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Yang E, Shankar K, Kumar S, Seo C, Moon I. Equilibrium Optimization Algorithm with Deep Learning Enabled Prostate Cancer Detection on MRI Images. Biomedicines 2023; 11:3200. [PMID: 38137421 PMCID: PMC10740673 DOI: 10.3390/biomedicines11123200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
The enlargement of the prostate gland in the reproductive system of males is considered a form of prostate cancer (PrC). The survival rate is considerably improved with earlier diagnosis of cancer; thus, timely intervention should be administered. In this study, a new automatic approach combining several deep learning (DL) techniques was introduced to detect PrC from MRI and ultrasound (US) images. Furthermore, the presented method describes why a certain decision was made given the input MRI or US images. Many pretrained custom-developed layers were added to the pretrained model and employed in the dataset. The study presents an Equilibrium Optimization Algorithm with Deep Learning-based Prostate Cancer Detection and Classification (EOADL-PCDC) technique on MRIs. The main goal of the EOADL-PCDC method lies in the detection and classification of PrC. To achieve this, the EOADL-PCDC technique applies image preprocessing to improve the image quality. In addition, the EOADL-PCDC technique follows the CapsNet (capsule network) model for the feature extraction model. The EOA is based on hyperparameter tuning used to increase the efficiency of CapsNet. The EOADL-PCDC algorithm makes use of the stacked bidirectional long short-term memory (SBiLSTM) model for prostate cancer classification. A comprehensive set of simulations of the EOADL-PCDC algorithm was tested on the benchmark MRI dataset. The experimental outcome revealed the superior performance of the EOADL-PCDC approach over existing methods in terms of different metrics.
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Jaferzadeh K, Rappaz B, Kim Y, Kim BK, Moon I, Marquet P, Turcatti G. Automated Dual-Mode Cell Monitoring To Simultaneously Explore Calcium Dynamics and Contraction-Relaxation Kinetics within Drug-Treated Stem Cell-Derived Cardiomyocytes. ACS Sens 2023. [PMID: 37335579 DOI: 10.1021/acssensors.3c00073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
This manuscript proposes a new dual-mode cell imaging system for studying the relationships between calcium dynamics and the contractility process of cardiomyocytes derived from human-induced pluripotent stem cells. Practically, this dual-mode cell imaging system provides simultaneously both live cell calcium imaging and quantitative phase imaging based on digital holographic microscopy. Specifically, thanks to the development of a robust automated image analysis, simultaneous measurements of both intracellular calcium, a key player of excitation-contraction coupling, and the quantitative phase image-derived dry mass redistribution, reflecting the effective contractility, namely, the contraction and relaxation processes, were achieved. Practically, the relationships between calcium dynamics and the contraction-relaxation kinetics were investigated in particular through the application of two drugs─namely, isoprenaline and E-4031─known to act precisely on calcium dynamics. Specifically, this new dual-mode cell imaging system enabled us to establish that calcium regulation can be divided into two phases, an early phase influencing the occurrence of the relaxation process followed by a late phase, which although not having a significant influence on the relaxation process affects significantly the beat frequency. In combination with cutting-edge technologies allowing the generation of human stem cell-derived cardiomyocytes, this dual-mode cell monitoring approach therefore represents a very promising technique, particularly in the fields of drug discovery and personalized medicine, to identify compounds likely to act more selectively on specific steps that compose the cardiomyocyte contractility.
