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Isaksson LJ, Summers P, Mastroleo F, Marvaso G, Corrao G, Vincini MG, Zaffaroni M, Ceci F, Petralia G, Orecchia R, Jereczek-Fossa BA. Automatic Segmentation with Deep Learning in Radiotherapy. Cancers (Basel) 2023; 15:4389. [PMID: 37686665 PMCID: PMC10486603 DOI: 10.3390/cancers15174389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
This review provides a formal overview of current automatic segmentation studies that use deep learning in radiotherapy. It covers 807 published papers and includes multiple cancer sites, image types (CT/MRI/PET), and segmentation methods. We collect key statistics about the papers to uncover commonalities, trends, and methods, and identify areas where more research might be needed. Moreover, we analyzed the corpus by posing explicit questions aimed at providing high-quality and actionable insights, including: "What should researchers think about when starting a segmentation study?", "How can research practices in medical image segmentation be improved?", "What is missing from the current corpus?", and more. This allowed us to provide practical guidelines on how to conduct a good segmentation study in today's competitive environment that will be useful for future research within the field, regardless of the specific radiotherapeutic subfield. To aid in our analysis, we used the large language model ChatGPT to condense information.
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Affiliation(s)
- Lars Johannes Isaksson
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (L.J.I.); (F.M.); (G.C.); (M.G.V.); (M.Z.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (F.C.); (G.P.)
| | - Paul Summers
- Division of Radiology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Federico Mastroleo
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (L.J.I.); (F.M.); (G.C.); (M.G.V.); (M.Z.); (B.A.J.-F.)
- Department of Translational Medicine, University of Piemonte Orientale (UPO), 20188 Novara, Italy
| | - Giulia Marvaso
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (L.J.I.); (F.M.); (G.C.); (M.G.V.); (M.Z.); (B.A.J.-F.)
| | - Giulia Corrao
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (L.J.I.); (F.M.); (G.C.); (M.G.V.); (M.Z.); (B.A.J.-F.)
| | - Maria Giulia Vincini
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (L.J.I.); (F.M.); (G.C.); (M.G.V.); (M.Z.); (B.A.J.-F.)
| | - Mattia Zaffaroni
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (L.J.I.); (F.M.); (G.C.); (M.G.V.); (M.Z.); (B.A.J.-F.)
| | - Francesco Ceci
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (F.C.); (G.P.)
- Division of Nuclear Medicine, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Giuseppe Petralia
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (F.C.); (G.P.)
- Precision Imaging and Research Unit, Department of Medical Imaging and Radiation Sciences, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Roberto Orecchia
- Scientific Directorate, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Barbara Alicja Jereczek-Fossa
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (L.J.I.); (F.M.); (G.C.); (M.G.V.); (M.Z.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (F.C.); (G.P.)
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Akhmet M, Tleubergenova M, Zhamanshin A. Dynamics of Hopfield-Type Neural Networks with Modulo Periodic Unpredictable Synaptic Connections, Rates and Inputs. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1555. [PMID: 36359644 PMCID: PMC9689789 DOI: 10.3390/e24111555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
In this paper, we rigorously prove that unpredictable oscillations take place in the dynamics of Hopfield-type neural networks (HNNs) when synaptic connections, rates and external inputs are modulo periodic unpredictable. The synaptic connections, rates and inputs are synchronized to obtain the convergence of outputs on the compact subsets of the real axis. The existence, uniqueness, and exponential stability of such motions are discussed. The method of included intervals and the contraction mapping principle are applied to attain the theoretical results. In addition to the analysis, we have provided strong simulation arguments, considering that all the assumed conditions are satisfied. It is shown how a new parameter, degree of periodicity, affects the dynamics of the neural network.
