Histopathology of tissue samples is used to determine the progression of cancer usually by staining and visual analysis. It is recognised that disease progression from healthy tissue to cancerous is accompanied by spectral signature changes in the infrared range. In this work, FTIR spectroscopic imaging in transmission using a focal plane array (96 x 96 pixels) has been applied to the characterisation of Barrett's esophageal adenocarcinoma. Spectral images were acquired in transmission mode. To correct optical aberrations, infrared transparent lenses were used of the same material as the slide on which biopsies were fixed. The lenses acted as an immersion objective, reducing scattering and improving spatial resolution.A novel mapping approach is presented where spectral images obtained with added lens are stitched together such that the dataset contained a representative section of the esophageal tissue. Images were also acquired in transmission mode using high-magnification optics for enhanced spatial resolution, and were also acquired using a germanium micro-ATR objective for comparison. The reduction of scattering was assessed using k-means clustering. The same tissue section map, which contained a region of high grade dysplasia was analysed using hierarchical clustering analysis. A reduction of the trough at 1077 cm -1 in the second derivative spectra was identified as an indicator of high grade dysplasia.In addition, the spatial resolution obtained with the added lens using high-magnification optics was assessed by measurements of a sharp interface of polymer laminate, which was also compared with the spatial resolution achieved in micro ATR-FTIR imaging. The resolution was determined from the change in absorbance of spectral bands from one side of the polymer interface to the other. In transmission mode using the lens, it was determined to be 12 µm and using micro-ATR, the resolution was 3 µm for the band at ca. 6 µm The spatial resolution was also assessed with and without the added lens, in normal and high-magnification mode using a USAF target.Spectroscopic images of cells in transmission using two lenses are also presented, which are necessary for correcting chromatic aberration and refraction in both the condenser and objective. The use of lenses is shown to be necessary in obtaining high-quality spectroscopic images of cells in transmission mode and proves the applicability of the pseudo hemisphere approach for this and other microfluidic systems.2

More reliable biomarkers using near-patient technologies are needed to improve early diagnosis and intervention for patients with renal disease. Infrared (IR) vibrational spectroscopy/microspectroscopy is an established analytical method that was first used in biomedical research over 20 years ago. With the advances in instrumentation, computational and mathematical techniques, this technology has now been applied to a variety of diseases; however, applications in nephrology are just beginning to emerge. In the present study, we used attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to analyze urine samples collected from rodent models of inflammatory glomerulonephritis (GN) as well as from patients with crescentic GN, with the aim of identifying potential renal biomarkers; several characteristic mid-IR spectral markers were identified in urine samples. Specifically, a 1545 cm−1 band increased in intensity with the progression and severity of GN in rats, mice and humans. Furthermore, its intensity declined significantly in response to corticosteroid treatment in nephritic rats. In conclusion, our results suggest that specific urinary FTIR biomarkers may provide a rapid, sensitive and novel non-invasive means of diagnosing inflammatory forms of GN, and for real-time monitoring of progress, and response to treatment.