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Ahamadzadeh E, Jaferzadeh K, Park S, Son S, Moon I. Automated analysis of human cardiomyocytes dynamics with holographic image-based tracking for cardiotoxicity screening. Biosens Bioelectron 2022; 195:113570. [PMID: 34455143 DOI: 10.1016/j.bios.2021.113570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 07/19/2021] [Accepted: 08/14/2021] [Indexed: 11/02/2022]
Abstract
This paper proposes a new non-invasive, low-cost, and fully automated platform to quantitatively analyze dynamics of human-induced pluripotent stem cell-derived cardiomyocytes (hiPS-CMs) at the single-cell level by holographic image-based tracking for cardiotoxicity screening. A dense Farneback optical flow method and holographic imaging informatics were combined to characterize the contractile motion of a single CM, which obviates the need for costly equipment to monitor a CM's mechanical beat activity. The reliability of the proposed platform was tested by single-cell motion characterization, synchronization analysis, motion speed measurement of fixed CMs versus live CMs, and noise sensitivity. The applicability of the motion characterization method was tested to determine the pharmacological effects of two cardiovascular drugs, isoprenaline (166 nM) and E-4031 (500 μM). The experiments were done using single CMs and multiple cells, and the results were compared to control conditions. Cardiomyocytes responded to isoprenaline by increasing the action potential (AP) speed and shortening the resting period, thus increasing the beat frequency. In the presence of E-4031, the AP speed was decreased, and the resting period was prolonged, thus decreasing the beat frequency. The findings offer insights into single hiPS-CMs' contractile motion and a deep understanding of their kinetics at the single-cell level for cardiotoxicity screening.
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Park S, Kim Y, Moon I. Automated phase unwrapping in digital holography with deep learning. BIOMEDICAL OPTICS EXPRESS 2021; 12:7064-7081. [PMID: 34858700 PMCID: PMC8606148 DOI: 10.1364/boe.440338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/08/2021] [Accepted: 10/14/2021] [Indexed: 05/28/2023]
Abstract
Digital holography can provide quantitative phase images related to the morphology and content of biological samples. After the numerical image reconstruction, the phase values are limited between -π and π; thus, discontinuity may occur due to the modulo 2π operation. We propose a new deep learning model that can automatically reconstruct unwrapped focused-phase images by combining digital holography and a Pix2Pix generative adversarial network (GAN) for image-to-image translation. Compared with numerical phase unwrapping methods, the proposed GAN model overcomes the difficulty of accurate phase unwrapping due to abrupt phase changes and can perform phase unwrapping at a twice faster rate. We show that the proposed model can generalize well to different types of cell images and has high performance compared to recent U-net models. The proposed method can be useful in observing the morphology and movement of biological cells in real-time applications.
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Kim E, Park S, Hwang S, Moon I, Javidi B. Deep Learning-based Phenotypic Assessment of Red Cell Storage Lesions for Safe Transfusions. IEEE J Biomed Health Inform 2021; 26:1318-1328. [PMID: 34388103 DOI: 10.1109/jbhi.2021.3104650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This study presents a novel approach to automatically perform instant phenotypic assessment of red blood cell (RBC) storage lesion in phase images obtained by digital holographic microscopy. The proposed model combines a generative adversarial network (GAN) with marker-controlled watershed segmentation scheme. The GAN model performed RBC segmentations and classifications to develop ageing markers, and the watershed segmentation was used to completely separate overlapping RBCs. Our approach achieved good segmentation and classification accuracy with a Dices coefficient of 0.94 at a high throughput rate of about 152 cells per second. These results were compared with other deep neural network architectures. Moreover, our image-based deep learning models recognized the morphological changes that occur in RBCs during storage. Our deep learning-based classification results were in good agreement with previous findings on the changes in RBC markers (dominant shapes) affected by storage duration. We believe that our image-based deep learning models can be useful for automated assessment of RBC quality, storage lesions for safe transfusions, and diagnosis of RBC-related diseases.
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Yi F, Park S, Moon I. High-throughput label-free cell detection and counting from diffraction patterns with deep fully convolutional neural networks. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-200328R. [PMID: 33686845 PMCID: PMC7939515 DOI: 10.1117/1.jbo.26.3.036001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
SIGNIFICANCE Digital holographic microscopy (DHM) is a promising technique for the study of semitransparent biological specimen such as red blood cells (RBCs). It is important and meaningful to detect and count biological cells at the single cell level in biomedical images for biomarker discovery and disease diagnostics. However, the biological cell analysis based on phase information of images is inefficient due to the complexity of numerical phase reconstruction algorithm applied to raw hologram images. New cell study methods based on diffraction pattern directly are desirable. AIM Deep fully convolutional networks (FCNs) were developed on raw hologram images directly for high-throughput label-free cell detection and counting to assist the biological cell analysis in the future. APPROACH The raw diffraction patterns of RBCs were recorded by use of DHM. Ground-truth mask images were labeled based on phase images reconstructed from RBC holograms using numerical reconstruction algorithm. A deep FCN, which is UNet, was trained on the diffraction pattern images to achieve the label-free cell detection and counting. RESULTS The implemented deep FCNs provide a promising way to high-throughput and label-free counting of RBCs with a counting accuracy of 99% at a throughput rate of greater than 288 cells per second and 200 μm × 200 μm field of view at the single cell level. Compared to convolutional neural networks, the FCNs can get much better results in terms of accuracy and throughput rate. CONCLUSIONS High-throughput label-free cell detection and counting were successfully achieved from diffraction patterns with deep FCNs. It is a promising approach for biological specimen analysis based on raw hologram directly.
