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Dr Antony Martin

Project Leader

Office - DVC (Research and Innovation)

Innovator, microscope builder, entrepreneur

Antony released albums and toured the world with Newcastle Indie Rock band Seabellies before honing his research and career focus at UON. Combining the study of mathematics and science in his undergraduate degree, Antony continued with his love for science, completing his PhD in crop phenomics bringing precision agriculture techniques to farmers.

Antony Martin

During his PhD, Antony worked both at UON and with scientists at the High Resolution Plant Phenomics Centre, CSIRO, where cutting edge agricultural techniques are being developed. This included exposure to high throughput 3D imaging/analysis platforms for plants, automated crop phenotyping for accelerated breeding and automation of some aspects of farm management. Antony’s thesis described breakthrough technologies using machine learning for rapid crop breeding and 3D imaging techniques for plant tissues with a focus on developing novel biofuel feedstocks.

Antony has presented his work around the world in France, Germany, Greece and China. “Another experience was travelling to Germany to work with the Max Planck Institute where I was exposed to a whole range of experiences that set up the skills and knowledge for what I’m working on with my colleagues now.” (Constructing 3D microscopes and building machine learning databases for rapid chemical phenotyping using optics.)

A powerhouse of collaboration

Having been old friends with colleague Jamie Flynn, and working alongside Will Palmer throughout their PhD research programs, a fortuitous collaboration was formed. “Jamie and I both seemed to go down similar sorts of paths, but he worked in medical science. It was just serendipitous that he was working in the building next to us, and we were always talking about the research we were doing and we actually found that the techniques that we were working on were almost identical in agricultural science and medical science. So combining those different views on the same problem was how we came up with the microscope and the clearing technique.”

The clearing and 3D imaging technique was first conducted on a model plant species, Tobacco, and was originally applied in plants to gain a fundamental understanding of the biomolecular, cellular and structural workings of high-value crops.

“There are a lot of fundamental similarities between plant cells and mammalian cells. But there are also some fundamental differences that make plants really hard to deal with. The fact that we were able to overcome all these difficulties with plants, such as hard-to-clear pigments, has meant that applying it back onto mammalian tissues is so much easier.”

The CLARITY light-sheet microscope was hand-built by Antony, Will and Jamie and it delivers clear, three-dimensional cellular images with unparalleled speed and precision.

Now he’s set up a company with Will and Jamie, sparked from Antony's early research at UON and further developed by the trio. Rapid Phenotyping Pty. Ltd. uses custom machine learning algorithms and patented processing technology to instantaneously measure the composition of anything you throw in front of it. “We’re starting with agriculture: wine, rice, wheat, fish oils. It’s also applicable in the medical field.”

Stay tuned for more on this exciting new development.

Read more about the development of the CLARITY microscope.

Innovator, microscope builder, entrepreneur

The CLARITY light-sheet microscope was hand-built by Antony Martin, Will Palmer and Jamie Flynn

Read more

Career Summary

Biography

Antony Martin is an innovative data specialist, with skills across STEM, working on solutions to large 3D imaging projects and sophisticated predictive modelling for rapid chemical analysis of biological tissues. Antony began his PhD work in agricultural sciences, using laser induced spectral readings to generate prediction models for the rapid detection of biofuel feedstock composition. He has since moved into the medical imaging field where he is paving the way for innovative 3D microscopy and image analysis in Australia. He is a founder of the Hunter Medical Research Institute (HMRI) Tissue Clearing and Lightsheet Microscopy Facility and founder/director of a start-up technology company, Rapid Phenotyping Pty. Ltd where he is applying his skills in sophisticated predictive modelling to solve problems for industry and in a clinical setting.

