMMRF
• Expertise & Instrumentation
• Structure & Operation
• Anatomy of the User-Experience:challenges & opportunities in eResearch
2
Atom ProbeTomography
10 nm
100 μm
4
Recent & Future Needs in Microscopy & Microanalysis
Need for aNational
ResearchFacility
www.ammrf.org.au
3
5
Activities - Instrument Usage: FY 05/06
6
TheAustralian Microscopy & Microanalysis Research Facility
• Established in 2007 under DEST ‘NCRIS’ program as an unincorporatedjoint venture between universities, PFRA’s, federal & state governments
• New collaborative research infrastructure initiative
• Builds on success of NANO established under the MNRF program
2002–2007 2007–2012
4
7
VISION
The AMMRF will be a user-focussed interdisciplinary organisation willenable the exploration of structure-function relationships in physical,chemical and biological sciences and will operate quality researchservices, research programs and research training. The AMMRF will beaccessible to all Australian researchers and will provide a quality userexperience.
MISSION
The AMMRF will provide Australia’s peak research facility for thecharacterisation of materials through macro, meso, nano and atomiclength scales by means of advanced microscopy & microanalysis.
“
”
TheAustralian Microscopy & Microanalysis Research Facility
8
Australian Microscopy & Microanalysis Research Facility
An Unincorporated JointVenture between
Research IntensiveAustralian Universities
[Top 50 Worldwide]
+ AMMRF Linked Laboratories & Linked Centres Program
5
9
ANUANU Characterisation Facility
A/Prof. Tim Senden
SARFSouth Australian RegionalFacility
Prof. Hans Griesser
UNSWElectron Microscope Unit
Prof. Paul Munroe
UQCentre for Microscopy andMicroanalysis
Prof. John Drennan
USydAustralian Key Centre forMicroscopy and Microanalysis
Prof. Simon Ringer
UWACentre for Microscopy,Characterisation and Analysis
Prof. Craig Atkins
Australian Microscopy & Microanalysis Research Facility
10
AMMRF Governance
6
11
AMMRF Governance: The Specialist Committees
12
The AMMRF Linked Laboratories
Australian Animal Health Laboratory(AAHL), Geelong
RMIT Microscopy & Microanalysis Facility, Melbourne
Advanced Analytical Centre,James Cook University, Townsville
Maquarie University,Optical Microcharacterisation Facility,Sydney
QUT, Analytical Electron MicroscopyFacility, Brisbane
7
13
The Facilities
14
Research: State of the Art Electron Microscopy andAtom Probe Tomography
Transmission Electron Microscopy Atom Probe Tomography
Nanoscience of Advanced Alloys [Design in Light Metals],
New Si-based ICT Devices, Interface Engineering
8
15
Multi-dimensional & multi-length scales
1. XRD
2. Spectral
3. Profiles
4. Analysis
1. SEM
2. TEM
3. LM
4. Scanning
1. Confocal
2. MicroCT
3. TEM
4. SEM/FIB
5. EDS/EELS
6. AtomProbe
1. Time +
– Confocal
– TEM
– MicroCT
– AtomProbe
2. Multi ROI
1D 2D 3D 4D
1. Correlative Image Creation
2. Data Analysis
– Support Vector Machines
– MultiANOVA
– FEM and CFD
5D and Higher
16
The User Experience
For merit-based access by publicly fundedresearchers, pricing is:
– $40/hr for flagship instruments;
– Up to $90/hr for other instruments.
Initial ScopingTechnical feasibility and scientific review through a direct or
teleconference meeting
TrainingOne-on-one or short course/workshop style. Full user support
may be provided for short or collaborative projects
Data acquisition and archivingResearcher uses instrumentation with staff support as
required
Analysis and InterpretationFollow up support is available for interpretation and analysis
Communication of resultsResults are disseminated in scientific literature
IdeaResearcher contacts NMMRF either through a web-based
portal or directly through a staff member
User may applyfor TAP funding
1. At least 30% of beamtime will be
available to external users.
2. Fast-track usage possible.
3. International users welcome
4. IP remains the property of the user,
unless another agreement is negotiated.
5. Generally, instruments will be accessible
to industry researchers at commercial
rates.
6. Alternative access arrangements are
through collaboration with publicly
funded researchers.