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Moon I, Jaferzadeh K, Kim Y, Javidi B. Noise-free quantitative phase imaging in Gabor holography with conditional generative adversarial network. OPTICS EXPRESS 2020; 28:26284-26301. [PMID: 32906903 DOI: 10.1364/oe.398528] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
This paper shows that deep learning can eliminate the superimposed twin-image noise in phase images of Gabor holographic setup. This is achieved by the conditional generative adversarial model (C-GAN), trained by input-output pairs of noisy phase images obtained from synthetic Gabor holography and the corresponding quantitative noise-free contrast-phase image obtained by the off-axis digital holography. To train the model, Gabor holograms are generated from digital off-axis holograms with spatial shifting of the real image and twin image in the frequency domain and then adding them with the DC term in the spatial domain. Finally, the digital propagation of the Gabor hologram with Fresnel approximation generates a super-imposed phase image for the C-GAN model input. Two models were trained: a human red blood cell model and an elliptical cancer cell model. Following the training, several quantitative analyses were conducted on the bio-chemical properties and similarity between actual noise-free phase images and the model output. Surprisingly, it is discovered that our model can recover other elliptical cell lines that were not observed during the training. Additionally, some misalignments can also be compensated with the trained model. Particularly, if the reconstruction distance is somewhat incorrect, this model can still retrieve in-focus images.
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Ahmadzadeh E, Jaferzadeh K, Shin S, Moon I. Automated single cardiomyocyte characterization by nucleus extraction from dynamic holographic images using a fully convolutional neural network. BIOMEDICAL OPTICS EXPRESS 2020; 11:1501-1516. [PMID: 32206425 PMCID: PMC7075611 DOI: 10.1364/boe.385218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 05/06/2023]
Abstract
Human-induced pluripotent stem cell-derived cardiomyocytes (hiPS-CMs) beating can be efficiently characterized by time-lapse quantitative phase imaging (QPIs) obtained by digital holographic microscopy. Particularly, the CM's nucleus section can precisely reflect the associated rhythmic beating pattern of the CM suitable for subsequent beating pattern characterization. In this paper, we describe an automated method to characterize single CMs by nucleus extraction from QPIs and subsequent beating pattern reconstruction and quantification. However, accurate CM's nucleus extraction from the QPIs is a challenging task due to the variations in shape, size, orientation, and lack of special geometry. To this end, we propose a novel fully convolutional neural network (FCN)-based network architecture for accurate CM's nucleus extraction using pixel classification technique and subsequent beating pattern characterization. Our experimental results show that the beating profile of multiple extracted single CMs is less noisy and more informative compared to the whole image slide. Applying this method allows CM characterization at the single-cell level. Consequently, several single CMs are extracted from the whole slide QPIs and multiple parameters regarding their beating profile of each isolated CM are efficiently measured.
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Moon I, Lee SP, Kim MK, Park JB, Kim HK, Kim YJ, Sohn DW. P1274 Early surgery versus watchful waiting in patients with moderate aortic stenosis and left ventricular systolic dysfunction. Eur Heart J Cardiovasc Imaging 2020. [DOI: 10.1093/ehjci/jez319.724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Aortic stenosis (AS) induces significant pressure overload to the left ventricle (LV) and its burden may increase if there is concomitant LV systolic dysfunction. Severe AS with LV systolic dysfunction is a class I indication for aortic valve replacement (AVR) irrespective of symptoms, however, this recommendation is not well established in those with moderate AS and LV systolic dysfunction. In this study, we sought to investigate the clinical impact of surgical AVR among patients with moderate AS and LV systolic dysfunction.