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Affiliation(s)
- Marat Akhmet
- Department of Mathematics, Middle East Technical University, Ankara 06531, Turkey
| | - Madina Tleubergenova
- Department of Mathematics, Aktobe Regional University, Aktobe 030000, Kazakhstan
- Institute of Information and Computational Technologies CS MES RK, Almaty 050010, Kazakhstan
| | - Akylbek Zhamanshin
- Department of Mathematics, Middle East Technical University, Ankara 06531, Turkey
- Department of Mathematics, Aktobe Regional University, Aktobe 030000, Kazakhstan
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Artificial intelligence in gastrointestinal and hepatic imaging: past, present and future scopes. Clin Imaging 2022; 87:43-53. [DOI: 10.1016/j.clinimag.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 03/09/2022] [Accepted: 04/11/2022] [Indexed: 11/19/2022]
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Abstract
Computed tomography (CT) scans usually include some disadvantages due to the nature of the imaging procedure, and these handicaps prevent accurate abdomen segmentation. Discontinuous abdomen edges, bed section of CT, patient information, closeness between the edges of the abdomen and CT, poor contrast, and a narrow histogram can be regarded as the most important handicaps that occur in abdominal CT scans. Currently, one or more handicaps can arise and prevent technicians obtaining abdomen images through simple segmentation techniques. In other words, CT scans can include the bed section of CT, a patient's diagnostic information, low-quality abdomen edges, low-level contrast, and narrow histogram, all in one scan. These phenomena constitute a challenge, and an efficient pipeline that is unaffected by handicaps is required. In addition, analysis such as segmentation, feature selection, and classification has meaning for a real-time diagnosis system in cases where the abdomen section is directly used with a specific size. A statistical pipeline is designed in this study that is unaffected by the handicaps mentioned above. Intensity-based approaches, morphological processes, and histogram-based procedures are utilized to design an efficient structure. Performance evaluation is realized in experiments on 58 CT images (16 training, 16 test, and 26 validation) that include the abdomen and one or more disadvantage(s). The first part of the data (16 training images) is used to detect the pipeline's optimum parameters, while the second and third parts are utilized to evaluate and to confirm the segmentation performance. The segmentation results are presented as the means of six performance metrics. Thus, the proposed method achieves remarkable average rates for training/test/validation of 98.95/99.36/99.57% (jaccard), 99.47/99.67/99.79% (dice), 100/99.91/99.91% (sensitivity), 98.47/99.23/99.85% (specificity), 99.38/99.63/99.87% (classification accuracy), and 98.98/99.45/99.66% (precision). In summary, a statistical pipeline performing the task of abdomen segmentation is achieved that is not affected by the disadvantages, and the most detailed abdomen segmentation study is performed for the use before organ and tumor segmentation, feature extraction, and classification.
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Chaudhari A, Kulkarni J. Cerebral edema segmentation using textural feature. Biocybern Biomed Eng 2019. [DOI: 10.1016/j.bbe.2019.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Cai W, He B, Hu M, Zhang W, Xiao D, Yu H, Song Q, Xiang N, Yang J, He S, Huang Y, Huang W, Jia F, Fang C. A radiomics-based nomogram for the preoperative prediction of posthepatectomy liver failure in patients with hepatocellular carcinoma. Surg Oncol 2019; 28:78-85. [PMID: 30851917 DOI: 10.1016/j.suronc.2018.11.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/15/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To develop and validate a radiomics-based nomogram for the preoperative prediction of posthepatectomy liver failure (PHLF) in patients with hepatocellular carcinoma (HCC). METHODS One hundred twelve consecutive HCC patients who underwent hepatectomy were included in the study pool (training cohort: n = 80, validation cohort: n = 32), and another 13 patients were included in a pilot prospective analysis. A total of 713 radiomics features were extracted from portal-phase computed tomography (CT) images. A logistic regression was used to construct a radiomics score (Rad-score). Then a nomogram, including Rad-score and other risk factors, was built with a multivariate logistic regression model. The discrimination, calibration and clinical utility of nomogram were evaluated. RESULTS The Rad-score could predict PHLF with an AUC of 0.822 (95% CI, 0.726-0.917) in the training cohort and of 0.762 (95% CI, 0.576-0.948) in the validation cohort; however, the approach could not completely outmatch the existing methods (CP [Child-Pugh], MELD [Model of End Stage Liver Disease], ALBI [albumin-bilirubin]). The individual predictive nomogram that included the Rad-score, MELD and performance status (PS) showed better discrimination with an AUC of 0.864 (95% CI, 0.786-0.942), which was higher than the AUCs of the conventional methods (nomogram vs CP, MELD, and ALBI at P < 0.001, P < 0.005, and P < 0.005, respectively). In the validation cohort, the nomogram discrimination was also superior to those of the other three methods (AUC: 0.896; 95% CI, 0.774-1.000). The calibration curves showed good agreement in both cohorts, and the decision curve analysis of the entire cohort revealed that the nomogram was clinically useful. A pilot prospective analysis showed that the radiomics nomogram could predict PHLF with an AUC of 0.833 (95% CI, 0.591-1.000). CONCLUSIONS A nomogram based on the Rad-score, MELD, and PS can predict PHLF.
