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Samples - Infrared microspectroscopy
Infrared microspectroscopy

Samples - Infrared microspectroscopy

What Type of Samples can be analysed on IRM?

The following section provides an overview of the types of samples that have been analysed on the IRM beamline at the Australian Synchrotron, from a range of research and industry applications. Recent publications are highlighted below each section, however for a complete list of publications relating to the IRM beamline, please follow the link under the publications tab. For any queries you might have relating to the analysis of your samples on the IRM beamline, please contact the beamline staff to discuss.  Below is a list highlighting some of the types of samples that have previously been analysed using the IRM beamline at the Australian Synchrotron:

  • Natural and Synthetic fibers (carbon fibers, silk, spider web, wool)
  • Insect wings and reptile skin
  • Food products (chia seed microcapsules, dairy products, bread)
  • Polymeric materials (bulk polymers and thin films)
  • Saliva and dental samples
  • Biological samples such as tissue sections, bone and single cells
  • Fingerprints
  • Nanoparticle coatings
  • Paint sections from historical paintings
  • Volcanic ash
  • Coral reef microfossils
  • Algae
  • Eucalyptus leaves
  • Pharmaceuticals
  • Soil samples
  • Geological samples

Sample preparation is largely varied and dependent both on your sample and the sampling mode to be performed (eg transmission, ATR).  More information relating to this can be found in the techniques section.

Biological & Biomedical Science:

Synchrotron radiation infrared microspectroscopy is particularly useful for monitoring molecular information of single cells and distinguishing complex biological tissue sections at a sub-cellular resolution. Many researchers are seeking single cell information, whether to reveal biological variability, monitor differences in cell cycles, stem cell differentiation or the cellular uptake and resulting biochemical and structural effects of various chemicals and therapeutics to highlight a few examples, where traditional globar sourced IR techniques would otherwise provide averaged information from a cell population.

For biological tissue, embedding and microtomed sections placed on an IR transmissive window such as CaF2 are commonly used for sample preparation (we have a microtome available for users here, at the Australian Synchrotron, or we recommend the facilities and services at Monash histology Platform ( Alternatively, the embedded biological material may be microtomed and analysed using ATR-FTIR.  Traditional sample preparation for cells involves fixing pre-treated cells onto an IR transmissive window for analysis in transmission mode.  More recently, it is possible to study live cells making use of the flow cells available. Below are a select few publications from groups who have used the IRM beamline, to provide an overview of some biological sample preparation and analysis.

Publications in biological and biomedical science:

Single cells

J.L. Denbigh, D. Perez-Guaita, R.R. Vernooij, M.J. Tobin, K.R. Bambery, Y. Xu, A.D. Southam, F.L. Khanim, M.T. Drayson, N.P. Lockyer, R. Goodacre and B.R. Wood “Probing the action of a novel anti-leukaemic drug therapy at the single cell level using modern vibrational spectroscopy techniques” Scientific Reports, 7, 2649 (2017)

M. Wongwattanakul, C. Hahnvajanawong, P. Tippayawat, S. Chio-Srichan, C. Leelayuwat, T. Limpaiboon, P. Jearanaikoon and Philip Heraud, “Classification of Gemcitabine resistant Cholangiocarcinoma cell lines using synchrotron FTIR microspectroscopy” Journal of Biophotonics, 10, 367-376

Tissue sections

D. Ye, P. Heraud, R. Parnpai and T. Li, “Reversal of Experimental Liver Damage after Transplantation of Stem-Derived Cells Detected by FTIR Spectroscopy” Stem Cells International, 2017, 4585169, (2017)

R.J. Tidy, V. Lam, N. Fimognari, J.C. Mamo and M. J. Hackett “FTIR studies of the similarities between pathology induced protein aggregation  in vivo  and chemically induced protein aggregation  ex vivo”  Vibrational Spectroscopy, 91, 68-79 (2017)

D.R Whelan and Toby D.M. Bell ”Correlative Synchrotron Fourier Transform Infrared Spectroscopy and Single Molecule Super Resolution Microscopy for the Detection of Composition and Ultrastructure Alterations in Single Cells” ACS Chemical Biology, 10, 2874-2883 (2015)

