Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

We first briefly review the state of the art of digital in-line holographic microscopy (DIHM) with numerical reconstruction and then discuss some technical issues, such as lateral and depth resolution, depth of field, twin image, four-dimensional tracking, and reconstruction algorithm. We then present a host of examples from microfluidics and biology of tracking the motion of spheres, algae, and bacteria. Finally, we introduce an underwater version of DIHM that is suitable for in situ studies in an ocean environment that show the motion of various plankton species.

Digital in-line holographic microscopy.

Three-dimensional imaging with micron resolution and simultaneous tracking of many (hundreds) objects (bubbles, beads, algae, bacteria etc.) is now possible in-situ not only with a benchtop microscope, but also remotely in such environments as the deep ocean with a submersible version of the instrument. The instrument is very simple in its hardware requirements and an efficient software package is available for real time reconstruction and image manipulation.

Digital In-line Holographic Microscopy

This tutorial-review introduces the fundamentals of polarized light interaction with biological tissues and presents some of the recent key polarization optical methods that have made possible the quantitative studies essential for biomedical diagnostics. Tissue structures and the corresponding models showing linear and circular birefringence, dichroism, and chirality are analyzed. As the basis for a quantitative description of the interaction of polarized light with tissues, the theory of polarization transfer in a random medium is used. This theory employs the modified transfer equation for Stokes parameters to predict the polarization properties of single- and multiple-scattered optical fields. The near-order of scatterers in tissues is accounted for to provide an adequate description of tissue polarization properties. Biomedical diagnostic techniques based on polarized light detection, including polarization imaging and spectroscopy, amplitude and intensity light scattering matrix measurements, and polarization-sensitive optical coherence tomography are described. Examples of biomedical applications of these techniques for early diagnostics of cataracts, detection of precancer, and prediction of skin disease are presented. The substantial reduction of light scattering multiplicity at tissue optical clearing that leads to a lesser influence of scattering on the measured intrinsic polarization properties of the tissue and allows for more precise quantification of these properties is demonstrated.

https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-21/issue-7/071114/Polarized-light-interaction-with-tissues/10.1117/1.JBO.21.7.071114.pdf

Polarized light interaction with tissues

Terahertz (THz = 1012 Hz) spectroscopy has shown great potential in biomedical research due to its unique features, such as the non-invasive and label-free identification of living cells and medical imaging. In this review, we summarized the advantages and progresses achieved in THz spectroscopy technology for blood cell detection, cancer cell characterization, bacterial identification and biological tissue discrimination, further introducing THz imaging systems and its progress in tissue imaging. We also highlighted the biological effects of THz radiation during its biological applications and the existing challenges and strategies to accelerate future clinical applications. The future prospects for THz spectroscopy will focus on developing rapid, label-free, and convenient biosensors for point-of-care tests and THz in vivo imaging.

/pdf/the-medical-application-of-terahertz-technology-in-non-22ktsyjokp.pdf

The medical application of terahertz technology in non-invasive detection of cells and tissues: opportunities and challenges

Water vapor noise in the air affects the accuracy of optical parameters extracted from terahertz (THz) time-domain spectroscopy. In this paper, a numerical method was proposed to eliminate water vapor noise from the THz spectra. According to the Van Vleck-Weisskopf function and the linear absorption spectrum of water molecules in the HITRAN database, we simulated the water vapor absorption spectrum and real refractive index spectrum with a particular line width. The continuum effect of water vapor molecules was also considered. Theoretical transfer function of a different humidity was constructed through the theoretical calculation of the water vapor absorption coefficient and the real refractive index. The THz signal of the Lacidipine sample containing water vapor background noise in the continuous frequency domain of 0.5-1.8 THz was denoised by use of the method. The results show that the optical parameters extracted from the denoised signal are closer to the optical parameters in the dry nitrogen environment.

Numerical method based on transfer function for eliminating water vapor noise from terahertz spectra.

