Radim Kolar

Brno University of Technology · Department of Biomedical Engineering

This work presents a novel fully automated method for retinal analysis in images acquired with a flood illuminated adaptive optics retinal camera (AO-FIO). The proposed processing pipeline consists of several steps: First, we register single AO-FIO images in a montage image capturing a larger retinal area. The registration is performed by combinati...

Theoretical models of retinal hemodynamics showed the modulation of retinal pulsatile patterns (RPPs) by heart rate (HR), yet in-vivo validation and scientific merit of this biological process is lacking. Such evidence is critical for result interpretation, study design, and (patho-)physiological modeling of human biology spanning applications in v...

Multispectral imaging is used in various applications including astronomy, industry, and agriculture. In retinal imaging, the single‐shot multispectral image stack is typically acquired and analyzed. This multispectral analysis can provide information on various structural or metabolic properties. This paper describes the multispectral improvement...

Cell viscoelastic properties are affected by the cell cycle, differentiation, pathological processes such as malignant transformation. Therefore, evaluation of the mechanical properties of the cells proved to be an approach to obtaining information on the functional state of the cells. Most of the currently used methods for cell mechanophenotypisat...

Dry powder inhalers are used by a large number of patients worldwide to treat respiratory diseases. The objective of this work is to experimentally investigate changes in aerosol particle diameter and particle number concentration of pharmaceutical aerosols generated by four dry powder inhalers under realistic inhalation and exhalation conditions....

Dry powder inhalers are used by a large number of patients worldwide to treat respiratory diseases. The objective of this work is to experimentally investigate changes in aerosol particle diameter and particle number concentration of pharmaceutical aerosols generated by five dry powder inhalers under realistic inhalation and exhalation conditions....

DNA double-strand breaks (DSBs), marked by ionizing radiation-induced (repair) foci (IRIFs), are the most serious DNA lesions and are dangerous to human health. IRIF quantification based on confocal microscopy represents the most sensitive and gold-standard method in radiation biodosimetry and allows research on DSB induction and repair at the mole...

This paper focuses on the analysis of image sequences acquired during fast photobleaching using a standard wide-field microscope. We show that the photobleaching rate estimated for each pixel is not constant for the whole field of view, but it provides a new spatially variant parametric image related to the cell structure and diffusion of fluoropho...

In this contribution, we focused on optimising a dynamic flow-based shear stress system to achieve a reliable platform for cell shear modulus (stiffness) and viscosity assessment using quantitative phase imaging. The estimation of cell viscoelastic properties is influenced by distortion of the shear stress waveform, which is caused by the propertie...

Assessment of retinal blood flow inside the optic nerve head (ONH) and the peripapillary area is an important task in retinal imaging. For this purpose, an experimental binocular video ophthalmoscope that acquires precisely synchronized video sequences of the optic nerve head and peripapillary area from both eyes has been previously developed. It e...

In this paper, a novel U-Net-based method for robust adherent cell segmentation for quantitative phase microscopy image is designed and optimised. We designed and evaluated four specific post-processing pipelines. To increase the transferability to different cell types, non-deep learning transfer with adjustable parameters is used in the post-proce...

Cell viscoelastic properties are affected by the cell cycle, differentiation, pathological processes such as malignant transformation. Therefore, evaluation of the mechanical properties of the cells proved to be an approach to obtaining information on the functional state of the cells. Most of the currently used methods for cell mechanophenotypisat...

Adaptive optics (AO) flood illumination camera acquires retinal images with a limited field of view, which can be extended by image alignment into one wide field of view montage image. The image alignment into a montage requires efficient and accurate image registration. Since manual registration is demanding and disadvantageous, automatic registra...

In this paper, U-Net-based method for robust adherent cell segmentation for quantitative phase microscopy image is designed and optimised. We designed and evaluated four specific post-processing pipelines. To increase the transferability to different cell types, non-deep learning transfer with adjustable parameters is used in the post-processing st...

During mechanical ventilation, a disparity between flow, pressure and volume demands of the patient and the assistance delivered by the mechanical ventilator often occurs. This paper introduces an alternative approach of simulating and evaluating patient–ventilator interactions with high fidelity using the electromechanical lung simulator xPULM™. T...

In this contribution, we focused on optimising a dynamic flow-based shear stress system to achieve a reliable platform for cell shear modulus (stiffness) and viscosity assessment using quantitative phase imaging. The estimation of cell viscoelastic properties is influenced by distortion of the shear stress waveform, which is caused by the propertie...