M.J. Hackett, J.B. Aitken, F. El-Assaad, J.A. McQuillan, E.A. Carter, H.J. Ball, M.J. Tobin, D. Paterson, M.D. de Jonge, R. Siegele, D.D. Cohen, S. Vogt, G.E. Grau, N.H. Hunt and P.A. Lay “Mechanisms of murine cerebral malaria: Multimodal imaging of altered cerebral metabolism and protein oxidation at hemorrhage sites” Science Advances, 1, e1500911-e1500911 (2015)

Bone sections

C. Vrahnas, P.R. Buenzli, T.A. Pearson, B.L. Pennypacker, M.J. Tobin, K.R. Bambery, L.T. Duong, N.A. Sims “Differing Effects of Parathyroid Hormone, Alendronate, and Odanacatib on Bone Formation and on the Mineralization Process in Intracortical and Endocortical Bone of Ovariectomized Rabbits” Calcified Tissue International, 103, 625-637 (2018)

C. Vrahnas, T.A. Pearson, A.R. Brunt, M.R. Forwood, K.R. Bambery, M.J. Tobin, T.J. Martin and N.A Sims “Anabolic action of parathyroid hormone (PTH) does not compromise bone matrix mineral composition or maturation” Bone, 93, 146-154, 2016

Dental and saliva samples

P. Seredin, D. Goloshchapov, Y. Ippolitov and P. Vongsvivut “Pathology-specific molecular profiles of saliva in patients with multiple dental caries—potential application for predictive, preventive and personalised medical services” EPMA Journal, 9, 195-203 (2018)

P. Seredin, D. Goloshchapov, V. Kashkarov, Y. Ippolitov, K. Bambery “The investigations of changes in mineral–organic and carbon–phosphate ratios in the mixed saliva by synchrotron infrared spectroscopy” Results in Physics, 6, 315-321 (2016)

Materials and Interfacial Science:

The information gained from infrared microspectroscopy, such as the heterogeneity of surface and bulk chemistries, orientation and structural conformation, and stability under conditions of interest, make its utility in materials science invaluable. Furthermore, temporally resolved rapid scan IR is now available, which will have particular benefits for material scientists who want to probe the kinetic chemical and structural effects to the sample as a result to exposure of a particular stimuli.

Methods for preparation and analysis of materials varies greatly depending on material properties and mode of analysis.  Below are a select few publications chosen to highlight a range of materials and the required sample preparations, which have been analysed on the IRM beamline at the Australian Synchrotron.

Publications in materials and interface science:


A. Oroumei, P. Lynch, M. Tobin and M. Naebe “Synchrotron X-ray scattering and IR-mapping studies of wet-spun lignin-derived carbon fibre precursor” Composites Science and Technology, 163,151-161, (2018)

S. Nunna, M. Maghe, S. Fakhrhoseini, B. Polisetti and M. Naebe “A Pathway to Reduce Energy Consumption in the Thermal Stabilization Process of Carbon Fiber Production” Energies, 11, 1145 (2018)

M. Ryu, H. Kobayashi, A. Balčytis, X. Wang, J. Vongsvivut, J. Li, N. Urayama, V. Mizeikis, M. Tobin, S. Juodkazis and J. Morikawa “Nanoscale chemical mapping of laser-solubilized silk” Materials Research Express, 4, 115028 (2017)

M. Ryu, A. Balčytis, X. Wang, J. Vongsvivut, Y. Hikima, J. Li, M.J. Tobin, S. Juodkazis, J. Morikawa, “Orientational Mapping Augmented Sub-Wavelength Hyper-Spectral Imaging of Silk” Scientific Reports, 7, 7419 (2017)

S. Nunna, C. Creighton, B. L. Fox, M. Naebe, M. Maghe, K. Bambery, M. J. Tobin, J. Vongsvivut, and N. Hameed, “The Effect of Thermally Induced Chemical Transformations on the Structure and Properties of Carbon Fiber Precursors,” Journal of Materials Chemistry A, 5, 7372-7382 (2017), doi: 10.1039/C7TA01022B.

