Radim Kolář - Profile on Academia.edu (original) (raw)

Papers by Radim Kolář

Computing in Cardiology (CinC), 2012, Dec 30, 2018

The experimental and preclinical studies of ischemia and reperfusion on animal models usually eva... more 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 challenging and prone to be expert-depending. Here, we describe a new approach for automatic IA and AR segmentation based on combination of Random Forest classifier and two-step pixel-wise k-means classification of image pixels. The evaluation has been performed on the set of 16 images from 8 rat hearts. We compared sizes of normal perfused tissues, viable area and IA (normalized to percentage of total area) obtained by our method with manually segmentation by biologist. We achieved mean absolute error of 2.59% with mean standard deviation of 1.61%.

Frontiers in Medicine, Mar 16, 2023

Based on our previously developed mono-color video-ophthalmoscope a multicolor video-ophthalmosco... more Based on our previously developed mono-color video-ophthalmoscope a multicolor video-ophthalmoscope was developed. Using narrow band transmission filters, this instrument allows to measure the pulsatile cardiac cycle induced blood volume changes in the human retina for any wavelength in the sensitivity range of the used CMOS-camera. In this key experiment, video sequences (8 s, 25 fps, 200 frames) of the optic nerve head (ONH) were acquire for seven wavelengths between 475 nm and 677 nm one after the other. After image registration of all frames of each video sequence (to compensate for eye movements) and trend correction (to compensate for slow intensity changes), the amplitude of the cardiac cycle induced light intensity changes (pulsatile absorption amplitude PAA) can be calculated for all seven wavelengths. The results confirmed that the spectral distribution of PAA (λ) follows the distribution of the light absorption of blood. The measured values correspond to the absorption of a thin blood layer of about 0.5 μm thickness.

Blind Source Separation of Retinal Pulsatile Patterns in Optic Nerve Head Video-Recordings

IEEE Transactions on Medical Imaging, Mar 1, 2021

Dynamic optical imaging of retinal hemodynamics is a rapidly evolving technique in vision and eye... more 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 display specific dynamic patterns that have been detected using manual or semi-automated methods. We propose a pioneering concept in retina video-imaging using blind source separation (BSS) serving as an automated localizer of distinct areas with temporally synchronized hemodynamics. The feasibility of BSS techniques (such as spatial principal component analysis and spatial independent component analysis) and K-means based post-processing method were successfully tested on the monocular and binocular video-ophthalmoscopic (VO) recordings of optic nerve head (ONH) in healthy subjects. BSSs automatically detected three spatially distinct reproducible areas, i.e. SVP, optic cup pulsations (OCP) that included areas of larger vessels in the nasal part of ONH, and “other” pulsations (OP). The K-means post-processing reduced a spike noise from the patterns’ dynamics while high linear dependence between the non-filtered and post-processed signals was preserved. Although the dynamics of all patterns were heart rate related, the morphology analysis demonstrated significant phase shifts between SVP and OCP, and between SVP and OP. In addition, we detected low frequency oscillations that may represent respiratory-induced effects in time-courses of the VO recordings.

Lecture notes in computational vision and biomechanics, 2015

The retinal nerve fiber layer (RNFL) is one of the most affected retinal structures due to the gl... more 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 the RNFL 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 rather expensive and still not widely available. On the other hand, fundus camera is considered as a common and fundamental diagnostic device utilized at many ophthalmic facilities worldwide. This contribution presents a novel approach to texture analysis enabling assessment of the RNFL thickness in widely used colour fundus photographs. The aim is to propose a regression model based on different texture features effective for description of changes in the RNFL textural appearance related to the variations of RNFL thickness. The performance evaluation uses OCT as a gold standard modality for validation of the proposed approach. The results show high correlation between the models predicted output and RNFL thickness directly measured by OCT. J. Odstrcilik ( ) • R.

Comprehensive automatic processing and analysis of adaptive optics flood illumination retinal images on healthy subjects

Biomedical Optics Express, Jan 30, 2023

This work presents a novel fully automated method for retinal analysis in images acquired with a ... more 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 combination of phase correlation and the scale-invariant feature transform method. A set of 200 AO-FIO images from 10 healthy subjects (10 images from left eye and 10 images from right eye) is processed into 20 montage images and mutually aligned according to the automatically detected fovea center. As a second step, the photoreceptors in the montage images are detected using a method based on regional maxima localization, where the detector parameters were determined with Bayesian optimization according to manually labeled photoreceptors by three evaluators. The detection assessment, based on Dice coefficient, ranges from 0.72 to 0.8. In the next step, the corresponding density maps are generated for each of the montage images. As a final step, representative averaged photoreceptor density maps are created for the left and right eye and thus enabling comprehensive analysis across the montage images and a straightforward comparison with available histological data and other published studies. Our proposed method and software thus enable us to generate AO-based photoreceptor density maps for all measured locations fully automatically, and thus it is suitable for large studies, as those are in pressing need for automated approaches. In addition, the application MATADOR (MATlab ADaptive Optics Retinal Image Analysis) that implements the described pipeline and the dataset with photoreceptor labels are made publicly available.