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Affiliation(s)
- Wei Cai
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China; Research Lab for Medical Imaging and Digital Surgery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Baochun He
- Research Lab for Medical Imaging and Digital Surgery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Min Hu
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wenyu Zhang
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China; Research Lab for Medical Imaging and Digital Surgery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Deqiang Xiao
- Research Lab for Medical Imaging and Digital Surgery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hao Yu
- Department of Radiology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qi Song
- School of Electronic Engineering and Computer Science, Washington State University, Pullman, WA, USA
| | - Nan Xiang
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Yang
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Songsheng He
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yaohuan Huang
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wenjie Huang
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Fucang Jia
- Research Lab for Medical Imaging and Digital Surgery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Chihua Fang
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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Chakraborty S, Chatterjee S, Ashour AS, Mali K, Dey N. Intelligent Computing in Medical Imaging. ADVANCEMENTS IN APPLIED METAHEURISTIC COMPUTING 2018. [DOI: 10.4018/978-1-5225-4151-6.ch006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Biomedical imaging is considered main procedure to acquire valuable physical information about the human body and some other biological species. It produces specialized images of different parts of the biological species for clinical analysis. It assimilates various specialized domains including nuclear medicine, radiological imaging, Positron emission tomography (PET), and microscopy. From the early discovery of X-rays, progress in biomedical imaging continued resulting in highly sophisticated medical imaging modalities, such as magnetic resonance imaging (MRI), ultrasound, Computed Tomography (CT), and lungs monitoring. These biomedical imaging techniques assist physicians for faster and accurate analysis and treatment. The present chapter discussed the impact of intelligent computing methods for biomedical image analysis and healthcare. Different Artificial Intelligence (AI) based automated biomedical image analysis are considered. Different approaches are discussed including the AI ability to resolve various medical imaging problems. It also introduced the popular AI procedures that employed to solve some special problems in medicine. Artificial Neural Network (ANN) and support vector machine (SVM) are active to classify different types of images from various imaging modalities. Different diagnostic analysis, such as mammogram analysis, MRI brain image analysis, CT images, PET images, and bone/retinal analysis using ANN, feed-forward back propagation ANN, probabilistic ANN, and extreme learning machine continuously. Various optimization techniques of ant colony optimization (ACO), genetic algorithm (GA), particle swarm optimization (PSO) and other bio-inspired procedures are also frequently conducted for feature extraction/selection and classification. The advantages and disadvantages of some AI approaches are discussed in the present chapter along with some suggested future research perspectives.
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Lin Y, Samei E. Development and validation of a segmentation-free polyenergetic algorithm for dynamic perfusion computed tomography. J Med Imaging (Bellingham) 2016; 3:033503. [PMID: 27610396 DOI: 10.1117/1.jmi.3.3.033503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/05/2016] [Indexed: 11/14/2022] Open
Abstract
Dynamic perfusion imaging can provide the morphologic details of the scanned organs as well as the dynamic information of blood perfusion. However, due to the polyenergetic property of the x-ray spectra, beam hardening effect results in undesirable artifacts and inaccurate CT values. To address this problem, this study proposes a segmentation-free polyenergetic dynamic perfusion imaging algorithm (pDP) to provide superior perfusion imaging. Dynamic perfusion usually is composed of two phases, i.e., a precontrast phase and a postcontrast phase. In the precontrast phase, the attenuation properties of diverse base materials (e.g., in a thorax perfusion exam, base materials can include lung, fat, breast, soft tissue, bone, and metal implants) can be incorporated to reconstruct artifact-free precontrast images. If patient motions are negligible or can be corrected by registration, the precontrast images can then be employed as a priori information to derive linearized iodine projections from the postcontrast images. With the linearized iodine projections, iodine perfusion maps can be reconstructed directly without the influence of various influential factors, such as iodine location, patient size, x-ray spectrum, and background tissue type. A series of simulations were conducted on a dynamic iodine calibration phantom and a dynamic anthropomorphic thorax phantom to validate the proposed algorithm. The simulations with the dynamic iodine calibration phantom showed that the proposed algorithm could effectively eliminate the beam hardening effect and enable quantitative iodine map reconstruction across various influential factors. The error range of the iodine concentration factors ([Formula: see text]) was reduced from [Formula: see text] for filtered back-projection (FBP) to [Formula: see text] for pDP. The quantitative results of the simulations with the dynamic anthropomorphic thorax phantom indicated that the maximum error of iodine concentrations can be reduced from [Formula: see text] for FBP to less than [Formula: see text] for pDP, which suggested that the proposed algorithm could not only effectively eliminate beam hardening artifacts but also significantly reduce the influence of the metal artifacts and accurately reconstruct the iodine map regardless of the influential factors. A segmentation-free polyenergetic dynamic perfusion imaging algorithm was proposed and validated via simulations. This method can accurately reconstruct artifact-free iodine maps for quantitative analyses.