Methods
From 2001 to 2017, we retrospectively but consecutively identified patients with moderate AS and LV systolic dysfunction from a single tertiary hospital. Moderate AS was defined as aortic valve area between 1.0 and 1.5cm2 and LV systolic dysfunction as LV ejection fraction less than 50%. The primary outcome was all-cause death and we additionally analyzed cardiac death as a secondary endpoint. The outcomes were compared between those who underwent early surgical AVR at the stage of moderate AS versus those who were followed without AVR at the outpatient clinic.
Results
Among a total of 257 patients with moderate AS and concomitant LV systolic dysfunction (70.0 ± 11.3 years, 63.4% of male), 34 patients received early AVR. Patients in the AVR group was younger than the observation group (64.2 ± 8.1 vs. 70.9 ± 11.5, respectively), and had a lower prevalence of hypertension and chronic kidney disease. During a mean of 3-year follow up, 112 patients (47.5%) died and the overall death rate was 15.367 per 100 person-year (PY). The AVR group showed a significantly lower rate of all-cause death than the observation group (5.241PY vs. 18.160PY, p-value = 0.002). After multivariable Cox proportional hazard regression adjusting for age, sex, comorbidities and laboratory data, early AVR at the stage of moderate AS significantly reduced the risk of all-cause death (hazard ratio [HR] 0.340, 95% confidence interval [CI] 0.117 - 0.985, p-value = 0.047). However, there was no risk reduction of cardiac death (HR 0.578 95% CI 0.150 - 2.231, p-value = 0.426).
Conclusions
In patients with moderate AS and LV systolic dysfunction, AVR reduces the risk of all-cause death. A prospective design study is warranted to confirm our findings in the near future.
Abstract P1274 Figure. Kaplan-Meier curves for deaths
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Park JB, Park CS, Choi YJ, Kwak S, Moon I, Hwang IC, Park JJ, Lee SP, Park JH, Cho GY. P785 Left ventricular geometry and myocardial contractility modulate impact of statins on prognosis in patients with acute heart failure. Eur Heart J Cardiovasc Imaging 2020. [DOI: 10.1093/ehjci/jez319.444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Funding Acknowledgements
N/A
Background/Introduction: The benefit of statins in patients with heart failure (HF) remains controversial and the mechanism of action is largely speculative. We investigated whether survival benefit with statins differs according to left ventricular (LV) geometry and myocardial contractility in acute HF patients.
Methods
We enrolled 1792 acute HF patients receiving statins and 2296 patients not receiving statins admitted from 2009 to 2016. The LV and right ventricular (RV) global longitudinal strain (GLS) was assessed as a measure of myocardial contractility. Patients were classified into 2 groups based on ischemic etiology of HF and further divided into 4 subgroups according to the median values of LV-GLS or RV-GLS. The primary outcome was 5-year all-cause mortality. The study protocol was approved by the ethics committee at each institute and complied with the Declaration of Helsinki. The need for written informed consent was waived.
Results
During the 5-year follow-up, 1740 (40.4%) patients died and they had more unfavorable baseline characteristics. Statin therapy was significantly associated with improved survival in overall patients and in both groups with and without ischemic etiology (all p <0.001). Patients with concentric remodeling/hypertrophy and eccentric hypertrophy demonstrated survival benefit with statin therapy (P = 0.033, 0.004, and 0.008, respectively), while those with normal geometry did not (p = 0.123). In the non-ischemic HF group, survival benefit with statin therapy was confined to patients with low LV-GLS (p = 0.045) or those with low RV-GLS p = 0.003). On the contrary, in ischemic HF group, survival benefit with statin therapy was observed in all patients regardless of the values of LV-GLS or RV-GLS. Significant interactions were present between statin use and diabetes mellitus and IHD (p for interaction = 0.027 and 0.003, respectively) regarding mortality.
Conclusions
LV geometry and myocardial contractility may modulate the effects of statins in patients with acute HF. These echocardiographic measures can provide prognostic information to guide tailored statin treatment in this population. Our findings may also help to develop more well-designed prospective studies, in terms of a more homogenous study population, to confirm survival benefit with statin therapy.