Qualifications

  • Doctor of Philosophy, University of Newcastle
  • Bachelor of Mathematics, University of Newcastle
  • Bachelor of Science (Biological Science), University of Newcastle
  • Bachelor of Science (Honours), University of Newcastle

Keywords

  • 3D imaging
  • Biofuels
  • Crop phenotyping
  • Infrared spectroscopy
  • Lightsheet microscopy
  • Machine learning
  • Plant breeding
  • Plant cell walls
  • Raman spectroscopy
  • Transcriptomics

Languages

  • English (Mother)

Fields of Research

Code Description Percentage
060702 Plant Cell and Molecular Biology 25
100101 Agricultural Biotechnology Diagnostics (incl. Biosensors) 50
170203 Knowledge Representation and Machine Learning 25

Professional Experience

Professional appointment

Dates Title Organisation / Department
17/03/2016 -  Project leader - 3D Tissue Clearing and Lightsheet Microscopy Facility

The newly founded 3D Tissue Clearing and Lightsheet Microscopy Facility, based at the Hunter Medical Research Institute (HMRI), has combined 3D tissue clearing methods with lightsheet microscopy technology to allow rapid 3D interrogation of biological systems and disease processes. This world-first facility is now being used by HMRI and UoN researchers to shed new light on diseases such as cancer, spinal cord injury, chronic pain, asthma, osteoarthritis, infertility, and kidney disease.

The University of Newcastle - Research and Innovation Division
Australia

Awards

Award

Year Award
2013 Winner of best seminar, Biological science RHD conference
Faculty of Science and Information Technology, University of Newcastle
2011 University Medallist
The University of Newcastle

Prize

Year Award
2010 Barry Boetcher Honours Prize
Faculty of Science and Information Technology, University of Newcastle

Recognition

Year Award
2015 F1000 prime article recommendation fopr publication: PEA-CLARITY: 3D molecular imaging of whole plant organs
The University of Newcastle - Research and Innovation Division

Scholarship

Year Award
2013 Farrer Memorial Travel Scholar
NSW Department of Primary Industries
2012 Office of the Cheif Executive (OCE) Postgraduate scholar, CSIRO
CSIRO - Commonwealth Scientific and Industrial Research Organisation
2010 Office of the Cheif Executive (OCE) Honours Scholar, CSIRO
CSIRO - Commonwealth Scientific and Industrial Research Organisation

Teaching

Code Course Role Duration
BIOL1003 Biology Professional Skills 1
Faculty of Science and Information Technology, University of Newcastle
Tutor 20/06/2015 - 28/08/2016
BIOL2002 Lab Skills in Biology
Faculty of Science and Information Technology, University of Newcastle
Tutor 20/07/2014 - 28/08/2016
BIOL3001 Advanced Lab Skills in Biology
Faculty of Science and IT, University of Newcastle
Tutor 20/02/2015 - 28/08/2016
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Journal article (6 outputs)

Year Citation Altmetrics Link
2016 Martin AP, Palmer WM, Brown C, Abel C, Lunn JE, Furbank RT, Grof CPL, 'A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C-4 model species', BIOTECHNOLOGY FOR BIOFUELS, 9 (2016) [C1]
DOI 10.1186/s13068-016-0457-6
Citations Scopus - 5Web of Science - 4
Co-authors Chris Grof
2015 Palmer WM, Martin AP, Flynn JR, Reed SL, White RG, Furbank RT, Grof CPL, 'PEA-CLARITY: 3D molecular imaging of whole plant organs', SCIENTIFIC REPORTS, 5 (2015) [C1]
DOI 10.1038/srep13492
Citations Scopus - 10Web of Science - 10
Co-authors Chris Grof, Jamie Flynn
2013 Martin AP, Palmer WM, Byrt CS, Furbank RT, Grof CPL, 'A holistic high-throughput screening framework for biofuel feedstock assessment that characterises variations in soluble sugars and cell wall composition in Sorghum bicolor', BIOTECHNOLOGY FOR BIOFUELS, 6 (2013) [C1]
DOI 10.1186/1754-6834-6-186
Citations Scopus - 15Web of Science - 13
Co-authors Chris Grof
2012 Li Z, Palmer WM, Martin AP, Wang R, Rainsford FW, Jin Y, et al., 'High invertase activity in tomato reproductive organs correlates with enhanced sucrose import into, and heat tolerance of, young fruit', Journal of Experimental Botany, 63 1155-1166 (2012) [C1]
Citations Scopus - 54Web of Science - 49
Co-authors Yong-Ling Ruan, John Patrick
2010 McCurdy DW, Dibley SJ, Cahyanegara R, Martin A, Patrick JW, 'Functional characterization and RNAi-mediated suppression reveals roles for hexose transporters in sugar accumulation by tomato fruit', Molecular Plant, 3 1049-1063 (2010) [C1]
DOI 10.1093/mp/ssq050
Citations Scopus - 25Web of Science - 23
Co-authors David Mccurdy, John Patrick
2010 Edwards J, Martin A, Andriunas FA, Offler CE, Patrick JW, McCurdy DW, 'GIGANTEA is a component of a regulatory pathway determining wall ingrowth deposition in phloem parenchyma transfer cells of Arabidopsis thaliana', The Plant Journal, 63 651-661 (2010) [C1]
DOI 10.1111/j.1365-313x.2010.04269.x
Citations Scopus - 22Web of Science - 21
Co-authors John Patrick, Tina Offler, David Mccurdy
Show 3 more journal articles
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Grants and Funding