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Affiliation(s)
- Yuan Lin
- Carestream Health Inc. , Division of Research and Innovations, 1049 Ridge Road West, Rochester, New York 14615, United States
| | - Ehsan Samei
- Duke University , Carl E. Ravin Advanced Imaging Lab, 2424 Erwin Road, Suite 302, Durham, North Carolina 27705, United States
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Polan DF, Brady SL, Kaufman RA. Tissue segmentation of computed tomography images using a Random Forest algorithm: a feasibility study. Phys Med Biol 2016; 61:6553-69. [PMID: 27530679 DOI: 10.1088/0031-9155/61/17/6553] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
There is a need for robust, fully automated whole body organ segmentation for diagnostic CT. This study investigates and optimizes a Random Forest algorithm for automated organ segmentation; explores the limitations of a Random Forest algorithm applied to the CT environment; and demonstrates segmentation accuracy in a feasibility study of pediatric and adult patients. To the best of our knowledge, this is the first study to investigate a trainable Weka segmentation (TWS) implementation using Random Forest machine-learning as a means to develop a fully automated tissue segmentation tool developed specifically for pediatric and adult examinations in a diagnostic CT environment. Current innovation in computed tomography (CT) is focused on radiomics, patient-specific radiation dose calculation, and image quality improvement using iterative reconstruction, all of which require specific knowledge of tissue and organ systems within a CT image. The purpose of this study was to develop a fully automated Random Forest classifier algorithm for segmentation of neck-chest-abdomen-pelvis CT examinations based on pediatric and adult CT protocols. Seven materials were classified: background, lung/internal air or gas, fat, muscle, solid organ parenchyma, blood/contrast enhanced fluid, and bone tissue using Matlab and the TWS plugin of FIJI. The following classifier feature filters of TWS were investigated: minimum, maximum, mean, and variance evaluated over a voxel radius of 2 (n) , (n from 0 to 4), along with noise reduction and edge preserving filters: Gaussian, bilateral, Kuwahara, and anisotropic diffusion. The Random Forest algorithm used 200 trees with 2 features randomly selected per node. The optimized auto-segmentation algorithm resulted in 16 image features including features derived from maximum, mean, variance Gaussian and Kuwahara filters. Dice similarity coefficient (DSC) calculations between manually segmented and Random Forest algorithm segmented images from 21 patient image sections, were analyzed. The automated algorithm produced segmentation of seven material classes with a median DSC of 0.86 ± 0.03 for pediatric patient protocols, and 0.85 ± 0.04 for adult patient protocols. Additionally, 100 randomly selected patient examinations were segmented and analyzed, and a mean sensitivity of 0.91 (range: 0.82-0.98), specificity of 0.89 (range: 0.70-0.98), and accuracy of 0.90 (range: 0.76-0.98) were demonstrated. In this study, we demonstrate that this fully automated segmentation tool was able to produce fast and accurate segmentation of the neck and trunk of the body over a wide range of patient habitus and scan parameters.
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Affiliation(s)
- Daniel F Polan
- Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI, USA. Department of Diagnostic Imaging, St Jude Children's Research Hospital, Memphis TN, USA
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Mala K, Sadasivam V, Alagappan S. Neural network based texture analysis of CT images for fatty and cirrhosis liver classification. Appl Soft Comput 2015. [DOI: 10.1016/j.asoc.2015.02.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Alper Selver M. Exploring Brushlet Based 3D Textures in Transfer Function Specification for Direct Volume Rendering of Abdominal Organs. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2015; 21:174-187. [PMID: 26357028 DOI: 10.1109/tvcg.2014.2359462] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Intuitive and differentiating domains for transfer function (TF) specification for direct volume rendering is an important research area for producing informative and useful 3D images. One of the emerging branches of this research is the texture based transfer functions. Although several studies in two, three, and four dimensional image processing show the importance of using texture information, these studies generally focus on segmentation. However, TFs can also be built effectively using appropriate texture information. To accomplish this, methods should be developed to collect wide variety of shape, orientation, and texture of biological tissues and organs. In this study, volumetric data (i.e., domain of a TF) is enhanced using brushlet expansion, which represents both low and high frequency textured structures at different quadrants in transform domain. Three methods (i.e., expert based manual, atlas and machine learning based automatic) are proposed for selection of the quadrants. Non-linear manipulation of the complex brushlet coefficients is also used prior to the tiling of selected quadrants and reconstruction of the volume. Applications to abdominal data sets acquired with CT, MR, and PET show that the proposed volume enhancement effectively improves the quality of 3D rendering using well-known TF specification techniques.
