Computational methods for the analysis of functional 4D-CT chest images.

Medical imaging is an important emerging technology that has been intensively used in the last few decades for disease diagnosis and monitoring as well as for the assessment of treatment effectiveness. Medical images provide a very large amount of valuable information that is too huge to be exploited by radiologists and physicians. Therefore, the design of computer-aided diagnostic (CAD) system, which can be used as an assistive tool for the medical community, is of a great importance. This dissertation deals with the development of a complete CAD system for lung cancer patients, which remains the leading cause of cancer-related death in the USA. In 2014, there were approximately 224,210 new cases of lung cancer and 159,260 related deaths. The process begins with the detection of lung cancer which is detected through the diagnosis of lung nodules (a manifestation of lung cancer). These nodules are approximately spherical regions of primarily high density tissue that are visible in computed tomography (CT) images of the lung. The treatment of these lung cancer nodules is complex, nearly 70% of lung cancer patients require radiation therapy as part of their treatment. Radiation-induced lung injury is a limiting toxicity that may decrease cure rates and increase morbidity and mortality treatment. By finding ways to accurately detect, at early stage, and hence prevent lung injury, it will have significant positive consequences for lung cancer patients. The ultimate goal of this dissertation is to develop a clinically usable CAD system that can improve the sensitivity and specificity of early detection of radiation-induced lung injury based on the hypotheses that radiated lung tissues may get affected and suffer decrease of their functionality as a side effect of radiation therapy treatment. These hypotheses have been validated by demonstrating that automatic segmentation of the lung regions and registration of consecutive respiratory phases to estimate their elasticity, ventilation, and texture features to provide discriminatory descriptors that can be used for early detection of radiation-induced lung injury. The proposed methodologies will lead to novel indexes for distinguishing normal/healthy and injured lung tissues in clinical decision-making. To achieve this goal, a CAD system for accurate detection of radiation-induced lung injury that requires three basic components has been developed. These components are the lung fields segmentation, lung registration, and features extraction and tissue classification. This dissertation starts with an exploration of the available medical imaging modalities to present the importance of medical imaging in today’s clinical applications. Secondly, the methodologies, challenges, and limitations of recent CAD systems for lung cancer detection are covered. This is followed by introducing an accurate segmentation methodology of the lung parenchyma with the focus of pathological lungs to extract the volume of interest (VOI) to be analyzed for potential existence of lung injuries stemmed from the radiation therapy. After the segmentation of the VOI, a lung registration framework is introduced to perform a crucial and important step that ensures the co-alignment of the intra-patient scans. This step eliminates the effects of orientation differences, motion, breathing, heart beats, and differences in scanning parameters to be able to accurately extract the functionality features for the lung fields. The developed registration framework also helps in the evaluation and gated control of the radiotherapy through the motion estimation analysis before and after the therapy dose. Finally, the radiation-induced lung injury is introduced, which combines the previous two medical image processing and analysis steps with the features estimation and classification step. This framework estimates and combines both texture and functional features. The texture features are modeled using the novel 7th-order Markov Gibbs random field (MGRF) model that has the ability to accurately models the texture of healthy and injured lung tissues through simultaneously accounting for both vertical and horizontal relative dependencies between voxel-wise signals. While the functionality features calculations are based on the calculated deformation fields, obtained from the 4D-CT lung registration, that maps lung voxels between successive CT scans in the respiratory cycle. These functionality features describe the ventilation, the air flow rate, of the lung tissues using the Jacobian of the deformation field and the tissues’ elasticity using the strain components calculated from the gradient of the deformation field. Finally, these features are combined in the classification model to detect the injured parts of the lung at an early stage and enables an earlier intervention

A CUDA-powered method for the feature extraction and unsupervised analysis of medical images

Funder: Università degli Studi di Milano - BicoccaAbstractImage texture extraction and analysis are fundamental steps in computer vision. In particular, considering the biomedical field, quantitative imaging methods are increasingly gaining importance because they convey scientifically and clinically relevant information for prediction, prognosis, and treatment response assessment. In this context, radiomic approaches are fostering large-scale studies that can have a significant impact in the clinical practice. In this work, we present a novel method, called CHASM (Cuda, HAralick &amp; SoM), which is accelerated on the graphics processing unit (GPU) for quantitative imaging analyses based on Haralick features and on the self-organizing map (SOM). The Haralick features extraction step relies upon the gray-level co-occurrence matrix, which is computationally burdensome on medical images characterized by a high bit depth. The downstream analyses exploit the SOM with the goal of identifying the underlying clusters of pixels in an unsupervised manner. CHASM is conceived to leverage the parallel computation capabilities of modern GPUs. Analyzing ovarian cancer computed tomography images, CHASM achieved up to $$\sim 19.5\times$$ ∼ 19.5 × and $$\sim 37\times$$ ∼ 37 × speed-up factors for the Haralick feature extraction and for the SOM execution, respectively, compared to the corresponding C++ coded sequential versions. Such computational results point out the potential of GPUs in the clinical research.</jats:p