Polymeric material

J.M. Uitto and C.J.R. Verbeek “The role of water in plasticizing thermally aggregated protein-based thermoplastics” Journal of Applied Polymer Science, 135, 46746 (2018)

R.A. Russell, L.J.R. Foster and P.J. Holden Carbon nanotube mediated miscibility of polyhydroxyalkanoate blends and chemical imaging using deuterium-labelled poly(3-hydroxyoctanoate)European Polymer Journal, 105, 150-157 (2018)

Jussi M. Uitto, Casparus J. R. Verbeek “Phase separation of plasticizers in thermally aggregated protein-based thermoplastics” Advances in Polymer Technology, 1-14 (2018)

C. Gavin, M.C. Lay and C.J. R  Verbeek “Conformational changes after foaming in a protein-based thermoplastic” Journal of Applied Polymer Science,135, 46005 (2018)

I.S.M.A. Tawakkal, M.J. Cran and S.W. Bigger “The influence of chemically treated natural fibers in poly(lactic acid) composites containing thymol” Polymer Composites, 39, 1261-1272 (2018)

J. Vongsvivut, V.K. Truong, M. Al Kobaisi, S. Maclaughlin, M.J. Tobin, R.J. Crawford and E.P. Ivanova “Synchrotron macro ATR-FTIR microspectroscopic analysis of silica nanoparticle-embedded polyester coated steel surfaces subjected to prolonged UV and humidity exposure” PLoS One, 12, e0188345 (2017)

T. Mukherjee, M.J. Tobin, L. Puskar, M-A. Sani, N. Kao, R.K. Gupta, M. Pannirselvam, N. Quazi and S. Bhattacharya “Chemically imaging the interaction of acetylated nanocrystalline cellulose (NCC) with a polylactic acid (PLA) polymer matrix” Cellulose, 24, 1717-1729 (2017)

K.J. van der Pal, G. Sauzier, M. Maric, W. van Bronswijk, K. Pitts and S.W. Lewis “The effect of environmental degradation on the characterisation of automotive clear coats by infrared spectroscopy” Talanta, 148, 715-720 (2016)

T.T.M. Ho, K.E. Bremmell, M. Krasowska, S.V. MacWilliams, C.J. E. Richard, D.N. Stringer, D.A. Beattie “In Situ ATR FTIR Spectroscopic Study of the Formation and Hydration of a Fucoidan/Chitosan Polyelectrolyte Multilayer” Langmuir, 31, 11249–11259 (2015)


R. Reis, M. Duke, A. Merenda, B. Winther-Jensen, L. Puskar, M.J. Tobin, J.D. Orbell, L. F. Dumée “Customizing the surface charge of thin-film composite membranes by surface plasma thin film polymerization” Journal of Membrane Science, 537, 1-10 (2017)

F.M. Allioux, L. He, F. She, P. D. Hodgson, L. Kong, L.F. Dumée “Investigation of hybrid ion-exchange membranes reinforced with non-woven metal meshes for electro-dialysis applications Investigation of hybrid ion-exchange membranes reinforced with non-woven metal meshes for electro-dialysis applications” Separation and Purification Technology, 147, 353–363 (2015)

L. He, L.F. Dumée, C. Feng, L. Velleman, R. Reis, F. She, W. Gao and L. Kong “Promoted water transport across graphene oxide–poly(amide) thin film composite membranes and their antibacterial activity” Desalination, 365, 126–135 (2015)

Food Science:

The use of FTIR microspectroscopy in food sciences enables one to probe various chemical and structural information relating to parameters such as food processing conditions, chemical composition, influence of storage and shelf life, probe for adulteration and aid in the development and optimisation of potentially new products.  Examples of food types analysed on the IRM beamline include cheeses, yoghurt, bread and chia seed oil microcapsules. We have temperature controlled stage accessories that enable measurements to be performed at refrigerated storage conditions, and use of the macro-ATR enables analysis without any sample preparation.

Publications in food science

Y. P. Timilsena, J. Vongsvivut, M. J. Tobin, R. Adhikari, C. Barrow, and B. Adhikari, “Investigation of Oil Distribution in Spray-Dried Chia Seed Oil Microcapsules Using Synchrotron-FTIR Microspectroscopy,” Food Chemistry, 275, 457-466 (2019).