Abstract P785 Figure. Multivariate Cox survival curves
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Kim Y, Sim M, Moon I. Secure storage and retrieval schemes for multiple encrypted digital holograms with orthogonal phase encoding multiplexing. OPTICS EXPRESS 2019; 27:22147-22160. [PMID: 31510508 DOI: 10.1364/oe.27.022147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Recent developments in 3D computational optical imaging such as digital holographic microscopy has ushered in a new era for biological research. Therefore, efficient and secure storage and retrieval of digital holograms is a challenging task for future cloud computing services. In this study, we propose a novel scheme to securely store and retrieve multiple encrypted digital holograms by using phase encoding multiplexing. In the proposed schemes, an encrypted hologram can only be accessed using a binary phase mask, which is the key to retrieve the image. In addition, it is possible to independently store, retrieve, and manage the encrypted digital holograms without affecting other groups of the encrypted holograms multiplexed using different sets of binary phase masks, due to the orthogonality properties of the Hadamard matrices with high autocorrelation and low cross-correlation. The desired encrypted holograms may also be searched for, removed, and added independently of other groups of the encrypted holograms. More and more 3D images or digital holograms can be securely and efficiently stored, retrieved, and managed.
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Jaferzadeh K, Hwang SH, Moon I, Javidi B. No-search focus prediction at the single cell level in digital holographic imaging with deep convolutional neural network. BIOMEDICAL OPTICS EXPRESS 2019; 10:4276-4289. [PMID: 31453010 PMCID: PMC6701551 DOI: 10.1364/boe.10.004276] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/11/2019] [Accepted: 07/23/2019] [Indexed: 05/05/2023]
Abstract
Digital propagation of an off-axis hologram can provide the quantitative phase-contrast image if the exact distance between the sensor plane (such as CCD) and the reconstruction plane is correctly provided. In this paper, we present a deep-learning convolutional neural network with a regression layer as the top layer to estimate the best reconstruction distance. The experimental results obtained using microsphere beads and red blood cells show that the proposed method can accurately predict the propagation distance from a filtered hologram. The result is compared with the conventional automatic focus-evaluation function. Additionally, our approach can be utilized at the single-cell level, which is useful for cell-to-cell depth measurement and cell adherent studies.
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Kim S, Kim H, Moon I, Kim M. Inter-Arm And Inter-Leg Blood Pressure Differences And Cardiovascular Outcomes In Patients After Percutaneous Coronary Intervention. Atherosclerosis 2019. [DOI: 10.1016/j.atherosclerosis.2019.06.468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Moon I, Jaferzadeh K, Ahmadzadeh E, Javidi B. Automated quantitative analysis of multiple cardiomyocytes at the single-cell level with three-dimensional holographic imaging informatics. JOURNAL OF BIOPHOTONICS 2018; 11:e201800116. [PMID: 30027630 DOI: 10.1002/jbio.201800116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/18/2018] [Indexed: 05/21/2023]
Abstract
Cardiomyocytes derived from human pluripotent stem cells are a promising tool for disease modeling, drug compound testing, and cardiac toxicity screening. Bio-image segmentation is a prerequisite step in cardiomyocyte image analysis by digital holography (DH) in microscopic configuration and has provided satisfactory results. In this study, we quantified multiple cardiac cells from segmented 3-dimensional DH images at the single-cell level and measured multiple parameters describing the beating profile of each individual cell. The beating profile is extracted by monitoring dry-mass distribution during the mechanical contraction-relaxation activity caused by cardiac action potential. We present a robust two-step segmentation method for cardiomyocyte low-contrast image segmentation based on region and edge information. The segmented single-cell contains mostly the nucleus of the cell since it is the best part of the cardiac cell, which can be perfectly segmented. Clustering accuracy was assessed by a silhouette index evaluation for k-means clustering and the Dice similarity coefficient (DSC) of the final segmented image. 3D representation of single of cardiomyocytes. The cell contains mostly the nucleus section and a small area of cytoplasm.
