scholarly journals The effect of deformation of absorbing scatterers on Mie-type signatures in infrared microspectroscopy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maren Anna Brandsrud ◽  
Reinhold Blümel ◽  
Johanne Heitmann Solheim ◽  
Achim Kohler
Keyword(s):  
Electromagnetic Radiation ◽  
Biological Samples ◽  
Numerical Aperture ◽  
Iterative Algorithms ◽  
Shape Resonance ◽  
Chaotic Scattering ◽  
Extinction Efficiency ◽  
Infrared Microspectroscopy ◽  
Spherical Scatterer ◽  
Absorbance Spectra

AbstractMie-type scattering features such as ripples (i.e., sharp shape-resonance peaks) and wiggles (i.e., broad oscillations), are frequently-observed scattering phenomena in infrared microspectroscopy of cells and tissues. They appear in general when the wavelength of electromagnetic radiation is of the same order as the size of the scatterer. By use of approximations to the Mie solutions for spheres, iterative algorithms have been developed to retrieve pure absorbance spectra. However, the question remains to what extent the Mie solutions, and approximations thereof, describe the extinction efficiency in practical situations where the shapes of scatterers deviate considerably from spheres. The aim of the current study is to investigate how deviations from a spherical scatterer can change the extinction properties of the scatterer in the context of chaos in wave systems. For this purpose, we investigate a chaotic scatterer and compare it with an elliptically shaped scatterer, which exhibits only regular scattering. We find that chaotic scattering has an accelerating effect on the disappearance of Mie ripples. We further show that the presence of absorption and the high numerical aperture of infrared microscopes does not explain the absence of ripples in most measurements of biological samples.

scholarly journals Mie scatter corrections in single cell infrared microspectroscopy

2016 ◽  
Vol 187 ◽  
pp. 235-257 ◽  
Author(s):  
Tatiana Konevskikh ◽  
Rozalia Lukacs ◽  
Reinhold Blümel ◽  
Arkadi Ponossov ◽  
Achim Kohler
Keyword(s):  
Iterative Algorithm ◽  
Single Cells ◽  
Scatter Correction ◽  
Numerical Aperture ◽  
Mie Scattering ◽  
Infrared Light ◽  
Approximation Formula ◽  
Meta Model ◽  
Independent Parameters ◽  
Absorbance Spectra

Strong Mie scattering signatures hamper the chemical interpretation and multivariate analysis of the infrared microscopy spectra of single cells and tissues. During recent years, several numerical Mie scatter correction algorithms for the infrared spectroscopy of single cells have been published. In the paper at hand, we critically reviewed existing algorithms for the correction of Mie scattering and suggest improvements. We developed an iterative algorithm based on Extended Multiplicative Scatter Correction (EMSC), for the retrieval of pure absorbance spectra from highly distorted infrared spectra of single cells. The new algorithm uses the van de Hulst approximation formula for the extinction efficiency employing a complex refractive index. The iterative algorithm involves the establishment of an EMSC meta-model. While existing iterative algorithms for the correction of resonant Mie scattering employ three independent parameters for establishing a meta-model, we could decrease the number of parameters from three to two independent parameters, which reduced the calculation time for the Mie scattering curves for the iterative EMSC meta-model by a factor of 10. Moreover, by employing the Hilbert transform for evaluating the Kramers–Kronig relations based on a FFT algorithm in Matlab, we further improved the speed of the algorithm by a factor of 100. For testing the algorithm we simulate distorted apparent absorbance spectra by utilizing the exact theory for the scattering of infrared light at absorbing spheres, taking into account the high numerical aperture of infrared microscopes employed for the analysis of single cells and tissues. In addition, the algorithm was applied to measured absorbance spectra of single lung cancer cells.

scholarly journals Extracting pure absorbance spectra in infrared microspectroscopy by modeling absorption bands as Fano resonances

2019 ◽  
Vol 150 (15) ◽  
pp. 154124 ◽  
Author(s):  
Alex J. Schofield ◽  
Reinhold Blümel ◽  
Achim Kohler ◽  
Rozalia Lukacs ◽  
Carol J. Hirschmugl
Keyword(s):  
Fano Resonances ◽  
Absorption Bands ◽  
Infrared Microspectroscopy ◽  
Absorbance Spectra

Does chaotic scattering affect the extinction efficiency in quasi-spherical scatterers?