Estimation of Time Delay Between Artery and Vein Pulsation using Experimental Video-Ophthalmoscope

The fundus observation by ophthalmoscope is a non-invasive approach for diagnosis of various reti... more 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 and the artery region. Data acquired by an experimental video-ophthalmoscope from five subjects with no eye diseases are analyzed. The analysis is based on the selection of artery and vein regions of interest and computation of averaged brightness within these regions for each frame. These extracted signals are filtered, interpolated and the trend is eliminated. Finally, the delays between artery and vein pulsation signals are determined using phase spectra. The measured delays are in the range of 15 to 95 ms, which is comparable with other published results.

Automatic Detection of Spontaneous Venous Pulsations Using Retinal Image Sequences

Lecture notes in computational vision and biomechanics, Oct 13, 2017

This paper proposes a method of automated detection and parameterization of spontaneous venous pu... more 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 detect glaucoma via detection of spontaneous venous pulsation.

Classification-based blood vessel segmentation in retinal images

Robust Automatic Montaging of Adaptive Optics Flood Illumination Retinal Images

Springer eBooks, 2021

Development of a binocular video-ophthalmoscope to compare parameters of heart beat induced blood volume changes between both eyes

Investigative Ophthalmology & Visual Science, Jul 13, 2018

bioRxiv (Cold Spring Harbor Laboratory), Aug 6, 2021

Cell viscoelastic properties are affected by the cell cycle, differentiation, pathological proces... more 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 mechanophenotypisation are limited by low robustness or the need for highly expert operation. In this paper, the system and method for viscoelasticity measurement using shear stress induction by fluid flow is described and tested. Quantitative Phase Imaging (QPI) is used for image acquisition because this technique enables to quantify optical path length delays introduced by the sample, thus providing a label-free objective measure of morphology and dynamics. Viscosity and elasticity determination were refined using a new approach based on the linear system model and parametric deconvolution. The proposed method allows high-throughput measurements during live cell experiments and even through a time-lapse, where we demonstrated the possibility of simultaneous extraction of shear modulus, viscosity, cell morphology, and QPI-derived cell parameters like circularity or cell mass. Additionally, the proposed method provides a simple approach to measure cell refractive index with the same setup, which is required for reliable cell height measurement with QPI, an essential parameter for viscoelasticity calculation. Reliability of the proposed viscoelasticity measurement system was tested in several experiments including cell types of different Young/shear modulus and treatment with cytochalasin D or docetaxel, and an agreement with atomic force microscopy was observed. The applicability of the proposed approach was also confirmed by a time-lapse experiment with cytochalasin D washout, where an increase of stiffness corresponded to actin repolymerisation in time. SIGNIFICANCE We present an approach for viscoelasticity measurement using QPI and shear stress induction by fluid flow. Our system builds and extends a recently published approach by parametric deconvolution, which allows us to eliminate the influence of the fluidic system and reliably measure both the shear modulus and viscosity of the cells in high throughput. Additionally, the proposed method enables to simultaneously determine cell refractive index map, cell dry mass map, and morphology, thereby enabling a multimodal cellular characterisation in a single measurement.

Cell Segmentation in Quantitative Phase Images with Improved Iterative Thresholding Method

Springer eBooks, Nov 30, 2020

Binocular video ophthalmoscope for simultaneous recording of sequences of the human retina to compare dynamic parameters

Proceedings of SPIE, Jul 28, 2017

A parallel video ophthalmoscope was developed to acquire short video sequences (25 fps, 250 frame... more A parallel video ophthalmoscope was developed to acquire short video sequences (25 fps, 250 frames) of both eyes simultaneously with exact synchronization. Video sequences were registered off-line to compensate for eye movements. From registered video sequences dynamic parameters like cardiac cycle induced reflection changes and eye movements can be calculated and compared between eyes.