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Selver MA. Segmentation of abdominal organs from CT using a multi-level, hierarchical neural network strategy. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2014; 113:830-852. [PMID: 24480371 DOI: 10.1016/j.cmpb.2013.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 11/09/2013] [Accepted: 12/17/2013] [Indexed: 06/03/2023]
Abstract
Precise measurements on abdominal organs are vital prior to the important clinical procedures. Such measurements require accurate segmentation of these organs, which is a very challenging task due to countless anatomical variations and technical difficulties. Although, several features with various classifiers have been designed to overcome these challenges, abdominal organ segmentation via classification is still an emerging field in order to reach desired precision. Recent studies on multiple feature-classifier combinations show that hierarchical systems outperform composite feature-single classifier models. In this study, how hierarchical formations can translate to improved accuracy, when large size feature spaces are involved, is explored for the problem of abdominal organ segmentation. As a result, a semi-automatic, slice-by-slice segmentation method is developed using a novel multi-level and hierarchical neural network (MHNN). MHNN is designed to collect complementary information about organs at each level of the hierarchy via different feature-classifier combinations. Moreover, each level of MHNN receives residual data from the previous level. The residual data is constructed to preserve zero false positive error until the last level of the hierarchy, where only most challenging samples remain. The algorithm mimics analysis behaviour of a radiologist by using the slice-by-slice iteration, which is supported with adjacent slice similarity features. This enables adaptive determination of system parameters and turns into the advantage of online training, which is done in parallel to the segmentation process. Proposed design can perform robust and accurate segmentation of abdominal organs as validated by using diverse data sets with various challenges.
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Affiliation(s)
- M Alper Selver
- Department of Electrical and Electronics Engineering, Dokuz Eylül University, İzmir 35160, Turkey.
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Reproducibility and Prognosis of Quantitative Features Extracted from CT Images. Transl Oncol 2014; 7:72-87. [PMID: 24772210 DOI: 10.1593/tlo.13844] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/27/2014] [Accepted: 02/11/2014] [Indexed: 12/25/2022] Open
Abstract
We study the reproducibility of quantitative imaging features that are used to describe tumor shape, size, and texture from computed tomography (CT) scans of non-small cell lung cancer (NSCLC). CT images are dependent on various scanning factors. We focus on characterizing image features that are reproducible in the presence of variations due to patient factors and segmentation methods. Thirty-two NSCLC nonenhanced lung CT scans were obtained from the Reference Image Database to Evaluate Response data set. The tumors were segmented using both manual (radiologist expert) and ensemble (software-automated) methods. A set of features (219 three-dimensional and 110 two-dimensional) was computed, and quantitative image features were statistically filtered to identify a subset of reproducible and nonredundant features. The variability in the repeated experiment was measured by the test-retest concordance correlation coefficient (CCCTreT). The natural range in the features, normalized to variance, was measured by the dynamic range (DR). In this study, there were 29 features across segmentation methods found with CCCTreT and DR ≥ 0.9 and R(2) Bet ≥ 0.95. These reproducible features were tested for predicting radiologist prognostic score; some texture features (run-length and Laws kernels) had an area under the curve of 0.9. The representative features were tested for their prognostic capabilities using an independent NSCLC data set (59 lung adenocarcinomas), where one of the texture features, run-length gray-level nonuniformity, was statistically significant in separating the samples into survival groups (P ≤ .046).
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Nanthagopal AP, Rajamony RS. A region-based segmentation of tumour from brain CT images using nonlinear support vector machine classifier. J Med Eng Technol 2012; 36:271-7. [DOI: 10.3109/03091902.2012.682638] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Sharma N, Aggarwal LM. Automated medical image segmentation techniques. J Med Phys 2011; 35:3-14. [PMID: 20177565 PMCID: PMC2825001 DOI: 10.4103/0971-6203.58777] [Citation(s) in RCA: 254] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2009] [Revised: 07/15/2009] [Accepted: 08/24/2009] [Indexed: 12/13/2022] Open
Abstract
Accurate segmentation of medical images is a key step in contouring during radiotherapy planning. Computed topography (CT) and Magnetic resonance (MR) imaging are the most widely used radiographic techniques in diagnosis, clinical studies and treatment planning. This review provides details of automated segmentation methods, specifically discussed in the context of CT and MR images. The motive is to discuss the problems encountered in segmentation of CT and MR images, and the relative merits and limitations of methods currently available for segmentation of medical images.