During mechanical ventilation, a disparity between flow, pressure or volume demands of the patient and the assistance delivered by the mechanical ventilator often occurs. Asynchrony effect and ventilator performance are frequently studied from ICU datasets or using commercially available lung simulators and test lungs. This paper introduces an alte...

Dynamic optical imaging of retinal hemodynamics is a rapidly evolving technique in vision and eye-disease research. Video-recording, which may be readily accessible and affordable, captures several distinct functional phenomena such as the spontaneous venous pulsations (SVP) of central vein or local arterial blood supply etc. These phenomena displa...

Purpose To measure parameters of the cardiac cycle-induced pulsatile light absorption signal (plethysmography signal) of the optic nerve head (ONH) and to compare parameters between normal subjects and patients with different stages of glaucoma. Patients and methods A recently developed video ophthalmoscope was used to acquire short video sequence...

Quantitative Phase Imaging (QPI) is a label-free microscopic technique, which provides images with high contrast, moreover, it provides quantitative cell mass measurements for each pixel. Segmentation of particular cells is an important step in the analysis of QPI image data. This paper presents a method for automatic cell segmentation in QPI image...

DNA double-strand breaks, marked by Ionizing Radiation-Induced (Repair) Foci (IRIF), are the most serious DNA lesions, dangerous to human health. IRIF quantification based on confocal microscopy represents the most sensitive and gold standard method in radiation biodosimetry and allows research of DSB induction and repair at the molecular and a sin...

Driver fatigue and stress significantly contribute to higher number of car accidents worldwide. Although, different detection approaches have been already commercialized and used by car producers (and third party companies), research activities in this field are still needed in order to increase the reliability of these alert systems. Also, in the...

The fundus observation by ophthalmoscope is a non-invasive approach for diagnosis of various retinal diseases. The vein and artery pulsation are usually clearly apparent on fundus and might be also important for medical practice. Thus our method focuses on these changes and analyzes the time delay between the pulsation signal detected in the vein a...

This paper describes an application of binocular video-ophthalmoscope for binocular eye movement analysis during target fixation. We analyze eye movements during monocular and binocular fixation and the changes in eye position for 73 subjects. We show that the standard deviations of differences between eye shifts for vertical and horizontal movemen...

Optical imaging of retinal hemodynamic function is an important part of ophthalmologic research. Development and inventing of imaging devices and data analysis methods are both just in progress. The current study innovatively implements two blind source separation (BSS) techniques (i.e. spatial Principal Component Analysis - sPCA; and spatial Indep...

Background Because of its non-destructive nature, label-free imaging is an important strategy for studying biological processes. However, routine microscopic techniques like phase contrast or DIC suffer from shadow-cast artifacts making automatic segmentation challenging. The aim of this study was to compare the segmentation efficacy of published s...

Fluorescence microscopy is a golden standard for contemporary biological studies. However, since fluorescent dyes cross-react with biological processes, a label-free approach is more desirable. The aim of this study is to create artificial, fluorescence-like nuclei labeling from label-free images using Convolution Neural Network (CNN), where traini...

The experimental and preclinical studies of ischemia and reperfusion on animal models usually evaluate the sizes of area at risk (AR) of infarction and infarct area (IA) as fundamental parameters. The authors usually don’t provide any detailed information about the image processing of their data, though the IA or AR segmentation is often challengin...

We describe a low-cost, easy to use binocular instrument to acquire retinal video sequences of both eyes simultaneously. After image registration, cardiac cycle-induced pulsatile light attenuation changes can be measured quantitatively with high spatial and temporal resolution. Parameters such as amplitude, pulse form, and time shift between light...

This paper proposes a method of automated detection and parameterization of spontaneous venous pulsation using raw video data acquired from retinal video-ophthalmoscope. Evaluation of magnitude of spontaneous venous pulsation has been proven to correlate with occurrence of glaucoma. Based on this relation a method is proposed that might help to det...

Background Optical coherence tomography (OCT) is a well established imaging technique with different applications in preclinical research and clinical practice. The main potential for its application lies in the possibility of noninvasively performing “optical biopsy”. Nevertheless, functional OCT imaging is also developing, in which perfusion imag...

Laser speckle contrast imaging (LSCI) is a noninvasive method, which uses scattered light to estimate the flow of a fluid containing scatterers. Thus, it can be especially used to estimate blood flow. Laser light is randomly scattered on the tissue and this refracted light interfere with reflected light, giving birth to laser speckle noise. As the...

