Miran Bürmen

University of Ljubljana · Faculty of Electrical Engineering

Structurally anisotropic materials are ubiquitous in several application fields, yet their accurate optical characterization remains challenging due to the lack of general models linking their scattering coefficients to the macroscopic transport observables and the need to combine multiple measurements to retrieve their direction-dependent values....

Structurally anisotropic materials are ubiquitous in several application fields, yet their accurate optical characterization remains challenging due to the lack of general models linking their scattering coefficients to the macroscopic transport observables, and the need to combine multiple measurements to retrieve their direction-dependent values....

Reflectance acquired with a multimode optical fiber probe can be related to optical properties of an investigated turbid medium by utilizing a light propagation model. During this step, a calibration of the light propagation model is required, as the modeled reflectance is normalized to the light energy of the source fiber, while the experimentally...

Lensless on-chip microscopy comprises a simple and compact setup in which the sample is placed close to the imaging sensor and illuminated by a coherent light source. The acquired in-line hologram carries information about the amplitude and phase image of the sample, which can be numerically reconstructed. Contrary to conventional microscopy, the r...

Significance: Current open-source Monte Carlo (MC) method implementations for light propagation modeling are many times tedious to build and require third-party licensed software that can often discourage prospective researchers in the biomedical optics community from fully utilizing the light propagation tools. Furthermore, the same drawback also...

We present a multi-layered and voxel-based Monte Carlo methods with auxiliary utilities implemented in Python for user-friendly, open-source and multi-purpose modeling of light propagation in turbid media based on PyOpenCL computational platform.

We corrected the label of the reduced scattering coefficient in Fig. 11 of our recently published paper (Biomed. Opt. Express 11, 3753 (2020)).

In this work, we introduce a framework for efficient and accurate Monte Carlo (MC) simulations of spatially resolved reflectance (SRR) acquired by optical fiber probes that account for all the details of the probe tip including reflectivity of the stainless steel and the properties of the epoxy fill and optical fibers. While using full details of t...

In this work, we revise the preparation procedure and conduct an in depth characterization of optical properties for the recently proposed silicone-based tissue-mimicking optical phantoms in the spectral range from 475 to 925 nm. The optical properties are characterized in terms of refractive index and its temperature dependence, absorption and red...

Monodisperse polystyrene microspheres are often utilized in optical phantoms since optical properties such as the scattering coefficient and the scattering phase function can be calculated using the Mie theory. However, the calculated values depend on the inherent physical parameters of the microspheres which include the size, refractive index, and...

Subdiffusive reflectance captured at short source-detector separations provides increased sensitivity to the scattering phase function and hence allows superficial probing of the tissue ultrastructure. Consequently, estimation of subdiffusive optical parameters has been the subject of many recent studies focusing on lookup-table-based (LUT) inverse...

Light propagation in biological tissues is frequently modeled by the Monte Carlo (MC) method, which requires processing of many photon packets to obtain adequate quality of the observed backscattered signal. The computation times further increase for detection schemes with small acceptance angles and hence small fraction of the collected backscatte...

We significantly improve the estimation of the absorption and reduced scattering coefficients, and second-order similarity parameter γ from spatially resolved reflectance by extending the inverse model with the third-order similarity parameter δ.

Measuring the three-dimensional point spread function (3D PSF) of imaging spectrometers is a challenging task since it requires a small, monochromatic and bright source. Here we introduce a powerful and practical new approach for 3D PSF measurement on the basis of a bright virtual monochromatic point-like source, which is formed by a collimated lig...

Estimation of optical properties from subdiffusive reflectance acquired at short source-detector separations is challenging due to the sensitivity to the underlying scattering phase function. In recent studies, a second-order similarity parameter γ has been increasingly used alongside the absorption and reduced scattering coefficients to account fo...

Analytical expressions for sampling the scattering angle from a phase function in Monte Carlo simulations of light propagation are available only for a limited number of phase functions. Consequently, numerical sampling methods based on tabulated values are often required instead. By using Monte Carlo simulated reflectance, we compare two existing...

2D point spread function (PSF) is a commonly used measure to assess the quality of various imaging systems. The most convenient way of 2D PSF measurement is taking an image of a light source with its size well below the diffraction limit of the imaging system. In this paper, we present a novel method that allows formation of such a virtual point-li...