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Jaferzadeh K, Moon I, Bardyn M, Prudent M, Tissot JD, Rappaz B, Javidi B, Turcatti G, Marquet P. Quantification of stored red blood cell fluctuations by time-lapse holographic cell imaging. BIOMEDICAL OPTICS EXPRESS 2018; 9:4714-4729. [PMID: 30319898 PMCID: PMC6179419 DOI: 10.1364/boe.9.004714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 05/03/2023]
Abstract
We propose methods to quantitatively calculate the fluctuation rate of red blood cells with nanometric axial and millisecond temporal sensitivity at the single-cell level by using time-lapse holographic cell imaging. For this quantitative analysis, cell membrane fluctuations (CMFs) were measured for RBCs stored at different storage times. Measurements were taken over the whole membrane for both the ring and dimple sections separately. The measurements show that healthy RBCs that maintain their discocyte shape become stiffer with storage time. The correlation analysis demonstrates a significant negative correlation between CMFs and the sphericity coefficient, which characterizes the morphological type of erythrocyte. In addition, we show the correlation results between CMFs and other morphological properties such as projected surface area, surface area, mean corpuscular volume, and mean corpuscular hemoglobin.
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Lata AA, Moon I, Kwon GR. P3‐345: MRI BRAIN IMAGE ENHANCEMENT USING CONTOURLET TRANSFORM ALONG WITH AN ENHANCEMENT FUNCTION. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.1706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Yi F, Moon I, Javidi B. Automated red blood cells extraction from holographic images using fully convolutional neural networks. BIOMEDICAL OPTICS EXPRESS 2017; 8:4466-4479. [PMID: 29082078 PMCID: PMC5654793 DOI: 10.1364/boe.8.004466] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/07/2017] [Accepted: 08/23/2017] [Indexed: 05/22/2023]
Abstract
In this paper, we present two models for automatically extracting red blood cells (RBCs) from RBCs holographic images based on a deep learning fully convolutional neural network (FCN) algorithm. The first model, called FCN-1, only uses the FCN algorithm to carry out RBCs prediction, whereas the second model, called FCN-2, combines the FCN approach with the marker-controlled watershed transform segmentation scheme to achieve RBCs extraction. Both models achieve good segmentation accuracy. In addition, the second model has much better performance in terms of cell separation than traditional segmentation methods. In the proposed methods, the RBCs phase images are first numerically reconstructed from RBCs holograms recorded with off-axis digital holographic microscopy. Then, some RBCs phase images are manually segmented and used as training data to fine-tune the FCN. Finally, each pixel in new input RBCs phase images is predicted into either foreground or background using the trained FCN models. The RBCs prediction result from the first model is the final segmentation result, whereas the result from the second model is used as the internal markers of the marker-controlled transform algorithm for further segmentation. Experimental results show that the given schemes can automatically extract RBCs from RBCs phase images and much better RBCs separation results are obtained when the FCN technique is combined with the marker-controlled watershed segmentation algorithm.
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Ahmadzadeh E, Jaferzadeh K, Lee J, Moon I. Automated three-dimensional morphology-based clustering of human erythrocytes with regular shapes: stomatocytes, discocytes, and echinocytes. JOURNAL OF BIOMEDICAL OPTICS 2017; 22:76015. [PMID: 28742920 DOI: 10.1117/1.jbo.22.7.076015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/05/2017] [Indexed: 05/08/2023]
Abstract
We present unsupervised clustering methods for automatic grouping of human red blood cells (RBCs) extracted from RBC quantitative phase images obtained by digital holographic microscopy into three RBC clusters with regular shapes, including biconcave, stomatocyte, and sphero-echinocyte. We select some good features related to the RBC profile and morphology, such as RBC average thickness, sphericity coefficient, and mean corpuscular volume, and clustering methods, including density-based spatial clustering applications with noise, k-medoids, and k-means, are applied to the set of morphological features. The clustering results of RBCs using a set of three-dimensional features are compared against a set of two-dimensional features. Our experimental results indicate that by utilizing the introduced set of features, two groups of biconcave RBCs and old RBCs (suffering from the sphero-echinocyte process) can be perfectly clustered. In addition, by increasing the number of clusters, the three RBC types can be effectively clustered in an automated unsupervised manner with high accuracy. The performance evaluation of the clustering techniques reveals that they can assist hematologists in further diagnosis.