2020 ◽  
Author(s):  
Maren Anna Brandsrud ◽  
Reinhold Blümel ◽  
Johanne Heitmann Solheim ◽  
Eirik Almklov Magnussen ◽  
Eivind Seim ◽  
...  
Keyword(s):  
Chaotic Scattering ◽  
Extinction Efficiency

An Efficient Statistic for Determining the Diameter of Thin Sectioned Uniform Spheres from Measurements of Biological Samples

1974 ◽  
Vol 32 ◽  
pp. 114-115
Author(s):  
W. R. Schucany ◽  
G. H. Kelsoe ◽  
V. F. Allison
Keyword(s):  
Biological Samples ◽  
Traditional Method ◽  
Cell Types ◽  
Accurate Estimation ◽  
Morphological Identification ◽  
Sectioned Material ◽  
Maximal Diameter ◽  
Similar Cell

Accurate estimation of the size of spheroid organelles from thin sectioned material is often necessary, as uniquely homogenous populations of organelles such as vessicles, granules, or nuclei often are critically important in the morphological identification of similar cell types. However, the difficulty in obtaining accurate diameter measurements of thin sectioned organelles is well known. This difficulty is due to the extreme tenuity of the sectioned material as compared to the size of the intact organelle. In populations where low variance is suspected the traditional method of diameter estimation has been to measure literally hundreds of profiles and to describe the “largest” as representative of the “approximate maximal diameter”.

Video-Enhanced Microscopy--Better Visibility of Plant Cell Structures

1982 ◽  
Vol 40 ◽  
pp. 182-185
Author(s):  
N.S. Allen ◽  
R.D. Allen
Keyword(s):  
Diffraction Pattern ◽  
Theoretical Basis ◽  
Numerical Aperture ◽  
Gain Control ◽  
Control Unit ◽  
Camera Control ◽  
Variable Gain ◽  
Contrast Method ◽  
Fine Detail ◽  
Cell Structures

Various methods of video-enhanced microscopy combine TV cameras with light microscopes creating images with improved resolution, contrast and visibility of fine detail, which can be recorded rapidly and relatively inexpensively. The AVEC (Allen Video-enhanced Contrast) method avoids polarizing rectifiers, since the microscope is operated at retardations of λ/9- λ/4, where no anomaly is seen in the Airy diffraction pattern. The iris diaphram is opened fully to match the numerical aperture of the condenser to that of the objective. Under these conditions, no image can be realized either by eye or photographically. Yet the image becomes visible using the Hamamatsu C-1000-01 binary camera, if the camera control unit is equipped with variable gain control and an offset knob (which sets a clamp voltage of a D.C. restoration circuit). The theoretical basis for these improvements has been described.

The Application of Ultra-Thin Sectioning Techniques to Non-Biological Samples

1968 ◽  
Vol 26 ◽  
pp. 332-333
Author(s):  
C. F. Oster
Keyword(s):  
Biological Sciences ◽  
Epoxy Resin ◽  
Cross Sections ◽  
Biological Samples ◽  
Industrial Applications ◽  
Photographic Film ◽  
Silver Particles ◽  
Thin Sectioning ◽  
Embedding Medium

Although ultra-thin sectioning techniques are widely used in the biological sciences, their applications are somewhat less popular but very useful in industrial applications. This presentation will review several specific applications where ultra-thin sectioning techniques have proven invaluable.The preparation of samples for sectioning usually involves embedding in an epoxy resin. Araldite 6005 Resin and Hardener are mixed so that the hardness of the embedding medium matches that of the sample to reduce any distortion of the sample during the sectioning process. No dehydration series are needed to prepare our usual samples for embedding, but some types require hardening and staining steps. The embedded samples are sectioned with either a prototype of a Porter-Blum Microtome or an LKB Ultrotome III. Both instruments are equipped with diamond knives.In the study of photographic film, the distribution of the developed silver particles through the layer is important to the image tone and/or scattering power. Also, the morphology of the developed silver is an important factor, and cross sections will show this structure.

Artefacts in the x-ray microanalysis of frozen-hydrated biological samples

1987 ◽  
Vol 45 ◽  
pp. 658-659
Author(s):  
Patrick Echlin
Keyword(s):  
Electron Scattering ◽  
Biological Samples ◽  
Fracture Face ◽  
Detailed Structure ◽  
X Ray ◽  
Morphological Appearance ◽  
The Poor ◽  
Freeze Dried

A number of papers have appeared recently which purport to have carried out x-ray microanalysis on fully frozen hydrated samples. It is important to establish reliable criteria to be certain that a sample is in a fully hydrated state. The morphological appearance of the sample is an obvious parameter because fully hydrated samples lack the detailed structure seen in their freeze dried counterparts. The electron scattering by ice within a frozen-hydrated section and from the surface of a frozen-hydrated fracture face obscures cellular detail. (Fig. 1G and 1H.) However, the morphological appearance alone can be quite deceptive for as Figures 1E and 1F show, parts of frozen-dried samples may also have the poor morphology normally associated with fully hydrated samples. It is only when one examines the x-ray spectra that an assurance can be given that the sample is fully hydrated.