Light propagation in biological tissues formulated within the framework of the radiative transport equation is frequently simulated by stochastic Monte Carlo simulations. Such methodology is used in numerous experimental settings including spatially resolved reflectance measurements conducted by optical fiber probes. In this paper, we analyse the i...

Properties of the short wave infrared (SWIR) imaging spectrograph and the front lens along with the misalignment of optical elements contribute to positionally variant displacements and blur that can significantly degrade the overall quality of the acquired images. In this work, we devise a complete routine for simultaneous displacement correction...

We propose and objectively evaluate an inverse Monte Carlo model for estimation of absorption and reduced scattering coefficients and similarity parameter γ from spatially resolved reflectance (SRR) profiles in the subdiffusive regime. The similarity parameter γ carries additional information on the phase function that governs the angular propertie...

Push-broom hyperspectral imaging systems are increasingly used for various medical, agricultural and military purposes. The acquired images contain spectral information in every pixel of the imaged scene collecting additional information about the imaged scene compared to the classical RGB color imaging. Due to the misalignment and imperfections in...

In this paper, diffuse reflectance hyperspectral images of a light beam propagating through a semi-infinite homogeneous layer were simulated by a modified version of the open source Monte Carlo (MC) for multi-layered tissues. Subsequently, the optical properties in terms of absorption and reduced scattering coefficients were extracted from the simu...

In this paper, the commonly used inverse Monte Carlo model based on absorption and reduced scattering coefficients is extended by a well-known similarity parameter γ (gamma), which carries additional information on the phase function. Sub-diffuse reflectance measurements at five source-detector separations were used to extract the absorption and re...

Characterization of spectral-spatial interdependence related error in the images acquired with an imaging spectrometer requires a 3D PSF measurement. In this contribution we introduce a 3D PSF measurement setup and demonstrate the error assessment.

We assess the properties of contact pressure applied by manually operated fiber-optic probes as a function of the operator, probe contact area, and sample stiffness. First, the mechanical properties of human skin sites with different skin structures, thicknesses, and underlying tissues were studied by in vivo indentation tests. According to the obt...

Light propagation models often simplify the interface between the optical fiber probe tip and tissue to a laterally uniform boundary with mismatched refractive indices. Such simplification neglects the precise optical properties of the commonly used probe tip materials, e.g. stainless steel or black epoxy. In this paper, we investigate the limitati...

Diffuse reflectance spectroscopy utilizing optical fiber probes is a useful and simple method for non-invasive determination of biological tissue optical properties. In order to extract the optical properties from the acquired diffuse reflectance spectra, an accurate light propagation model, such as Monte Carlo, is required. The results obtained by...

Hyperspectral imaging systems effectively collect information across the spectral and two spatial dimensions by employing three main components: the front lens, the light-diffraction element and a camera. Imperfections in these components introduce spectral and spatial dependent distortions in the recorded hyperspectral image. These can be characte...

In this study, we assess the properties of the contact pressure applied by manually operated probes as a function of the operator, probe contact area, and sample stiffness. For this purpose, three different human skin-like phantoms with different well-defined mechanical properties were used. To gain relevant statistics of the contact pressure prope...

Diffuse reflectance spectroscopy is a popular approach for non-invasive assessment of optical properties in turbid media. The acquired spectra are analyzed by various light propagation models or by purely empirical methods. In this study, we quantitatively asses the experimental data and Monte Carlo lookup table-based inverse models by extracting t...

Cancer is the main cause of canine morbidity and mortality. The existing evaluation of tumors requires an experienced veterinarian and usually includes invasive procedures (e.g., fine-needle aspiration) that can be unpleasant for the dog and the owner. We investigate visible and near-infrared diffuse reflectance spectroscopy (DRS) as a noninvasive...

In this paper, we propose a novel method for spectral and spatial calibration and resolution enhancement of hyperspectral images by a two-step procedure. The spectral and spatial variability of the hyperspectral imaging system response function is characterized by a global parametric model, which is derived from a pair of calibration images corresp...

Swine ascariasis results in milk spot livers which are manually removed from the slaughter line. In this paper, we propose and objectively assess a novel automated method for detection of milk spot livers based on digital color imaging, visible and near infrared spectroscopy and multispectral measurements. A commercial digital color camera based sy...

