An open‐source code for Mie extinction extended multiplicative signal correction for infrared microscopy spectra of cells and tissues. Issue 8 (14th March 2019)

• Record Type: Journal Article
• Authors: Solheim, Johanne H.; Gunko, Evgeniy; Petersen, Dennis; Großerüschkamp, Frederik; Gerwert, Klaus; Kohler, Achim
• Is Part Of: Journal of biophotonics. Volume 12:Issue 8(2019)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2019-03-14
• Subjects: extended multiplicative signal correction -- infrared microscopy -- Mie scattering -- open‐source algorithm -- preprocessing; Photonics -- Periodicals; Optical materials -- Periodicals; Optics -- Periodicals; Medical instruments and apparatus -- Periodicals; 621.3605
• DOI: 10.1002/jbio.201800415
• Languages: English
• ISSNs: 1864-063X

Abstract

Abstract : Infrared spectroscopy of single cells and tissue is affected by Mie scattering. During recent years, several methods have been proposed for retrieving pure absorbance spectra from such measurements, while currently no user‐friendly version of the state‐of‐the‐art algorithm is available. In this work, an open‐source code for correcting highly scatter‐distorted absorbance spectra of cells and tissues is presented, as well as several improvements of the latest version of the Mie correction algorithm based on extended multiplicative signal correction (EMSC) published by Konevskikh et al. In order to test the stability of the code, a set of apparent absorbance spectra was simulated. To this purpose, pure absorbance spectra based on a Matrigel spectrum are simulated. Scattering contributions where obtained by mimicking the scattering features observed in a set of experimentally obtained spectra . It can be concluded that the algorithm is not depending strongly on the reference spectrum used for initializing the algorithm and retrieves well the underlying pure absorbance spectrum. The calculation time of the algorithm is considerably improved with respect to the resonant Mie scattering EMSC algorithm used by the community today. Abstract : Infrared spectroscopy of single cells and tissue is affected by Mie scattering. During recent years, several methods have been proposed for retrieving pure absorbance spectra from such measurements. A new and improved version of the state‐of‐the‐art Mie correction code is now available as open‐source code at https://gitlab.com/BioSpecNorway/me-emsc . The improved version is faster than the previous versions and employs an optimization criterion in the iterative algorithm.