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Yi F, Jeoung Y, Moon I. Three-dimensional image authentication scheme using sparse phase information in double random phase encoded integral imaging. APPLIED OPTICS 2017; 56:4381-4387. [PMID: 29047866 DOI: 10.1364/ao.56.004381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In recent years, many studies have focused on authentication of two-dimensional (2D) images using double random phase encryption techniques. However, there has been little research on three-dimensional (3D) imaging systems, such as integral imaging, for 3D image authentication. We propose a 3D image authentication scheme based on a double random phase integral imaging method. All of the 2D elemental images captured through integral imaging are encrypted with a double random phase encoding algorithm and only partial phase information is reserved. All the amplitude and other miscellaneous phase information in the encrypted elemental images is discarded. Nevertheless, we demonstrate that 3D images from integral imaging can be authenticated at different depths using a nonlinear correlation method. The proposed 3D image authentication algorithm can provide enhanced information security because the decrypted 2D elemental images from the sparse phase cannot be easily observed by the naked eye. Additionally, using sparse phase images without any amplitude information can greatly reduce data storage costs and aid in image compression and data transmission.
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Jaferzadeh K, Gholami S, Moon I. Lossless and lossy compression of quantitative phase images of red blood cells obtained by digital holographic imaging. APPLIED OPTICS 2016; 55:10409-10416. [PMID: 28059271 DOI: 10.1364/ao.55.010409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this paper, we evaluate lossless and lossy compression techniques to compress quantitative phase images of red blood cells (RBCs) obtained by an off-axis digital holographic microscopy (DHM). The RBC phase images are numerically reconstructed from their digital holograms and are stored in 16-bit unsigned integer format. In the case of lossless compression, predictive coding of JPEG lossless (JPEG-LS), JPEG2000, and JP3D are evaluated, and compression ratio (CR) and complexity (compression time) are compared against each other. It turns out that JP2k can outperform other methods by having the best CR. In the lossy case, JP2k and JP3D with different CRs are examined. Because some data is lost in a lossy way, the degradation level is measured by comparing different morphological and biochemical parameters of RBC before and after compression. Morphological parameters are volume, surface area, RBC diameter, sphericity index, and the biochemical cell parameter is mean corpuscular hemoglobin (MCH). Experimental results show that JP2k outperforms JP3D not only in terms of mean square error (MSE) when CR increases, but also in compression time in the lossy compression way. In addition, our compression results with both algorithms demonstrate that with high CR values the three-dimensional profile of RBC can be preserved and morphological and biochemical parameters can still be within the range of reported values.
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Jaferzadeh K, Moon I. Human red blood cell recognition enhancement with three-dimensional morphological features obtained by digital holographic imaging. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:126015. [PMID: 28006044 DOI: 10.1117/1.jbo.21.12.126015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/28/2016] [Indexed: 05/20/2023]
Abstract
The classification of erythrocytes plays an important role in the field of hematological diagnosis, specifically blood disorders. Since the biconcave shape of red blood cell (RBC) is altered during the different stages of hematological disorders, we believe that the three-dimensional (3-D) morphological features of erythrocyte provide better classification results than conventional two-dimensional (2-D) features. Therefore, we introduce a set of 3-D features related to the morphological and chemical properties of RBC profile and try to evaluate the discrimination power of these features against 2-D features with a neural network classifier. The 3-D features include erythrocyte surface area, volume, average cell thickness, sphericity index, sphericity coefficient and functionality factor, MCH and MCHSD, and two newly introduced features extracted from the ring section of RBC at the single-cell level. In contrast, the 2-D features are RBC projected surface area, perimeter, radius, elongation, and projected surface area to perimeter ratio. All features are obtained from images visualized by off-axis digital holographic microscopy with a numerical reconstruction algorithm, and four categories of biconcave (doughnut shape), flat-disc, stomatocyte, and echinospherocyte RBCs are interested. Our experimental results demonstrate that the 3-D features can be more useful in RBC classification than the 2-D features. Finally, we choose the best feature set of the 2-D and 3-D features by sequential forward feature selection technique, which yields better discrimination results. We believe that the final feature set evaluated with a neural network classification strategy can improve the RBC classification accuracy.