Near-infrared scanning holography with a Fresnel zone plate (FZP) coded aperture has potential applications in imaging through turbid media. However, the nonnegative intensity-distribution function of the FZP coded aperture introduces the background artifacts into the reconstructed images, reducing the contrast and the signal-to-noise ratio (SNR) of the images. A novel method termed as the composite hologram is proposed to reduce the artifacts. The computer simulations showed that the contrast and the SNR of the reconstructed images had improvements of at least 50.2% and 5.58-dB, respectively, compared with the conventional method. The composite hologram of a metal ring with a 6.0-mm diameter made by a wire with a 0.4-mm diameter immersing in 1% intralipid solution was recorded, and the reconstruction was performed numerically. The experimental results demonstrated that the contrast and the SNR of the reconstructed image had improvements of at least 32.3% and 2.51-dB, respectively.

Method for reduction of background artifacts of images in scanning holography with a Fresnel-zone-plate coded aperture.

The degree of polarization (DOP) can be used to characterize the polarization-maintaining ability of a beam of polarized light propagating through a turbid medium. Experiments on polystyrene (PST) sphere suspensions show that, the linearly polarized light propagating through the PST sphere suspension of Rayleigh scatterers has better polarization-maintaining ability, whereas the circularly polarized light propagating through the PST sphere suspension of Mie scatterers has better polarization-maintaining ability. Moreover, helicity flipping occurs to the circularly polarized light propagating in the extremely weak PST sphere suspensions or on the surface of suspensions. In addition, the DOP is dependent on the wavelength of incident light. The results can be helpful to image in turbid media by use of diffuse backscattered light.

Experimentally determined characteristics of the degree of polarization of backscattered light from polystyrene sphere suspensions

The optical activity of glucose molecules is important for diagnosing and monitoring blood glucose of diabetes. In order to accurately detect the diabetes at an early stage, there is an urgent need to develop innovative detection methods. By use of Mueller matrix decomposition (MMD), we have studied the optical activity of glucose molecules in three types of turbid media—polystyrene (PST) sphere suspension, chicken blood, and the vein blood of diabetic patients. The experimental setup to obtain the Mueller matrix in the forward detection geometry has been used. The experimental results show that the rotation angle has linear relationship with the concentration of the glucose when the scattering coefficient of the PST sphere suspension remains unchanged, whereas the scattering effect enlarges the rotation angle. Furthermore, optical rotation abides by Drude’s dispersion equation. The decomposition method has also been found useful applications in quantifying the optical rotations of blood glucose in diabetic patients. The diabetic severity status can be distinguished with the rotation angle of glucose and also is in accordance with the clinical diagnosis. Thus, the method of MMD has promising applications in diabetic diagnosis and monitoring.

https://www.spiedigitallibrary.org/journals/Journal-of-Biomedical-Optics/volume-19/issue-04/046015/Mueller-matrix-decomposition-for-determination-of-optical-rotation-of-glucose/10.1117/1.JBO.19.4.046015.pdf

Mueller matrix decomposition for determination of optical rotation of glucose molecules in turbid media

A principal component analysis (PCA) method was used here to analyze three materials: glucose, intralipids, and water. The time-domain signal, frequency-domain information, refractive index, extinction coefficient, and dielectric function of these three substances were selected as original variables. We find that it is possible to analyze the similarity between different materials via the cluster distance in the principal component (PC) space and to analyze the difference between samples of the same material via the centroid distance, and the clustering effects of different original variables in PCA may be analyzed via the ratio of centroid distances. Because the thickness of solid-state matters and the concentration of liquid matters are related to the PC, the terahertz time-domain spectroscopy may be combined with PCA to perform visual classification on the materials, thus facilitating substance identification. Sample thickness and concentration may be deduced from the PC score of the materials.

Ping Sun

Papers

Numerical method based on transfer function for eliminating water vapor noise from terahertz spectra.

Method for reduction of background artifacts of images in scanning holography with a Fresnel-zone-plate coded aperture.

Experimentally determined characteristics of the degree of polarization of backscattered light from polystyrene sphere suspensions

Mueller matrix decomposition for determination of optical rotation of glucose molecules in turbid media

Terahertz data combined with principal component analysis applied for visual classification of materials