Paper – FTIR of biological materials

Using Fourier transform IR spectroscopy to analyze biological materials
Matthew J Baker, Júlio Trevisan, Paul Bassan, Rohit Bhargava, Holly J Butler, Konrad M Dorling, Peter R Fielden, Simon W Fogarty, Nigel J Fullwood, Kelly A Heys, Caryn Hughes, Peter Lasch, Pierre L Martin-Hirsch, Blessing Obinaju, Ganesh D Sockalingum, Josep Sulé-Suso, Rebecca J Strong, Michael J Walsh, Bayden R Wood, Peter Gardner & Francis L Martin
Nature Protocols 9 (2014) 1771–1791

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Paper – Quantum cascade laser microscopy of tissue microarrays

Open Access

Large scale infrared imaging of tissue micro arrays (TMAs) using a tunable Quantum Cascade Laser (QCL) based microscope
Paul Bassan, Miles J. Weida, Jeremy Rowlette and Peter Gardner
Analyst (2014)


Chemical imaging in the field of vibrational spectroscopy is developing into a promising tool to complement digital histopathology. Applications include screening of biopsy tissue via automated recognition of tissue/cell type and disease state based on the chemical information from the spectrum. For integration into clinical practice, data acquisition needs to be speeded up to implement a rack based system where specimens are rapidly imaged to compete with current visible scanners where 100’s of slides can be scanned overnight. Continue reading

Paper – High-throughput tissue imaging

Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging
Paul Bassan, Ashwin Sachdeva, Jonathan H. Shanks, Mick D. Brown, Noel W. Clarke and Peter Gardner
Proc. SPIE 9041, Medical Imaging 2014: Digital Pathology, 90410D 9041 (2014)


Fourier transform infrared (FT-IR) chemical imaging has been demonstrated as a promising technique to complement histopathological assessment of biomedical tissue samples. Current histopathology practice involves preparing thin tissue sections and staining them using hematoxylin and eosin (H&E) after which a histopathologist manually assess the tissue architecture under a visible microscope. Studies have shown that there is disagreement between operators viewing the same tissue suggesting that a complementary technique for verification could improve the robustness of the evaluation, and improve patient care. Continue reading

Paper – FTIR analysis of blood serum

Open Access

Assessing the challenges of Fourier transform infrared spectroscopic analysis of blood serum
Caryn Hughes, Michael Brown, Graeme Clemens, Alex Henderson, Geraldine Monjardez, Noel W. Clarke and Peter Gardner
Journal of Biophotonics (2014) [OPEN ACCESS]


There are many approaches to measuring the infrared spectrum of a blood serum sample. Naturally, each approach will have both advantages and disadvantages. We report on the progress of the application of infrared spectroscopy in the field of blood serum analysis towards clinical application, with a focus on prostate cancer. In order to perform a high-powered study with clinical relevance, choosing the most suitable approach must undergo careful consideration. We review the possibilities of using different sample preparation methods and speculate upon the potential pitfalls of both transmission and attenuated total reflectance (ATR) techniques.

Paper – Paraffin removal from FFPE sections

Assessment of paraffin removal from prostate FFPE sections using transmission mode FTIR-FPA imaging
Caryn Hughes, Lydia Gaunt, Michael Brown, Noel W. Clarke and Peter Gardner
Anal. Methods (2014)


Formalin-fixed paraffin-embedded (FFPE) tissue sections are routinely analysed for biochemical discrimination by vibrational spectroscopy techniques in the spectral pathology community. In these experiments, it is usually desirable to remove the paraffin from the tissue. This is most commonly performed by the use of xylene but other solvents such as hexane are also used. It is thought that the removal of unbound paraffin wax by such solvents also leaches out lipids native to the tissue, leading to the perception by some that any subsequent analysis on remaining lipids of dewaxed tissue may be unreliable. The scope of the study was to make an assessment of whether a dewaxing protocol can demonstrate that paraffin wax is reliably removed in relation to the detectable limits of transmission mode infrared spectroscopy. Continue reading

Paper – FTIR through glass

Transmission FTIR chemical imaging on glass substrates: applications in infrared spectral histopathology
Paul Bassan, Joe Mellor, Jonathan Shapiro, Kaye J. Williams, Michael Lisanti and Peter Gardner
Anal. Chem. (2014)


Fourier transform infrared chemical imaging in transmission mode has traditionally been performed on expensive mid-IR transparent windows such as barium/calcium fluoride, which are more fragile than glass making preparation in the histopathology laboratories more cumbersome. A solution is presented here by using cheap glass substrates for the FTIR chemical imaging which has a high-wavenumber transmission window allowing measurement of the C–H, N–H and O–H stretches occurring at ca. 2500–3800 cm–1. The “fingerprint” region of the IR spectrum occurring below 1800 cm–1 is not obtainable, however we demonstrate that a wealth of information is contained in the high wavenumber range using 71 patients on a breast tissue microarray (TMA) as a model for investigation. Importantly we demonstrate that the tissue can be classified into four basic tissue cell-types and that using just the epithelial cells, reasonable discrimination of normal and malignant tissue can be found.

Paper – Whole organ, label-free imaging

Whole organ cross-section chemical imaging using label-free mega-mosaic FTIR microscopy
Paul Bassan, Ashwin Sachdeva, Jonathan H. Shanks, Mick D. Brown, Noel W. Clarke and Peter Gardner Analyst (2013)


FTIR chemical imaging has been demonstrated as a promising technique to construct automated systems to complement histopathological evaluation of biomedical tissue samples. The rapid chemical imaging of large areas of tissue has previously been a limiting factor in this application. Consequently, smaller areas of tissue have previously had to be sampled, possibly introducing sampling bias and potentially missing diagnostically important areas. In this report a high spatial resolution chemical image of a whole prostate cross section is shown comprising 66 million pixels. Each pixel represents an area 5.5 × 5.5 μm2 of tissue and contains a full infrared spectrum providing a chemical fingerprint. The data acquisition time was 14 hours, thus showing that a clinical time frame of hours rather than days has been achieved.

Graphical abstract: Whole organ cross-section chemical imaging using label-free mega-mosaic FTIR microscopy