FR-IR Molecular Microanalysis System

1990 ◽  
Vol 48 (2) ◽  
pp. 270-271
Author(s):  
John A. Reffner ◽  
William T. Wihlborg
Keyword(s):  
Fourier Transform ◽  
Fourier Transform Infrared ◽  
Integrated System ◽  
Morphological Examination ◽  
Fully Integrated ◽  
Ir Microscopy ◽  
Normal Functions ◽  
Infrared Microspectroscopy ◽  
Infrared Spectral ◽  
Ft Ir

The IRμs™ is the first fully integrated system for Fourier transform infrared (FT-IR) microscopy. FT-IR microscopy combines light microscopy for morphological examination with infrared spectroscopy for chemical identification of microscopic samples or domains. Because the IRμs system is a new tool for molecular microanalysis, its optical, mechanical and system design are described to illustrate the state of development of molecular microanalysis. Applications of infrared microspectroscopy are reviewed by Messerschmidt and Harthcock.Infrared spectral analysis of microscopic samples is not a new idea, it dates back to 1949, with the first commercial instrument being offered by Perkin-Elmer Co. Inc. in 1953. These early efforts showed promise but failed the test of practically. It was not until the advances in computer science were applied did infrared microspectroscopy emerge as a useful technique. Microscopes designed as accessories for Fourier transform infrared spectrometers have been commercially available since 1983. These accessory microscopes provide the best means for analytical spectroscopists to analyze microscopic samples, while not interfering with the FT-IR spectrometer’s normal functions.

On resolving fine periodic microstructures in the optical microscope

1989 ◽  
Vol 47 ◽  
pp. 364-365
Author(s):  
W.S. Putnam ◽  
C. Viney
Keyword(s):  
Liquid Crystalline ◽  
Numerical Aperture ◽  
Polarized Light ◽  
Normal Incidence ◽  
Optical Microscope ◽  
Angle Of Incidence ◽  
Resolution Limit ◽  
Crystalline Materials ◽  
Periodic Microstructures ◽  
Liquid Crystalline Materials

Many sheared liquid crystalline materials (fibers, films and moldings) exhibit a fine banded microstructure when observed in the polarized light microscope. In some cases, for example Kevlar® fiber, the periodicity is close to the resolution limit of even the highest numerical aperture objectives. The periodic microstructure reflects a non-uniform alignment of the constituent molecules, and consequently is an indication that the mechanical properties will be less than optimal. Thus it is necessary to obtain quality micrographs for characterization, which in turn requires that fine detail should contribute significantly to image formation.It is textbook knowledge that the resolution achievable with a given microscope objective (numerical aperture NA) and a given wavelength of light (λ) increases as the angle of incidence of light at the specimen surface is increased. Stated in terms of the Abbe resolution criterion, resolution improves from λ/NA to λ/2NA with increasing departure from normal incidence.

Performance Evaluation of a Novel Type of Low-Energy Electron Microscope

1990 ◽  
Vol 48 (1) ◽  
pp. 354-355
Author(s):  
Bertholdand Senftinger ◽  
Helmut Liebl
Keyword(s):  
Electron Microscope ◽  
High Resolution ◽  
Field Strength ◽  
Numerical Aperture ◽  
Low Energy ◽  
Energy Electron ◽  
High Resolution Imaging ◽  
Lens System ◽  
Resolution Imaging ◽  
Low Energy Electron

During the last few years the investigation of clean and adsorbate-covered solid surfaces as well as thin-film growth and molecular dynamics have given rise to a constant demand for high-resolution imaging microscopy with reflected and diffracted low energy electrons as well as photo-electrons. A recent successful implementation of a UHV low-energy electron microscope by Bauer and Telieps encouraged us to construct such a low energy electron microscope (LEEM) for high-resolution imaging incorporating several novel design features, which is described more detailed elsewhere.The constraint of high field strength at the surface required to keep the aberrations caused by the accelerating field small and high UV photon intensity to get an improved signal-to-noise ratio for photoemission led to the design of a tetrode emission lens system capable of also focusing the UV light at the surface through an integrated Schwarzschild-type objective. Fig. 1 shows an axial section of the emission lens in the LEEM with sample (28) and part of the sample holder (29). The integrated mirror objective (50a, 50b) is used for visual in situ microscopic observation of the sample as well as for UV illumination. The electron optical components and the sample with accelerating field followed by an einzel lens form a tetrode system. In order to keep the field strength high, the sample is separated from the first element of the einzel lens by only 1.6 mm. With a numerical aperture of 0.5 for the Schwarzschild objective the orifice in the first element of the einzel lens has to be about 3.0 mm in diameter. Considering the much smaller distance to the sample one can expect intense distortions of the accelerating field in front of the sample. Because the achievable lateral resolution depends mainly on the quality of the first imaging step, careful investigation of the aberrations caused by the emission lens system had to be done in order to avoid sacrificing high lateral resolution for larger numerical aperture.

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