J. Vongsvivut  & K.V Truong, N.Hameed, D.A. Beattie, M. Krasowska, S. Gras, G. Watson, J. Watson, D. Perez-Guaita, P. Heraud, B. Wood, J. Morikawa, S Juodkazis, E.Ivanova and  M. Tobin “Recent Advances in Macro ATR-FTIR Microspectroscopic Technique for High Resolution Surface Characterisation at Australian Synchrotron IR Beamline” MT3C.5. 10.1364/MICS.2018.MT3C.5. (2018)

Geological and Environmental Sciences:

A range of samples relating to geological and environmental science can be analysed on the IRM beamline including but not limited to soil samples, rocks, volcanic ash, plants, algae, coral and pollutants.  A range of recently published articles from environmental and geological sciences, with data obtained on the IRM beamline, is highlighted below.

Publications in geological and environmental science

M. Brenna, SJ. Cronin, I.E.M. Smith, P.M.E. Tollan, J.M. Scott, D.J. Prior, K. Bambery and I.A. Ukstins “Olivine xenocryst diffusion reveals rapid monogenetic basaltic magma ascent following complex storage at Pupuke Maar, Auckland Volcanic Field, New Zealand” Earth and Planetary Science Letters, 499, 1322 (2108)

K. Petrou, D. Nielson and P Heraud, “Single-Cell Biomolecular Analysis of Coral Algal Symbionts Reveals Opposing Metabolic Responses to Heat Stress and Expulsion” Frontiers in Marine Science, 5, Article 110 (2018)

D.R. Viete, B.R. Hacker, M.B. Allen, G.G.E. Seward, M.J. Tobin, C.S. Kelley, G. Cinque and A.R. Duckworth “Metamorphic records of multiple seismic cycles during subduction” Science Advances, 4, eaaq0234 (2018)

Felix W. von Aulock, Ben M. Kennedy, Anton Maksimenko, Fabian B. Wadsworth, Yan Lavallée “Outgassing from Open and Closed Magma Foams”  Frontiers in Earth Science, 5, 46 (2017)

F.a Li, S.C. Srivatsa, W. Batchelor and S Bhattacharya “A study on growth and pyrolysis characteristics of microalgae using Thermogravimetric Analysis-Infrared Spectroscopy and synchrotron Fourier Transform Infrared Spectroscopy” Bioresource Technology, 229, 1-10 (2017)

C.W. Harris, E. Silvester, G.N. Rees, J. Pengelly and L. Puskar, "Proteins are a major component of dissolved organic nitrogen (DON) leached from terrestrially aged Eucalyptus camaldulensis leaves" Environmental Chemistry, 13, 877-887 (2106)

A. Auer, J.D.L. White and M.J. Tobin “Variable H2O content in magmas from the Tongariro Volcanic Centre and its relation to crustal storage and magma ascent” Journal of Volcanology and Geothermal Research, 325, 203-210 (2016)

A. Levett, E. Gagen, J. Shuster, L. Rintoul, M. Tobin, J. Vongsvivut, K. Bambery, P. Vasconcelos and G. Southam “Evidence of biogeochemical processes in iron duricrust formation” Journal of South American Earth Sciences, 71, 131-142 (2016)

A. Auer, C.E. Martin, J.M. Palin, J.D.L. White, M. Nakagawa and C. Stirling “The evolution of hydrous magmas in the Tongariro Volcanic 10 ka Pahoka-Mangamate eruptions” New Zealand Journal of Geology and Geophysics, 58, 364-384 (2015)

C. Vogel, C. Adam, R. Sekine, T. Schiller, E. Lipiec and D. McNaughton “Determination of Phosphorus Fertilizer Soil Reactions by Raman and Synchrotron Infrared Microspectroscopy” Applied Spectroscopy, 67, 1165-1170 (2013)

Zoology and Entomology:

Analysis of insect wings is well established on the infrared microspectroscopy beamline, along with reptile skin.  A variety of information can be obtained such as chemical and spatial composition and spatial distribution, low fouling and antibacterial properties, influence of geographical distribution, and effects of environmental pollutants.  Use of the macro-ATR attachment is popular for insect wing analysis due to the ability to analyse these without any sample preparation or embedding required.