Blind Source Separation of Different Retinal Pulsatile Patterns from Simultaneous Long-term Binocular Ophthalmoscopic Video-records

2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

Optical imaging of retinal hemodynamic function is an important part of ophthalmologic research. ... more 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 Independent Component Analysis – sICA) in application of an automatic detection and segmentation of a distinct Optic Disc (OD) areas with different hemodynamic properties from a simultaneous binocular video-ophthalmoscopic records. Both methods detected 3 different spatial patterns mostly symmetric over both eyes stable and reproducible over investigated participants, i.e. central Spontaneous Vessel Pulsations (SVPs), inner OD intensity pulsations and other OD pulsations. Dynamics of all mentioned patterns has a periodic character with similar main frequency (possibly corresponding to subject-specific heart rate) but shifted phase decreasing patterns’ mutual high cross-correlations. The sICA estimates a higher rate of phase shifts than sPCA.

Multispectral retinal video‐ophthalmoscope with fiber optic illumination

Journal of Biophotonics

Retinal pulsatile shift enhancement with blind source separation

Investigative Ophthalmology & Visual Science, Jul 22, 2019

Robust Automatic Montaging of Adaptive Optics Flood Illumination Retinal Images

Medical Image Understanding and Analysis, 2021

Comparison and practical review of segmentation approaches for label-free microscopy

This dataset contains microscopic images of PNT1A cell line captured by multiple microcopic witho... more This dataset contains microscopic images of PNT1A cell line captured by multiple microcopic without use of any labeling and a manually annotated ground truth for subsequent use in segmentation algorithms. Dataset also includes images reconstructed according to the methods described below in order to ease further segmentation. See Vicar et al. Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison. BMC Bioinformatics (2019) 20:360. DOI 10.1186/s12859-019-2880-8 Code using this dataset is available at https://github.com/tomasvicar/Cell-segmentation-methods-comparison <strong>Materials and methods </strong> Cells were cultured in RPMI-1640 medium supplemented with antibiotics (penicillin 100 U/ml and streptomycin 0.1 mg/ml) with 10% fetal bovine serum. Prior microscopy acquisition, cells were maintained at 37 cenigrade in a humidified incubator with 5% CO2. Intentionally, high passage number of cells was used (>30) in order to d...

Cell Segmentation in Quantitative Phase Images with Improved Iterative Thresholding Method

8th European Medical and Biological Engineering Conference, 2020

Eye movement analysis using a binocular video-ophthalmoscope

2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2019

This paper describes an application of binocular video-ophthalmoscope for binocular eye movement ... more 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 movements are higher for binocular fixation with respect to monocular fixation. We also present different examples of eye movement visualization.

Computing in Cardiology (CinC), 2012, Dec 30, 2018

The experimental and preclinical studies of ischemia and reperfusion on animal models usually eva... more 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 challenging and prone to be expert-depending. Here, we describe a new approach for automatic IA and AR segmentation based on combination of Random Forest classifier and two-step pixel-wise k-means classification of image pixels. The evaluation has been performed on the set of 16 images from 8 rat hearts. We compared sizes of normal perfused tissues, viable area and IA (normalized to percentage of total area) obtained by our method with manually segmentation by biologist. We achieved mean absolute error of 2.59% with mean standard deviation of 1.61%.

Frontiers in Medicine, Mar 16, 2023

Based on our previously developed mono-color video-ophthalmoscope a multicolor video-ophthalmosco... more Based on our previously developed mono-color video-ophthalmoscope a multicolor video-ophthalmoscope was developed. Using narrow band transmission filters, this instrument allows to measure the pulsatile cardiac cycle induced blood volume changes in the human retina for any wavelength in the sensitivity range of the used CMOS-camera. In this key experiment, video sequences (8 s, 25 fps, 200 frames) of the optic nerve head (ONH) were acquire for seven wavelengths between 475 nm and 677 nm one after the other. After image registration of all frames of each video sequence (to compensate for eye movements) and trend correction (to compensate for slow intensity changes), the amplitude of the cardiac cycle induced light intensity changes (pulsatile absorption amplitude PAA) can be calculated for all seven wavelengths. The results confirmed that the spectral distribution of PAA (λ) follows the distribution of the light absorption of blood. The measured values correspond to the absorption of a thin blood layer of about 0.5 μm thickness.