Review of the existing studies on the contact pressure-induced changes in the optical properties of biological tissues showed that the reported changes in transmittance, reflectance, absorption, and scattering coefficient are vastly inconsistent. In order to gain more insight into the contact pressure-induced changes observed in biomedical applicat...

Push-broom hyperspectral imaging system ideally disperses the spectral and spatial information in two orthogonal directions preferably aligned with the columns and rows of the imaging sensor. Due to the imperfections in the camera lens and in particular the optical components of spectrograph, wavelength dependent spectral and spatial distortions al...

Contact pressure induced by manually operated fiber optic probes can significantly affect the optical properties of the studied tissue. If the contact pressure and the changes in optical properties are measured properly, then the complementary information can be used to obtain additional insight into the tissue physiology. However, as reliable asse...

A significant part of the uniformity degradation in the acquired hyperspectral images can be attributed to the coregistration distortions and spectrally and spatially dependent resolution arising from the misalignments and the operation principle of the spectrograph based hyperspectral imaging system. The aim of this study was the development and v...

Acquiring near infrared spectra in vivo usually requires a fiber-optic probe to be pressed against the tissue. The applied pressure can significantly affect the optical properties of the underlying tissue, and thereby the acquired spectra. The existing studies consider these effects to be distortions. In contrast, we hypothesize that the pressure-i...

Among the variety of available hyperspectral imaging systems, the line-scan technique stands out for its short acquisition time and good signal-to-noise ratio. However, due to imperfections in the camera lens and, in particular, optical components of the imaging spectrograph, the acquired images are spatially and spectrally distorted, which can sig...

Dental caries remains one of the most prevalent chronic diseases of modern society. The initial stages of dental caries are characterized by demineralization of enamel, resulting in subclinical lesions, which are difficult to diagnose. If detected early enough, such demineralization can be arrested and reversed by noninvasive means through well-est...

Hyper-spectral imaging has gained recognition as an important non-invasive research tool in the field of biomedicine. Among the variety of available hyperspectral imaging systems, systems comprising an imaging spectrograph, lens, wideband illumination source and a corresponding camera stand out for the short acquisition time and good signal to nois...

Spatial resolution of hyperspectral imaging systems can vary significantly due to axial optical aberrations that originate from wavelength-induced index-of-refraction variations of the imaging optics. For systems that have a broad spectral range, the spatial resolution will vary significantly both with respect to the acquisition wavelength and with...

Dental caries is a disease characterized by demineralization of enamel crystals leading to the penetration of bacteria into the dentine and pulp. Early detection of enamel demineralization resulting in increased enamel porosity, commonly known as white spots, is a difficult diagnostic task. Laser induced autofluorescence was shown to be a useful me...

Despite major improvements in dental healthcare and oral hygiene, dental caries remains one of the most prevalent oral diseases and represents the primary cause of oral pain and tooth loss. The initial stages of dental caries are characterized by demineralization of enamel crystals and are difficult to diagnose. Near infrared (NIR) hyperspectral im...

Near infrared (NIR) diffuse reflectance spectroscopy is a rapid noninvasive spectroscopic technique extensively used in the field of biomedicine. The main challenges of the NIR spectroscopy lie in the analysis of the acquired spectral information, requiring prior knowledge on the influence of various tissue parameters on the spectra. In this paper,...

Accurate and objective evaluation of vertebral body deformations represents an important part of the clinical diagnostics and therapy of pathological conditions affecting the spine. Although modern clinical practice is oriented towards threedimensional (3D) imaging techniques, the established methods for the evaluation of vertebral body deformation...

Despite major improvements in dental healthcare and technology, dental caries remains one of the most prevalent chronic diseases of modern society. The initial stages of dental caries are characterized by demineralization of enamel crystals, commonly known as white spots, which are difficult to diagnose. Near-infrared (NIR) hyperspectral imaging is...

In this study, we propose and evaluate a method for spectral characterization of acousto-optic tunable filter (AOTF) hyperspectral imaging systems in the near-infrared (NIR) spectral region from 900 nm to 1700 nm. The proposed spectral characterization method is based on the SRM-2035 standard reference material, exhibiting distinct spectral feature...