Summary

Number of grants 5
Total funding $384,339

Click on a grant title below to expand the full details for that specific grant.


20171 grants / $31,100

3D imaging of biomedical tissue samples$31,100

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Doctor Antony Martin
Scheme Project Grant
Role Lead
Funding Start 2017
Funding Finish 2017
GNo G1700784
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON Y

20164 grants / $353,239

Virtual Biobank$160,000

Funding body: Australian National Data Service

Funding body Australian National Data Service
Project Team Doctor Jamie Flynn, Doctor Antony Martin, Mr Will Palmer
Scheme Research Grant
Role Investigator
Funding Start 2016
Funding Finish 2016
GNo G1601108
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON Y

A 3D Virtual Biobank for Medical Tissue Samples$160,000

Funding body: Australian National Data Service

Funding body Australian National Data Service
Project Team

Antony Martin, Jamie Flynn, William Palmer, Bill Pascoe, Vicki Picasso, Aaron Scott, Lloyd Handyside

Scheme Unknown
Role Lead
Funding Start 2016
Funding Finish 2017
GNo
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON N

Development of a high-throughput sample processing station$30,190

Funding body: NSW Department of Industry

Funding body NSW Department of Industry
Project Team

Antony Martin, William Palmer, Jamie Flynn, Jarrah Peddie, Phil Clausen, Adrian Wills

Scheme TechVoucher
Role Lead
Funding Start 2016
Funding Finish 2016
GNo
Type Of Funding Aust Competitive - Commonwealth
Category 1CS
UON N

Bringing CLARITY to Brain Cancer$3,049

Funding body: Mark Hughes Foundation

Funding body Mark Hughes Foundation
Project Team

Antony Martin, Jamie Flynn, William Palmer, Craig Geyde

Scheme Pilot grants
Role Lead
Funding Start 2016
Funding Finish 2016
GNo
Type Of Funding Donation - Aust Non Government
Category 3AFD
UON N
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Research Projects

3D Tissue Clearing and Lightsheet Microscopy Facility 2015 - 2017


3D Virtual Biobank for Medical Tissue Samples 2016 - 2017


Rapid chemical testing platform 2016 - 2017


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News

Sahil Harriram and Dr Antony Martin

Collaborative space Three76 throws open its doors to innovation

October 28, 2016

A brand new innovation space run by the University of Newcastle (UON) will officially open its doors to welcome its first clients this week, marking an exciting step for the Hunter as part of the Integrated Innovation Network (I2N) announced earlier this year.

Hand-built microscope gives greater clarity

March 2, 2016

Three young University of Newcastle (UON) biologists have hand-built a state-of-the-art laser microscope at HMRI that delivers clear three-dimensional cellular images with unparalleled speed and precision.

Dr Antony Martin

Positions

Project Leader
Tissue clearing/Lightsheet microscopy
Office - DVC (Research and Innovation)
Research and Innovation Division

Project Management
Tissue clearing/Lightsheet microscopy
Office - DVC (Research and Innovation)
Research and Innovation Division

Contact Details

Email antony.martin@newcastle.edu.au
Phone 0240420468
Mobile 0401922699

Office

Room 3613
Building Hunter medical research institute (HMRI)
Location Level 3 East

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