Correlation Between Hippocampus MRI Radiomic Features and Resting-State Intrahippocampal Functional Connectivity in Alzheimer’s Disease

Alzheimer’s disease (AD) is a neurodegenerative disease with main symptoms of chronic primary memory loss and cognitive impairment. The study aim was to investigate the correlation between intrahippocampal functional connectivity (FC) and MRI radiomic features in AD. A total of 67 AD patients and 44 normal controls (NCs) were enrolled in this study. Using the seed-based method of resting-state functional MRI (rs-fMRI), the whole-brain FC with bilateral hippocampus as seed was performed, and the FC values were extracted from the bilateral hippocampus. We observed that AD patients demonstrated disruptive FC in some brain regions in the left hippocampal functional network, including right gyrus rectus, right anterior cingulate and paracingulate gyri, bilateral precuneus, bilateral angular gyrus, and bilateral middle occipital gyrus. In addition, decreased FC was detected in some brain regions in the right hippocampal functional network, including bilateral anterior cingulate and paracingulate gyri, right dorsolateral superior frontal gyrus, and right precentral gyrus. Bilateral hippocampal radiomics features were calculated and selected using the A.K. software. Finally, Pearson’s correlation analyses were conducted between these selected features and the bilateral hippocampal FC values. The results suggested that two gray level run-length matrix (RLM) radiomic features and one gray level co-occurrence matrix (GLCM) radiomic feature weakly associated with FC values in the left hippocampus. However, there were no significant correlations between radiomic features and FC values in the right hippocampus. These findings present that the AD group showed abnormalities in the bilateral hippocampal functional network. This is a prospective study that revealed the weak correlation between the MRI radiomic features and the intrahippocampal FC in AD patients

Feature-preserving Reduction and Visualization of Industrial CT data using GLCM texture analysis and Mass-spring Model Deformation

학위논문 (박사)-- 서울대학교 대학원 : 전기·컴퓨터공학부, 2014. 8. 신영길.본 논문에서는 3D 볼륨 데이터에서 중요한 영역을 보존하면서 크기를 줄이는 방법을 제안한다. 볼륨 데이터에서 어느 부분이 중요한 영역인지를 결정하기 위해 질감 분석 방법 중 하나인 GLCM 균일도를 이용한 중요도 측정 모델을 제안하고, 이를 기반으로 한 MSM 기반의 볼륨 변형을 수행한다. 중요도가 반영된 볼륨 변형 과정을 통해, 중요한 영역은 상대적으로 크기가 확장되는 반면, 덜 중요한 영역은 줄어들게 된다. 이로 인해, 일반적으로 손실률이 높은 균일 다운샘플링을 이용한 압축 후에도 작은 크기의 중요한 특징점들이 손실되지 않고 보존될 수 있다. 실측 산업 영상 데이터를 이용한 실험을 통해, 그냥 균일 다운샘플링을 이용한 압축 결과에서는 사라진 작은 기공이나 수축 균열 형태의 결함 영역이 제안 방법에서는 보존되는 것을 확인할 수 있었다. 이 변형 볼륨을 원래 형태로 가시화하기 위해선 역변형 과정을 추가로 수행해야 하지만, 이 계산은 가시화 과정에 간단하게 추가할 수 있으며, 결과를 얻기 위한 소요시간에 유의미한 영향을 미치지 않는다.Non-destructive testing is a method which examines the internal structures of industrial components such as various machine parts without dissecting them. Recently, 3D CT based analysis enables more accurate inspection than traditional X-ray based tests. However, manipulating volumetric data acquired by CT is still challenging due to its huge size of the volume data. This dissertation proposes a novel method that reduces the size of 3D volume data while preserving important features in the data. Our method quantifies the importance of features in the 3D data based on gray level co-occurrence matrix (GLCM) texture analysis and represents the volume data using a simple mass-spring model. According to the measured importance value, blocks containing important features expand while other blocks shrink. After deformation, small features are exaggerated on deformed volume space, and more likely to survive during the uniform volume reduction. Experimental results showed that our method well preserved the small features of the original volume data during the reduction without any artifact comparing with the previous methods. Although additional inverse deformation process was required for the rendering of the deformed volume data, the rendering speed of the deformed volume data was much faster than that of the original volume data.초록 i 목차 iii 그림 목차 vi 표 목차 x 1장 서론 1 1.1 볼륨 렌더링 1 1.2 비파괴검사 2 1.3 연구 내용 4 1.4 논문의 구성 6 2장 관련 연구 7 2.1 볼륨 렌더링 알고리즘 7 2.1.1 볼륨 데이터의 특성 7 2.1.2 표면 추출 기법 8 2.1.3 직접 볼륨 렌더링 10 2.2 압축 볼륨 렌더링 17 2.2.1 벡터 양자화 18 2.2.2 변환 부호화 19 2.2.3 다중-해상도 기반 기법 23 2.2.4 볼륨 변형 기반 방법 25 2.3 질량-스프링 기반 볼륨 변형 모델 27 2.4 산업용 CT 영상의 중요 특징점 측량 방법 30 3장 중요도 측정 기법 32 3.1 명암도 동시발생 행렬 32 3.2 GLCM 균일도 기반 중요도 모델 36 3.3 공기 영역 제거 44 4장 볼륨 변형, 축소 및 가시화 47 4.1 질량-스프링 모델 기반 볼륨 변형 47 4.2 볼륨 축소 54 4.3 역변형 및 렌더링 55 5장 실험 및 결과 58 5.1 화질 평가 60 5.2 속도 평가 65 5.3 파라미터 연구 69 6장 결론 74 6.1 요약 74 6.2 향후 연구 75 참고문헌 77 Abstract 83Docto