Blind Source Separation of Retinal Pulsatile Patterns in Optic Nerve Head Video-Recordings

IEEE Transactions on Medical Imaging, Mar 1, 2021

Dynamic optical imaging of retinal hemodynamics is a rapidly evolving technique in vision and eye... more 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 display specific dynamic patterns that have been detected using manual or semi-automated methods. We propose a pioneering concept in retina video-imaging using blind source separation (BSS) serving as an automated localizer of distinct areas with temporally synchronized hemodynamics. The feasibility of BSS techniques (such as spatial principal component analysis and spatial independent component analysis) and K-means based post-processing method were successfully tested on the monocular and binocular video-ophthalmoscopic (VO) recordings of optic nerve head (ONH) in healthy subjects. BSSs automatically detected three spatially distinct reproducible areas, i.e. SVP, optic cup pulsations (OCP) that included areas of larger vessels in the nasal part of ONH, and “other” pulsations (OP). The K-means post-processing reduced a spike noise from the patterns’ dynamics while high linear dependence between the non-filtered and post-processed signals was preserved. Although the dynamics of all patterns were heart rate related, the morphology analysis demonstrated significant phase shifts between SVP and OCP, and between SVP and OP. In addition, we detected low frequency oscillations that may represent respiratory-induced effects in time-courses of the VO recordings.

Lecture notes in computational vision and biomechanics, 2015

The retinal nerve fiber layer (RNFL) is one of the most affected retinal structures due to the gl... more 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 the RNFL 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 rather expensive and still not widely available. On the other hand, fundus camera is considered as a common and fundamental diagnostic device utilized at many ophthalmic facilities worldwide. This contribution presents a novel approach to texture analysis enabling assessment of the RNFL thickness in widely used colour fundus photographs. The aim is to propose a regression model based on different texture features effective for description of changes in the RNFL textural appearance related to the variations of RNFL thickness. The performance evaluation uses OCT as a gold standard modality for validation of the proposed approach. The results show high correlation between the models predicted output and RNFL thickness directly measured by OCT. J. Odstrcilik ( ) • R.

Comprehensive automatic processing and analysis of adaptive optics flood illumination retinal images on healthy subjects

Biomedical Optics Express, Jan 30, 2023

This work presents a novel fully automated method for retinal analysis in images acquired with a ... more 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 combination of phase correlation and the scale-invariant feature transform method. A set of 200 AO-FIO images from 10 healthy subjects (10 images from left eye and 10 images from right eye) is processed into 20 montage images and mutually aligned according to the automatically detected fovea center. As a second step, the photoreceptors in the montage images are detected using a method based on regional maxima localization, where the detector parameters were determined with Bayesian optimization according to manually labeled photoreceptors by three evaluators. The detection assessment, based on Dice coefficient, ranges from 0.72 to 0.8. In the next step, the corresponding density maps are generated for each of the montage images. As a final step, representative averaged photoreceptor density maps are created for the left and right eye and thus enabling comprehensive analysis across the montage images and a straightforward comparison with available histological data and other published studies. Our proposed method and software thus enable us to generate AO-based photoreceptor density maps for all measured locations fully automatically, and thus it is suitable for large studies, as those are in pressing need for automated approaches. In addition, the application MATADOR (MATlab ADaptive Optics Retinal Image Analysis) that implements the described pipeline and the dataset with photoreceptor labels are made publicly available.

Estimation of Time Delay Between Artery and Vein Pulsation using Experimental Video-Ophthalmoscope

The fundus observation by ophthalmoscope is a non-invasive approach for diagnosis of various reti... more 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 and the artery region. Data acquired by an experimental video-ophthalmoscope from five subjects with no eye diseases are analyzed. The analysis is based on the selection of artery and vein regions of interest and computation of averaged brightness within these regions for each frame. These extracted signals are filtered, interpolated and the trend is eliminated. Finally, the delays between artery and vein pulsation signals are determined using phase spectra. The measured delays are in the range of 15 to 95 ms, which is comparable with other published results.

Automatic Detection of Spontaneous Venous Pulsations Using Retinal Image Sequences

Lecture notes in computational vision and biomechanics, Oct 13, 2017

This paper proposes a method of automated detection and parameterization of spontaneous venous pu... more 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 detect glaucoma via detection of spontaneous venous pulsation.

Classification-based blood vessel segmentation in retinal images

Robust Automatic Montaging of Adaptive Optics Flood Illumination Retinal Images

Springer eBooks, 2021

Development of a binocular video-ophthalmoscope to compare parameters of heart beat induced blood volume changes between both eyes