Publications in zoology and entomology

S.Cheeseman, S.Owen, VKTruong, D Meyer, S Hock Ng, J Vongsvivut, D.Linklater, M. Tobin, M. Werner, V.A. Baulin, P. Luque, R. Marchant, S. Juodkazis, R.J. Crawford and E.P. Ivanova “Pillars of Life: Is There a Relationship between Lifestyle Factors and the Surface Characteristics of Dragonfly Wings?” ACS Omega, 3, 6036-6046 (2018)

S. Stuhr, V.K. Truong, J. Vongsvivut, T. Senkbeil, Y. Yang, M. Al Kobaisi, V.A. Baulin, M.Werner, S. Rubanov, M.J. Tobin, P. Cloetens, A. Rosenhahn, R.N. Lamb, P. Luque, R. Marchant and E.P. Ivanova, “Structure and Chemical Organization in Damselfly Calopteryx haemorrhoidalis Wings: A Spatially Resolved FTIR and XRF Analysis with Synchrotron Radiation” Scientific Reports, 8, 8413 (2018)

V.K Truong, J. Vongsvivut, N.M. Geeganagamage, M.J. Tobin, P. Luque, V. Baulin, M. Werner, S. Maclaughlin, R.J. Crawford and E.P. Ivanova “Study of melanin localization in the mature male Calopteryx haemorrhoidalis damselfly wings” Journal of Synchrotron Radiation, 25, 874-877 (2018)

Vi.K. Truong, N.M. Geeganagamage, V.A. Baulin, J. Vongsvivut, M.J. Tobin, P. Luque, R.J. Crawford and E.P. Ivanova “The susceptibility of Staphylococcus aureus CIP 65.8 and Pseudomonas aeruginosa ATCC 9721 cells to the bactericidal action of nanostructured Calopteryx haemorrhoidalis damselfly wing surfaces” Applied Microbiology and Biotechnology, 101, 4683-4690 (2017)

G.S. Watson, D.W. Green, B.W. Cribb, C.L. Brown, C.R. Meritt, M.J. Tobin, J. Vongsvivut, M. Sun, A. Liang and J.A. Watson “Insect Analogue to the Lotus Leaf: A Planthopper Wing Membrane Incorporating a Low-Adhesion, Nonwetting, Superhydrophobic, Bactericidal, and Biocompatible Surface” ACS Applied Materials & Interfaces, 9, 24381-24392 (2017)

D.E. Mainwaring, S.H. Nguyen, H. Webb, T. Jakubov, M. Tobin, R.N. Lamb, A.H.-F. Wu, R. Marchant, R.J. Crawford and E.P. Ivanova “The nature of inherent bactericidal activity: insights from the nanotopology of three species of dragonfly” Nanoscale, 8, 6527-6534 (2016)

Forensic Science:

The infrared microspectroscopy beamline can been used for research in the forensic science arena for such purposes as fingerprint analysis, drug detection, human hair fiber analysis, and analysis of the authenticity of multilayered polymeric security cards to name a few examples.  The technique is of particular use to forensic science where spatially correlating specific chemical information using non-destructive methods is of critical importance.

Publications in forensic science

B.N. Dorakumbura, R.E. Boseley, T. Becker, D.E. Martin, A. Richter, M.J. Tobin, W. Van Bronswjik, J Vongsvivut, M.J. Hackett and S.W. Lewis, “Revealing the spatial distribution of chemical species within latent fingermarks using vibrational spectroscopy” Analyst, 143, 3961-4208 (2018)

M. Maric, W. van Bronswijk, S.W. Lewis and K. Pitts “Synchrotron FTIR characterisation of automotive primer surface paint coatings for forensic purposes” Talenta, 118, 156-161  (2014)

P. Fritz, W. van Bronswjik, K. Lepkova, S.W. Lewis, K.F. Lim, D.E. Martin and L. Puskar “Infrared microscopy studies of the chemical composition of latent fingermark residues” Microchemical Journal, 111, 40-46 (2013)

M. Maric, W. van Bronswijk, S.W. Lewis, K. Pitts and D.E. Martin “Characterisation of chemical component migration in automotive paint by synchrotron infrared imaging” Forensic Science International, 228, 165-169 (2013)

S. Zadnik, W. van Bronswijk,  A.A. Frick, P. Fritz and S.W. Lewis “Fingermark simulants and their inherent problems: a comparison with latent fingermark deposits” Journal of Forensic Identification, 63, 593-608 (2013)

History & Cultural Heritage:

The IRM beamline has been used by those involved in cultural heritage to probe a range of factors including the chemical analysis of pigments, paints, material etc in order to determine the historical period and geographical location that a historical object might originate from, as well as product authenticity or adulteration.  Below is a list of publications where the researchers used the IRM beamline to investigate their historical items.