9
17
The Travel & Access Program (TAP)
An electronic applicationform can be found online
TAP provides funds for instrumenttime and travel and accommodation costs
Grants – typically $2-5k. Provide initialaccess to instruments – springboard to
larger fund opportunities – ARC etc.
18
The User Experience: where does eResearch fit in?
1. The Idea 2. Registration
3. New User Meeting
4. Training
5. Data Acquisition and Archiving
6. Data
Visualisation
and Analysis
7. Publication
everywhere
10
19
What are we doing? Telemicroscopy
Perth
Brisbane
Sydney
Adelaide
Melbourne
Darwin
USA
Japan
UQ
AMMRF
ATP
Hobart
UMelb
Canberra
ANU
CSIRO
Backbone
AARNet links
PASSIVETelepresence
ACTIVETelepresence
20
1. Internal to Unit
- GB Ethernet [GB switches/routers etc]
- Fast processors [dual processors standard on workstations]
- Plenty of local HD storage [200GB scratch spaces / 1000GB main store]
- Fast drives [SCSI 320] 10,000rpm or 15,000rpm
- Data pipelines [several workstations]
2. External to Unit
- High speed links [GrangeNet]
- Good communications links
Perth
Brisbane
Sydney
Adelaide
Melbourne
Darwin
USA
Japan
UQ
AMMRF
ATP
Hobart
UMelb
Canberra
ANU
CSIRO
What are we doing? Data Transport
11
21
• ARC Special Research Initiative Project
• Collaboration between:
- The University of Queensland eResearch Group
- NANO/AMMRF
- JEOL Australasia, APAC, MAMS
• Primary Objectives: pilot a national, distributed image database
- To develop a pilot Web portal for users to capture and store selectedimage/data/metadata
• Other Objectives: to explore . . .
- Remote instrument and booking systems
- Telemicroscopy services
- Automation (HPC) for image/data processing and annotation tools
What are we doing? GRANI Grid-enabled National Archive of Nanostructural Imagery
22
What are we doing?GRANI collaboration with APAC
• Link to the National Data Centre in Canberra• Long term large-scale data storage and backup• Hundreds of TB indexed
30 days
12
23
24
What are we doing?Collaborative Telemicroscopy Support Services
13
25
Future Challenges:Should we now…
1. Deploy and install middleware across all AMMRF nodes?
2. Extend data/metadata capture to a wider range of instruments?
3. Expand Portal – grid-enabled registry of image processing services?
4. Support future trends in Characterisation:– Higher resolution, high throughput – combinatorial, robotics– Greater simulation/computational modelling– Remote steering of experiments via telepresence– 3D, time series data/video – cameras, sensors– Integration of related data – databases, characterisation techniques– Publication of raw data + methodology
5. Progress materials informatics field in Australia?
We need help to do this!
26
But…What aren’t we doing?
UserExperience
1. The Idea 2. Registration
3. New User Meeting
4. Training
5. Data Acquisition and Archiving
6. Data
Visualisation
and Analysis
7. Publication
Key Challenges
eResearch
14
27www.hickerphoto.com
28
eResearch
Enabling the gateway to discovery
• Large & very large (nx10 GB) data sets
• Real space data
• Complex, evolving software platforms for analysis
• Novel scripting required
• These software platforms often represent a barrierfor users (scientists)
• An easy win for eResearch:Support data analysis from selected flagship
instrumentation
Transforming data into information
15
29
eResearch in microscopy & microanalysis:Challenges & Opportunities
• Well supported National Research Facilities are needed for access to awell supported user experience in microscopy & microanalysis
• Large multi-dimensional & multi-scale data generated
• eResearch plays a pervasive role across the user-experience
- User contact & registration
- bookings & metadata
- data archiving
- data visualisation & analysis
• Convergence of scale of experiments and simulation - conduit to HPC
• Data analysis by facility specialists using advanced software in
collaboration with users
• Extend/develop the GRANI pilot project for data archiving via
national data centre
5.16?
30
Acknowledgements
Prof. Jane Hunter
The University of QLD
Brendan Mauger
The University of QLD
Dr Allan Jones
Chair, eResearch Committee,AMMRFThe University of Sydney
Prof. John Drennan
Scientific Director, AMMRFThe University of QLD
Dr Peter Hines
The University of Sydney
Vanessa Zeman
The University of Sydney
Uli Eichhorn
The University of Sydney
Ms. Rosie Hicks
COO, AMMRF
16
31