Investigative Ophthalmology & Visual Science, Jul 13, 2018

bioRxiv (Cold Spring Harbor Laboratory), Aug 6, 2021

Cell viscoelastic properties are affected by the cell cycle, differentiation, pathological proces... more 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 mechanophenotypisation are limited by low robustness or the need for highly expert operation. In this paper, the system and method for viscoelasticity measurement using shear stress induction by fluid flow is described and tested. Quantitative Phase Imaging (QPI) is used for image acquisition because this technique enables to quantify optical path length delays introduced by the sample, thus providing a label-free objective measure of morphology and dynamics. Viscosity and elasticity determination were refined using a new approach based on the linear system model and parametric deconvolution. The proposed method allows high-throughput measurements during live cell experiments and even through a time-lapse, where we demonstrated the possibility of simultaneous extraction of shear modulus, viscosity, cell morphology, and QPI-derived cell parameters like circularity or cell mass. Additionally, the proposed method provides a simple approach to measure cell refractive index with the same setup, which is required for reliable cell height measurement with QPI, an essential parameter for viscoelasticity calculation. Reliability of the proposed viscoelasticity measurement system was tested in several experiments including cell types of different Young/shear modulus and treatment with cytochalasin D or docetaxel, and an agreement with atomic force microscopy was observed. The applicability of the proposed approach was also confirmed by a time-lapse experiment with cytochalasin D washout, where an increase of stiffness corresponded to actin repolymerisation in time. SIGNIFICANCE We present an approach for viscoelasticity measurement using QPI and shear stress induction by fluid flow. Our system builds and extends a recently published approach by parametric deconvolution, which allows us to eliminate the influence of the fluidic system and reliably measure both the shear modulus and viscosity of the cells in high throughput. Additionally, the proposed method enables to simultaneously determine cell refractive index map, cell dry mass map, and morphology, thereby enabling a multimodal cellular characterisation in a single measurement.

Cell Segmentation in Quantitative Phase Images with Improved Iterative Thresholding Method

Springer eBooks, Nov 30, 2020

Binocular video ophthalmoscope for simultaneous recording of sequences of the human retina to compare dynamic parameters

Proceedings of SPIE, Jul 28, 2017

A parallel video ophthalmoscope was developed to acquire short video sequences (25 fps, 250 frame... more A parallel video ophthalmoscope was developed to acquire short video sequences (25 fps, 250 frames) of both eyes simultaneously with exact synchronization. Video sequences were registered off-line to compensate for eye movements. From registered video sequences dynamic parameters like cardiac cycle induced reflection changes and eye movements can be calculated and compared between eyes.

Blind Source Separation of Different Retinal Pulsatile Patterns from Simultaneous Long-term Binocular Ophthalmoscopic Video-records

2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

Optical imaging of retinal hemodynamic function is an important part of ophthalmologic research. ... more 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 Independent Component Analysis – sICA) in application of an automatic detection and segmentation of a distinct Optic Disc (OD) areas with different hemodynamic properties from a simultaneous binocular video-ophthalmoscopic records. Both methods detected 3 different spatial patterns mostly symmetric over both eyes stable and reproducible over investigated participants, i.e. central Spontaneous Vessel Pulsations (SVPs), inner OD intensity pulsations and other OD pulsations. Dynamics of all mentioned patterns has a periodic character with similar main frequency (possibly corresponding to subject-specific heart rate) but shifted phase decreasing patterns’ mutual high cross-correlations. The sICA estimates a higher rate of phase shifts than sPCA.

Multispectral retinal video‐ophthalmoscope with fiber optic illumination

Journal of Biophotonics

Retinal pulsatile shift enhancement with blind source separation

Investigative Ophthalmology & Visual Science, Jul 22, 2019

Robust Automatic Montaging of Adaptive Optics Flood Illumination Retinal Images

Medical Image Understanding and Analysis, 2021

Comparison and practical review of segmentation approaches for label-free microscopy

This dataset contains microscopic images of PNT1A cell line captured by multiple microcopic witho... more This dataset contains microscopic images of PNT1A cell line captured by multiple microcopic without use of any labeling and a manually annotated ground truth for subsequent use in segmentation algorithms. Dataset also includes images reconstructed according to the methods described below in order to ease further segmentation. See Vicar et al. Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison. BMC Bioinformatics (2019) 20:360. DOI 10.1186/s12859-019-2880-8 Code using this dataset is available at https://github.com/tomasvicar/Cell-segmentation-methods-comparison <strong>Materials and methods </strong> Cells were cultured in RPMI-1640 medium supplemented with antibiotics (penicillin 100 U/ml and streptomycin 0.1 mg/ml) with 10% fetal bovine serum. Prior microscopy acquisition, cells were maintained at 37 cenigrade in a humidified incubator with 5% CO2. Intentionally, high passage number of cells was used (>30) in order to d...

Cell Segmentation in Quantitative Phase Images with Improved Iterative Thresholding Method

8th European Medical and Biological Engineering Conference, 2020

Eye movement analysis using a binocular video-ophthalmoscope

2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2019

This paper describes an application of binocular video-ophthalmoscope for binocular eye movement ... more 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 movements are higher for binocular fixation with respect to monocular fixation. We also present different examples of eye movement visualization.