Publications in history and cultural heritage:

D. Creagh, V. Otieno-Alego, A. Treasure, M Kubik and D Hallam “The use of radiation in the study of cultural heritage artefacts” Radiation Physics and Chemistry, 137, 2116-224 (2017)

A. Hunt, P.S. Thomas, D. James, B. David, J.-M. Geneste, J.-J. Delannoy and B.H. Stuart “The characterisation of pigments used in X-ray rock art at Dalakngalarr 1, central-western Arnhem Land” Microchemical Journal, 126, 524-529 (2016)

R.A. Goodall, L. Puskar, K. Fisher, E. McCartney and H. Privett, "Investigation of historical dart poisons using synchrotron based infrared microscopy and spectroscopy" Vibrational Spectroscopy, 78, 66-74 (2015)

G. Osmond, B Ebert and J. Drennan “Zinc oxide-centred deterioration in 20th century Vietnamese paintings by Nguyễ Trọng Kiệm (1933–1991)” AICCM Bulletin, 34, 4-14

P. Dredge, M.R. Schilling, G. Gautier, J. Mazurek, T. Learner and R. Wuhrer “Lifting the Lids off Ripolin: A Collection of Paint From Sidney Nolan's Studio” Journal of the American Institute for Conservation, 52, 227-235

Sample preparation facilities


Limited space is available inside the IR Cabin for sample preparation, however the synchrotron has both a Chemistry and a Biochemistry laboratory on-site. These are equipped with fume cupboards, fridges, freezers, pellet press, ovens, stereo microscopes with camera, UV-Vis spectrometer and balances. A microtome is also available onsite. Please consult IR Beamline staff if you require specific equipment for sample preparation so we can ensure you have access to it over your beamtime. If it is something we do not have, you may have to supply your own equipment.

In addition to the above, PC2 cell culture facilities are also available for use. The Biochemistry lab is PC2 compliant and set-up for bacterial and GMO work, and a PC2 Tissue Culture laboratory is available for mammalian cell work. Facilities include a Class II Laminar Flow Biosafety Cabinet, CO2 incubator, inverted microscope, autoclave, centrifuges, fridge, freezer and water bath. Users requiring access to these facilities should contact IR beamline staff when submitting their proposal if it involves the handling of live biological material.

Please note that in special circumstances site access can be given earlier than your scheduled experiment if you require time to prepare your samples onsite e.g. you require the microtome or the PC2 laboratory.

Sample stages & environments

Each microscope is equipped with a motorised sample stage and can accommodate samples up to approximately XxY = 10x10 cm in size. Maximum sample thickness is restricted to 10 mm by the vertical travel limits of the stage and the working distance of the objective optic. The stage is fitted with interchangeable plates which can be adapted for different sample shapes and sizes. 

Typical sample sizes accommodated within these plates are listed below, however more specific information relating to sample requirements according to the mode of IRM to be performed (eg ATR, reflection) may be found in the techniques section:

  • 13 mm or 22 mm diameter optical windows (transmission)
  • 25x76 mm (1”x3”) microscope slides (reflectance)
  • 50x76 mm sample chambers (e.g the sample compression cell)

To reduce the background variations produced by the presence of water or carbon dioxide in the atmosphere, each microscope stage is surrounded by a perspex box continuously purged by dry air. In addition, use of the Linkam FTIR600 sample stage also allows the immediate environment surrounding a sample to be controlled; samples are placed within a small chamber in the heating block that can be purged by either nitrogen or argon gas. This stage can be used for samples in either transmission or reflection mode.

For specific requirements relating to sample mounting, please consult the IR beamline staff.