Background: Analysis of fast temporal changes on retinas has become an important part of diagnostic video-ophthalmology. It enables investigation of the hemodynamic processes in retinal tissue, e.g. blood-vessel diameter changes as a result of blood-pressure variation, spontaneous venous pulsation influenced by intracranial-intraocular pressure di...

Isolated cardiomyocytes have been used as valid and useful model in experimental cardiology research for decades. The cell contraction function is usually measured via expensive and complex instruments which can either damage the cell or take much time for setting up. In contrary, recent development of optical microscopy and digital cameras suggest...

This paper describes a novel methodology for eye fixation measurement using a unique videoophthalmoscope setup and advanced image registration approach. The representation of the eye movements via Poincare plot is also introduced. The properties, limitations and perspective of this methodology are finally discussed.

The analysis of fast temporal changes of the human retina can be used to get insight to normal physiological behavior and to detect pathological deviations. This can be important for the early detection of glaucoma and other eye diseases. We developed a small, lightweight, USB powered video ophthalmoscope that allows taking video sequences of the h...

This paper describes experiments and methodology for flow rate estimation using optical coherence tomography and dilution method in single fiber setup. The single fiber is created from custom made glass capillary and polypropylene hollow fiber. As a data source, measurements on single fiber phantom with continuous flow of carrier medium and bolus o...

This study presents three methods for absolute quantification in ultrasound perfusion analysis based on bolus tracking. The first two methods deconvolve the perfusion time sequence with a measured AIF, using a nonparametric or a parametric model of the tissue residue function, respectively. The third method is a simplified approach avoiding deconvo...

The retinal nerve fiber layer (RNFL) is one of the most affected retinal structures due to the glaucoma disease. Progression of this disease results in theRNFL atrophy that can be detected as the decrease of the layer’s thickness. Usually, the RNFL thickness can be assessed by optical coherence tomography (OCT). However, an examination using OCT is...

This paper deals with the retinal blood vessel segmentation in fundus video-sequences acquired by experimental fundus video camera. Quality of acquired video-sequences is relatively low and fluctuates across particular frames. Especially, due to the low resolution, poor signal-to-noise ratio, and varying illumination conditions within the frames, a...

This paper deals with the design of optical system for simultaneous iris and retina acquirement of a human eye. This unique combination in one particular apparatus can be used for medical (ophthalmology) as well as for biometric purposes. Scanning in one cycle could significantly save the work time in comparison with separate scanning of each part...

Images of ocular fundus are routinely utilized in ophthalmology. Since an examination using fundus camera is relatively fast and cheap procedure, it can be used as a proper diagnostic tool for screening of retinal diseases such as the glaucoma. One of the glaucoma symptoms is progressive atrophy of the retinal nerve fiber layer (RNFL) resulting in...

This paper describes new registration approach for registration of low SNR retinal image sequences. We combine two approaches - Fourier-based method for large shift correction and Lucas-Kanade tracking for small shift and rotation correction. We also propose method for evaluation of registration results, which uses spatial variation of minimum valu...

A statistical analysis of 1st and 2nd harmonic echoes backscattered from contrast media using Rician inverse Gaussian (RiIG) envelope model is described. Knowledge of statistics of the scattered signal may contribute to perfusion analysis. A range of ultrasound contrast agent (UCA) concentrations is examined. The RiIG distribution was fitted to ima...

This paper presents the successful creation of new phantom for optical coherence tomography (OCT) aimed on perfusion simulation. The phantom is created from syringe pump and polypropylene hollow fiber with porous walls embeded in the glass capillary to provide small outer environment. Its function was tested by gold nanorods as a flowing medium and...

Automatic assessment of retinal vessels plays an important role in the diagnosis of various eye, as well as systemic diseases. A public screening is highly desirable for prompt and effective treatment, since such diseases need to be diagnosed at an early stage. Automated and accurate segmentation of the retinal blood vessel tree is one of the chall...

This paper deals with registration of retinal images, which were taken by high-resolution digital colour fundus cameras. The proposed method describes successful application of phase correlation method. It combines several basic steps — global correction of shift, rotation and scaling, detection of landmarks, their correspondences and finally image...

A new signal model and processing method for quantitative ultrasound perfusion analysis is presented, called bolus-and-burst. The method has the potential to provide absolute values of blood flow, blood volume, and mean transit time. Furthermore, it provides an estimate of the local arterial input function which characterizes the arterial tree, all...

Dynamic contrast-enhanced ultrasound (DCE-US) imaging is a promising diagnostic method, which enables the evaluation of tissue perfusion via different parameters. The mean transit time and time-to-peak parameters are the main time parameters and their values depend on the model used for the approximation of the noisy perfusion curves. In this paper...