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Affiliation(s)
- Neeraj Sharma
- School of Biomedical Engineering, Institute of Technology, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221 005, UP, India
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SHI Z, He L. Current Status and Future Potential of Neural Networks Used for Medical Image Processing. ACTA ACUST UNITED AC 2011. [DOI: 10.4304/jmm.6.3.244-251] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Linguraru MG, Sandberg JK, Li Z, Shah F, Summers RM. Automated segmentation and quantification of liver and spleen from CT images using normalized probabilistic atlases and enhancement estimation. Med Phys 2010; 37:771-83. [PMID: 20229887 DOI: 10.1118/1.3284530] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE To investigate the potential of the normalized probabilistic atlases and computer-aided medical image analysis to automatically segment and quantify livers and spleens for extracting imaging biomarkers (volume and height). METHODS A clinical tool was developed to segment livers and spleen from 257 abdominal contrast-enhanced CT studies. There were 51 normal livers, 44 normal spleens, 128 splenomegaly, 59 hepatomegaly, and 23 partial hepatectomy cases. 20 more contrast-enhanced CT scans from a public site with manual segmentations of mainly pathological livers were used to test the method. Data were acquired on a variety of scanners from different manufacturers and at varying resolution. Probabilistic atlases of livers and spleens were created using manually segmented data from ten noncontrast CT scans (five male and five female). The organ locations were modeled in the physical space and normalized to the position of an anatomical landmark, the xiphoid. The construction and exploitation of liver and spleen atlases enabled the automated quantifications of liver/spleen volumes and heights (midhepatic liver height and cephalocaudal spleen height) from abdominal CT data. The quantification was improved incrementally by a geodesic active contour, patient specific contrast-enhancement characteristics passed to an adaptive convolution, and correction for shape and location errors. RESULTS The livers and spleens were robustly segmented from normal and pathological cases. For the liver, the Dice/Tanimoto volume overlaps were 96.2%/92.7%, the volume/height errors were 2.2%/2.8%, the root-mean-squared error (RMSE) was 2.3 mm, and the average surface distance (ASD) was 1.2 mm. The spleen quantification led to 95.2%/91% Dice/Tanimoto overlaps, 3.3%/ 1.7% volume/height errors, 1.1 mm RMSE, and 0.7 ASD. The correlations (R2) with clinical/manual height measurements were 0.97 and 0.93 for the spleen and liver, respectively (p < 0.0001). No significant difference (p > 0.2) was found comparing interobserver and automatic-manual volume/height errors for liver and spleen. CONCLUSIONS The algorithm is robust to segmenting normal and enlarged spleens and livers, and in the presence of tumors and large morphological changes due to partial hepatectomy. Imaging biomarkers of the liver and spleen from automated computer-assisted tools have the potential to assist the diagnosis of abdominal disorders from routine analysis of clinical data and guide clinical management.
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Affiliation(s)
- Marius George Linguraru
- Imaging Biomarkers and Computer-Aided Diagnosis Laboratory, Radiology and Imaging Sciences, Clinical Center National Institutes of Health, 10 Center Drive Bethesda, Maryland 20892, USA.
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Campadelli P, Casiraghi E, Esposito A. Liver segmentation from computed tomography scans: a survey and a new algorithm. Artif Intell Med 2008; 45:185-96. [PMID: 19059767 DOI: 10.1016/j.artmed.2008.07.020] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2007] [Revised: 07/24/2008] [Accepted: 07/25/2008] [Indexed: 12/23/2022]
Abstract
OBJECTIVE In the recent years liver segmentation from computed tomography scans has gained a lot of importance in the field of medical image processing since it is the first and fundamental step of any automated technique for the automatic liver disease diagnosis, liver volume measurement, and 3D liver volume rendering. METHODS In this paper we report a review study about the semi-automatic and automatic liver segmentation techniques, and we describe our fully automatized method. RESULTS The survey reveals that automatic liver segmentation is still an open problem since various weaknesses and drawbacks of the proposed works must still be addressed. Our gray-level based liver segmentation method has been developed to tackle all these problems; when tested on 40 patients it achieves satisfactory results, comparable to the mean intra- and inter-observer variation. CONCLUSIONS We believe that our technique outperforms those presented in the literature; nevertheless, a common test set with its gold standard traced by experts, and a generally accepted performance measure are required to demonstrate it.
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Affiliation(s)
- Paola Campadelli
- Università degli Studi di Milano, Dipartimento di Scienze dell'Informazione, Via Comelico 39/41, 20135 Milano, Italy
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Rodríguez R, Castillo PJ, Guerra V, Azuela JHS, Suáreza AG, Izquierdo E. A comparison between two robust techniques for segmentation of blood vessels. Comput Biol Med 2008; 38:931-40. [PMID: 18672232 DOI: 10.1016/j.compbiomed.2008.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 06/04/2008] [Accepted: 06/18/2008] [Indexed: 10/21/2022]
Abstract
Image segmentation plays an important role in image analysis. According to several authors, segmentation terminates when the observer's goal is satisfied. For this reason, a unique method that can be applied to all possible cases does not yet exist. In this paper, we have carried out a comparison between two current segmentation techniques, namely the mean shift method, for which we propose a new algorithm, and the so-called spectral method. In this investigation the important information to be extracted from an image is the number of blood vessels (BV) present in the image. The results obtained by both strategies were compared with the results provided by manual segmentation. We have found that using the mean shift segmentation an error less than 20% for false positives (FP) and 0% for false negatives (FN) was observed, while for the spectral method more than 45% for FP and 0% for FN were obtained. We discuss the advantages and disadvantages of both methods.
