Acquisition and Analysis in Biomedical Vibrational Spectroscopy

Data Acquisition and Analysis in Biomedical Vibrational Spectroscopy 

Present data acquisition and/or analysis tools such as OPUS (Bruker Optics), Perkin Elmer s Spotlight software (Perkin Elmer), Resolutions Pro (Varian), Grams (Thermo Fisher Scientific), The Unscrambler (CAMO), CytoSpec (www.cytospec.com) and various Matlab (The MathWorks) toolboxes allow for the easy recording and evaluation of infrared (IR) spectra. However, care has to be taken concerning the particular choice of data acquisition parameters, pre-treatment of spectra and data analysis procedures. With the attempt to move biomedical IR spectroscopy from bench top to bedside further questions of reproducibility and standardisation arise. 

This chapter is intended to assist the procedure of biomedical vibrational spectroscopy in the context of synchrotron IR spectroscopy. It starts with the recording of spectra in standardised settings and continues through the assessment of spectral (and system) quality, spectral pre-processing up to data analysis (both quantitative and classification analysis). For the latter part, the main emphasis is placed on the role of independent validation. 

The migration of research results of IR spectroscopy to practical applications requires a high level of spectral quality and reproducibility. Standardisation and optimisation of the measurement conditions and measurement parameters are therefore considered to be necessary prerequisites for further technological progress. In this section we will discuss systematic factors, which potentially impact the spectral quality and reproducibility, such as sample preparation, the optical set-up, the problem of water vapour absorption, and aspects of spectral and spatial resolution. 

Optical material After sectioning, the tissue slices are mounted on IR transparent supportive substrates such as Cap2 windows for transmission-type measurements. Cap2 is a popular window material in IR spectroscopy because it is almost insoluble in water and thus allows post-staining of the sections by haematoxylin and eosin (H E). Furthermore, compared with other window 

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