The retinal ganglion axons are an important part of the visual system, which can be directly observed by fundus camera. The layer they form together inside the retina is the retinal nerve fiber layer (RNFL). This paper describes results of a texture RNFL analysis in color fundus photographs and compares these results with quantitative measurement o...

Dynamic contrast enhanced ultrasound (DCE-US) imaging is a promising modality for noninvasive assessment of various tissue kinetic parameters (e.g. time-to-peak, mean transit time (MTT), blood flow etc.). These parameters can be used for diagnosis of pathological tissue functions caused by different diseases. Fast bolus method is based on the fast...

This paper describes an experimental evaluation of the statistical properties of microbubbles by the means of Nakagami probability distribution. The first and second harmonic images are used for statistical analysis of backscattered signals from saline with different concentration of microbubbles (SonoVue). There were no differences between the sha...

The paper presents a new perfusion analysis method using ultrasound which combines burst-replenishment and bolustracking acquisition methods. It allows absolute quantification of the mean transit time, blood flow and blood volume. It is based on the concept of arterial input function and tissue residue function and is formulated as a blind-deconvol...

An automatic method of segmenting the retinal vessel tree and estimating status of retinal neural fibre layer (NFL) from high resolution fundus camera images is presented. First, reliable blood vessel segmentation, using 2D directional matched filtering, enables to remove areas occluded by blood vessels thus leaving remaining retinal area available...

Since images of ocular fundus are commonly available in ophthalmic practice, automatic assessment of the retinal nerve fiber layer (RNFL) can be useful for early diagnosis of glaucoma. This contribution presents a texture analysis method for the description of RNFL status and proposes appropriate textural features for medical diagnosis. The method...

Two approaches to evaluation of the retinal nerve fibre layer (RNFL) status are compared in the contribution: detection of the local existence of the RNFL in the fundus camera (FC) images versus the objective measurement of the RNFL thickness at identical retinal locations by the optical coherence tomography (OCT). The local detection results based...

The paper presents an overview of image analysis activities of the Brno DAR group in the medical application area of retinal imaging. Particularly, illumination correction and SNR enhancement by registered averaging as preprocessing steps are briefly described; further mono-and multimodal registration methods developed for specific types of oph-tha...

This paper describes a method for registration of images in ultrasound sequences when contrast agent is administrated in blood stream. The proposed method is based on mu-tual information, image enhancement and automatic selec-tion of multi-reference images. The registration process and the properties of the normalized mutual information are in-vest...

A method for correction of non-uniform illumination in colour fundus images based on the B-spline approximation of the illumination surface is presented. The control points for B-splines are determined from an original image, sepa- rately from the red, green and blue channel. The estimated illumination surface is used in a multiplicative model for...

This paper is focused on multimodal and multidimensional image data registration: the three-dimensional retinal optical coherence tomographic (OCT) data and two-dimensional color images of fundus. The registration of these two modalities is not common in retinal image processing, but it might help to remove the moving artifacts in OCT and correct t...

This paper describes a new method for detection biffurcation points of retinal vascular tree. This approach uses Hessian matrix for blood vessel segmentation, followed by morphological thinning and binary matched filtering. These bifurcation points are consequently used as landmarks for rigid image registration based on the iterative closest point...

A method for segmentation of vessel structure in colour retinal fundus images is presented, based on 2D matched filtering correlating the local image areas with 2D masks obtained via averaging of brightness profiles of vessels for several different vessel widths.Each of the basic masks is rotated in twelve different directions; this way, 60 masks f...

This paper describes method for analysis of the texture created by retinal nerve fibers (RNF) via Markov Random Fields. The Causal Autoregressive Random (CAR) model is used to create a feature vector describing the changes in texture due to losses in RNF layer. It is shown that features based on CAR model can be used for discrimination between heal...

The texture analysis of the retinal nerve fiber layer (RNFL) in colour fundus images is a promising tool for early glau-coma diagnosis. This paper describes model-based method for detection of changes in the RNFL. The method utilizes Gaussian Markov random fields (GMRF) and the least-square error (LSE) estimate for the local RNFL texture modelling....

It has been shown that besides positron emission tomography, single photon emission computed tomography and magnetic resonance imaging; contrast echocardiography can be used for qualitative and quantitative myocardial perfusion assessment. In this review, the properties of ultrasound contrast agents, imaging techniques and acquisition methods are s...