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Affiliation(s)
- Roberto Rodríguez
- Digital Signal Processing Group, Institute of Cybernetics, Mathematics & Physics (ICIMAF), CP 10 400, Havana, Cuba
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Sharma N, Ray AK, Sharma S, Shukla KK, Pradhan S, Aggarwal LM. Segmentation and classification of medical images using texture-primitive features: Application of BAM-type artificial neural network. J Med Phys 2008; 33:119-26. [PMID: 19893702 PMCID: PMC2772042 DOI: 10.4103/0971-6203.42763] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Accepted: 05/28/2008] [Indexed: 11/23/2022] Open
Abstract
The objective of developing this software is to achieve auto-segmentation and tissue characterization. Therefore, the present algorithm has been designed and developed for analysis of medical images based on hybridization of syntactic and statistical approaches, using artificial neural network (ANN). This algorithm performs segmentation and classification as is done in human vision system, which recognizes objects; perceives depth; identifies different textures, curved surfaces, or a surface inclination by texture information and brightness. The analysis of medical image is directly based on four steps: 1) image filtering, 2) segmentation, 3) feature extraction, and 4) analysis of extracted features by pattern recognition system or classifier. In this paper, an attempt has been made to present an approach for soft tissue characterization utilizing texture-primitive features with ANN as segmentation and classifier tool. The present approach directly combines second, third, and fourth steps into one algorithm. This is a semisupervised approach in which supervision is involved only at the level of defining texture-primitive cell; afterwards, algorithm itself scans the whole image and performs the segmentation and classification in unsupervised mode. The algorithm was first tested on Markov textures, and the success rate achieved in classification was 100%; further, the algorithm was able to give results on the test images impregnated with distorted Markov texture cell. In addition to this, the output also indicated the level of distortion in distorted Markov texture cell as compared to standard Markov texture cell. Finally, algorithm was applied to selected medical images for segmentation and classification. Results were in agreement with those with manual segmentation and were clinically correlated.
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Affiliation(s)
- Neeraj Sharma
- School of Biomedical Engineering, Institute of Technology, Banaras Hindu University, Varanasi (UP), India
| | - Amit K. Ray
- School of Biomedical Engineering, Institute of Technology, Banaras Hindu University, Varanasi (UP), India
| | - Shiru Sharma
- School of Biomedical Engineering, Institute of Technology, Banaras Hindu University, Varanasi (UP), India
| | - K. K. Shukla
- Department of Computer Engineering, Institute of Technology, Banaras Hindu University, Varanasi (UP), India
| | - Satyajit Pradhan
- Department of Radiotherapy and Radiation Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi (UP), India
| | - Lalit M. Aggarwal
- Department of Radiotherapy and Radiation Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi (UP), India
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Selver MA, Kocaoğlu A, Demir GK, Doğan H, Dicle O, Güzeliş C. Patient oriented and robust automatic liver segmentation for pre-evaluation of liver transplantation. Comput Biol Med 2008; 38:765-84. [PMID: 18550045 DOI: 10.1016/j.compbiomed.2008.04.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 04/06/2008] [Accepted: 04/08/2008] [Indexed: 12/21/2022]
Abstract
Identifying liver region from abdominal computed tomography-angiography (CTA) data sets is one of the essential steps in evaluation of transplantation donors prior to the hepatic surgery. However, due to gray level similarity of adjacent organs, injection of contrast media and partial volume effects; robust segmentation of the liver is a very difficult task. Moreover, high variations in liver margins, different image characteristics with different CT scanners and atypical liver shapes make the segmentation process even harder. In this paper, we propose a three stage (i.e. pre-processing, classification, post-processing); automatic liver segmentation algorithm that adapts its parameters according to each patient by learning the data set characteristics in parallel to segmentation process to address all the challenging aspects mentioned above. The efficiency in terms of the time requirement and the overall segmentation performance is achieved by introducing a novel modular classification system consisting of a K-Means based simple classification system and an MLP based complex one which are combined with a data-dependent and automated switching mechanism that decides to apply one of them. Proposed approach also makes the design of the overall classification system fully unsupervised that depends on the given CTA series only without requiring any given training set of CTA series. The segmentation results are evaluated by using area error rate and volume calculations and the success rate is calculated as 94.91% over a data set of diverse CTA series of 20 patients according to the evaluation of the expert radiologist. The results show that, the proposed algorithm gives better results especially for atypical liver shapes and low contrast studies where several algorithms fail.
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Affiliation(s)
- M Alper Selver
- Electrical and Electronics Engineering Department, Dokuz Eylül University, Buca, Izmir 35160, Turkey.