Construction of a standardized near infrared (NIR) hyper-spectral teeth database is a first step in the development of a reliable diagnostic tool for quantification and early detection of dental diseases. The standardized diffuse reflectance hyper-spectral database was constructed by imaging 12 extracted human teeth with natural lesions of various...

Despite major improvements in dental healthcare and technology, dental caries remains one of the most prevalent chronic diseases of modern society. The initial stages of dental caries are characterized by demineralization of enamel crystals, commonly known as white spots which are difficult to diagnose. If detected early enough, such demineralizati...

Dental caries is a disease characterized by demineralization of enamel crystals leading to the penetration of bacteria into the dentin and pulp. If left untreated, the disease can lead to pain, infection and tooth loss. Early detection of enamel demineralization resulting in increased enamel porosity, commonly known as white spots, is a difficult d...

Every imaging system requires a geometric calibration to yield accurate optical measurements. Geometric calibration typically involves imaging of a known calibration object and finding the parameters of a camera model and a model of optical aberrations. Optical aberrations can vary significantly across the wide spectral ranges of hyperspectral imag...

The goal of this article is to present a novel method for spectral characterization and calibration of spectrometers and hyper-spectral imaging systems based on non-collinear acousto-optical tunable filters. The method characterizes the spectral tuning curve (frequency–wavelength characteristic) of the AOTF (Acousto-Optic Tunable Filter) filter by...

Near-infrared spectroscopy is a promising, rapidly developing, reliable and noninvasive technique, used extensively in the biomedicine and in pharmaceutical industry. With the introduction of acousto-optic tunable filters (AOTF) and highly sensitive InGaAs focal plane sensor arrays, real-time high resolution hyper-spectral imaging has become feasib...

Optical aberrations present an important problem in optical measurements. Geometrical calibration of an imaging system is therefore of the utmost importance for achieving accurate optical measurements. In hyper-spectral imaging systems, the problem of optical aberrations is even more pronounced because optical aberrations are wavelength dependent....

Near-infrared spectroscopy is a promising, rapidly developing, reliable and noninvasive technique, used extensively in the biomedicine and in pharmaceutical industry. With the introduction of acousto-optic tunable filters (AOTF) and highly sensitive InGaAs focal plane sensor arrays, real-time high resolution hyper-spectral imaging has become feasib...

Coated pellets typically used for filling pharmaceutical capsules and pressing tablets are increasingly replacing powder especially because of the better compression and flow characteristics and superior drug release rate management. However, the highly complex multivariable coating process needs to be well-controlled in order to ensure high produc...

In this paper, we present a cost-effective method for fast and accurate in-line weighing of hard gelatin capsules based on the optimized capacitance sensor and real-time processing of the capsule capacitance profile resulting from 5000 capacitance measurements per second. First, the effect of the shape and size of the capacitive sensor on the sensi...

Automatic visual inspection of pharmaceutical pellets is of utmost importance for monitoring, controlling and improving coating process. To reach this goal, we propose a visual inspection system for estimation of mean aspect ratio, circularity, equivalent spherical diameter and coating thickness of pharmaceutical pellets. The proposed system was as...

The unique properties of light emitting diodes (LED) offer significant advantages in terms of lifetime, source control, and response time all of which are potentially very important for various illumination applications. However, a number of factors such as the initial variability of the optical properties in a batch, high temperature dependence of...

Visualization of subcutaneous veins is very difficult with the naked eye, but important for diagnosis of medical conditions and different medical procedures such as catheter insertion and blood withdrawal. Moreover, recent studies showed that the images of subcutaneous veins could be used for biometric identification. The majority of methods used f...

Nowadays, after nearly half a century of rapid and sustained development of light-emitting diodes (LEDs), conventional light sources such as incandescent and fluorescent lamps are beginning to be replaced by LEDs. Therefore, understanding and assessing all the relevant factors that affect the quality of LEDs is becoming increasingly important for d...

The unique properties of LEDs offer significant advantages in terms of lifetime, intensity and color control, response time and efficiency, all of which are very important for illumination in machine vision applications. However, there are some drawbacks of LEDs, such as the high thermal dependency and temporal degradation of the intensity and colo...