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Yi F, Moon I, Javidi B. Cell morphology-based classification of red blood cells using holographic imaging informatics. BIOMEDICAL OPTICS EXPRESS 2016; 7:2385-99. [PMID: 27375953 PMCID: PMC4918591 DOI: 10.1364/boe.7.002385] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/22/2016] [Accepted: 05/23/2016] [Indexed: 05/23/2023]
Abstract
We present methods that automatically select a linear or nonlinear classifier for red blood cell (RBC) classification by analyzing the equality of the covariance matrices in Gabor-filtered holographic images. First, the phase images of the RBCs are numerically reconstructed from their holograms, which are recorded using off-axis digital holographic microscopy (DHM). Second, each RBC is segmented using a marker-controlled watershed transform algorithm and the inner part of the RBC is identified and analyzed. Third, the Gabor wavelet transform is applied to the segmented cells to extract a series of features, which then undergo a multivariate statistical test to evaluate the equality of the covariance matrices of the different shapes of the RBCs using selected features. When these covariance matrices are not equal, a nonlinear classification scheme based on quadratic functions is applied; otherwise, a linear classification is applied. We used the stomatocyte, discocyte, and echinocyte RBC for classifier training and testing. Simulation results demonstrated that 10 of the 14 RBC features are useful in RBC classification. Experimental results also revealed that the covariance matrices of the three main RBC groups are not equal and that a nonlinear classification method has a much lower misclassification rate. The proposed automated RBC classification method has the potential for use in drug testing and the diagnosis of RBC-related diseases.
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Moon I, Yi F, Han M, Lee J. Efficient asymmetric image authentication schemes based on photon counting-double random phase encoding and RSA algorithms. APPLIED OPTICS 2016; 55:4328-4335. [PMID: 27411183 DOI: 10.1364/ao.55.004328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Recently, double random phase encoding (DRPE) has been integrated with the photon counting (PC) imaging technique for the purpose of secure image authentication. In this scheme, the same key should be securely distributed and shared between the sender and receiver, but this is one of the most vexing problems of symmetric cryptosystems. In this study, we propose an efficient asymmetric image authentication scheme by combining the PC-DRPE and RSA algorithms, which solves key management and distribution problems. The retrieved image from the proposed authentication method contains photon-limited encrypted data obtained by means of PC-DRPE. Therefore, the original image can be protected while the retrieved image can be efficiently verified using a statistical nonlinear correlation approach. Experimental results demonstrate the feasibility of our proposed asymmetric image authentication method.
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Jaferzadeh K, Moon I, Gholami S. Enhancing fractal image compression speed using local features for reducing search space. Pattern Anal Appl 2016. [DOI: 10.1007/s10044-016-0551-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Moon I, Yi F, Rappaz B. Automated tracking of temporal displacements of a red blood cell obtained by time-lapse digital holographic microscopy. APPLIED OPTICS 2016; 55:A86-94. [PMID: 26835962 DOI: 10.1364/ao.55.000a86] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Red blood cell (RBC) phase images that are numerically reconstructed by digital holographic microscopy (DHM) can describe the cell structure and dynamics information beneficial for a quantitative analysis of RBCs. However, RBCs investigated with time-lapse DHM undergo temporal displacements when their membranes are loosely attached to the substrate during sedimentation on a glass surface or due to the microscope drift. Therefore, we need to develop a tracking algorithm to localize the same RBC among RBC image sequences and dynamically monitor its biophysical cell parameters; this information is helpful for studies on RBC-related diseases and drug tests. Here, we propose a method, which is a combination of the mean-shift algorithm and Kalman filter, to track a single RBC and demonstrate that the optical path length of the single RBC can be continually extracted from the tracked RBC. The Kalman filter is utilized to predict the target RBC position in the next frame. Then, the mean-shift algorithm starts execution from the predicted location, and a robust kernel, which is adaptive to changes in the RBC scale, shape, and direction, is designed to improve the accuracy of the tracking. Finally, the tracked RBC is segmented and parameters such as the RBC location are extracted to update the Kalman filter and the kernel function for mean-shift tracking; the characteristics of the target RBC are dynamically observed. Experimental results show the feasibility of the proposed algorithm.
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