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Rodríguez R. Binarization of medical images based on the recursive application of mean shift filtering : Another algorithm. Adv Appl Bioinform Chem 2008; 1:1-12. [PMID: 21918602 PMCID: PMC3169934 DOI: 10.2147/aabc.s3206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Binarization is often recognized to be one of the most important steps in most high-level image analysis systems, particularly for object recognition. Its precise functioning highly determines the performance of the entire system. According to many researchers, segmentation finishes when the observer's goal is satisfied. Experience has shown that the most effective methods continue to be the iterative ones. However, a problem with these algorithms is the stopping criterion. In this work, entropy is used as the stopping criterion when segmenting an image by recursively applying mean shift filtering. Of this way, a new algorithm is introduced for the binarization of medical images, where the binarization is carried out after the segmented image was obtained. The good performance of the proposed method; that is, the good quality of the binarization, is illustrated with several experimental results. In this paper a comparison was carried out among the obtained results with this new algorithm with respect to another developed by the author and collaborators previously and also with Otsu's method.
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Affiliation(s)
- Roberto Rodríguez
- Digital Signal Processing Group, Institute of Cybernetics, Mathematics and Physics (ICIMAF), La Habana, Cuba
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A Strategy for Atherosclerosis Image Segmentation by Using Robust Markers. J INTELL ROBOT SYST 2007. [DOI: 10.1007/s10846-007-9156-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Campadelli P, Casiraghi E. Liver Segmentation from CT Scans: A Survey. APPLICATIONS OF FUZZY SETS THEORY 2007. [DOI: 10.1007/978-3-540-73400-0_66] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Rodríguez R, Alarcón TE, Pacheco O. A new strategy to obtain robust markers for blood vessels segmentation by using the watersheds method. Comput Biol Med 2006; 35:665-86. [PMID: 16124989 DOI: 10.1016/j.compbiomed.2004.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2003] [Revised: 06/01/2004] [Accepted: 06/01/2004] [Indexed: 10/25/2022]
Abstract
The watersheds method is a powerful segmentation tool developed in mathematical morphology. In order to prevent its over-segmentation, in this paper, we present a new strategy to obtain robust markers for segmentation of blood vessels from malignant tumors. For this purpose, we introduced a new algorithm. We propose a two-stage segmentation strategy which involves: (1) extracting an approximate region containing the blood vessel and part of the background near the blood vessel, and (2) segmenting the blood vessel from the background within this region. The approach effectively reduces the influence of peripheral background intensities on the extraction of a blood vessel region. In this application the important information to be extracted from images is only the number of blood vessels present in the images. The proposed strategy was tested on manual segmentation, where segmentation errors less than 10% for false positives and 0% for false negatives are observed. It is demonstrated by extensive experimentation, by using real images, that the proposed strategy was suitable for our application in the environment of a personal computer.
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Affiliation(s)
- Roberto Rodríguez
- Institute of Cybernetics, Mathematics and Physics (ICIMAF), Group of Digital Signal Processing, Calle 15 No. 551 e/ C y D CP 10400, La Habana, Cuba.
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Lee CC, Chung PC, Tsai HM. Identifying multiple abdominal organs from CT image series using a multimodule contextual neural network and spatial fuzzy rules. ACTA ACUST UNITED AC 2003; 7:208-17. [PMID: 14518735 DOI: 10.1109/titb.2003.813795] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Identifying abdominal organs is one of the essential steps in visualizing organ structure to assist in teaching, clinical training, diagnosis, and medical image retrieval. However, due to partial volume effects, gray-level similarities of adjacent organs, contrast media affect, and the relatively high variations of organ position and shape, automatically identifying abdominal organs has always been a high challenging task. To conquer these difficulties, this paper proposes combining a multimodule contextual neural network and spatial fuzzy rules and fuzzy descriptors for automatically identifying abdominal organs from a series of CT image slices. The multimodule contextual neural network segments each image slice through a divide-and-conquer concept, embedded within multiple neural network modules, where the results obtained from each module are forwarded to other modules for integration, in which contextual constraints are enforced. With this approach, the difficulties arising from partial volume effects, gray-level similarities of adjacent organs, and contrast media affect can be reduced to the extreme. To address the issue of high variations in organ position and shape, spatial fuzzy rules and fuzzy descriptors are adopted, along with a contour modification scheme implementing consecutive organ region overlap constraints. This approach has been tested on 40 sets of abdominal CT images, where each set consists of about 40 image slices. We have found that 99% of the organ regions in the test images are correctly identified as its belonging organs, implying the high promise of the proposed method.
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Affiliation(s)
- Chien-Cheng Lee
- Department of Electrical Engineering, National Cheng-Kung University, Tainan, 70101 Taiwan, ROC
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