Massive training artificial immune recognition system for lung nodules detection

In the early detection and diagnosis of lung nodule, computer aided detection (CAD) has become crucial to assist radiologists in interpreting medical images and decision making. However, some limitations have been found in the existing CAD algorithms for detecting lung nodules, such as imprecision classification due to inaccurate segmentation and lengthy computation time. In this research, Massive Training Artificial Immune Recognition System (MTAIRS) is proposed to detect lung nodules on Computed Tomography (CT) scans. MTAIRS is developed based on the pixel machine learning and artificial immune-based system-Artificial Immune Recognition System (AIRS). Two versions of proposed algorithms have been investigated in the study: MTAIRS 1 and MTAIRS 2. Since segmentation and feature calculation are not implemented in the pixel-based machine learning, the loss of information can be avoided during the data training in MTAIRS 1 and MTAIRS 2. The experiment and analysis find that MTAIRS 1 and MTAIRS 2 have successfully reduced the computation time and accomplished good accuracy in the detection of lung nodules on CT scans compared to other well-known pixel-based classification algorithms. Furthermore, MTAIRS 1 and MTAIRS 2 are investigated to improve their performance in eliminating the false positives. A weighted non-linear affinity function is employed in the training of MTAIRS 1 and MTAIRS 2 to replace Euclidean distance in affinity measurement. The enhanced algorithms named, E-MTAIRS 1 and E-MTAIRS 2 are capable to reduce the false positives in the non-nodule classification while maintaining the accuracy in nodule detection. In order to further provide comparative analysis of pixel-based classification algorithms in lung nodules detection, a pixel-based evaluation method of Kullback Leibler (KL) divergence is proposed in this study. Based on the pixel-based quantitative analysis, MTAIRS 1 performs better in the elimination of false positives, while MTAIRS 2 in lung nodules detection. The average detection accuracy for both MTAIRS algorithms is 95%

A Locally Adaptive Regularization Based on Anisotropic Diffusion for Deformable Image Registration of Sliding Organs

We propose a deformable image registration algorithm that uses anisotropic smoothing for regularization to find correspondences between images of sliding organs. In particular, we apply the method for respiratory motion estimation in longitudinal thoracic and abdominal computed tomography scans. The algorithm uses locally adaptive diffusion tensors to determine the direction and magnitude with which to smooth the components of the displacement field that are normal and tangential to an expected sliding boundary. Validation was performed using synthetic, phantom, and 14 clinical datasets, including the publicly available DIR-Lab dataset. We show that motion discontinuities caused by sliding can be effectively recovered, unlike conventional regularizations that enforce globally smooth motion. In the clinical datasets, target registration error showed improved accuracy for lung landmarks compared to the diffusive regularization. We also present a generalization of our algorithm to other sliding geometries, including sliding tubes (e.g., needles sliding through tissue, or contrast agent flowing through a vessel). Potential clinical applications of this method include longitudinal change detection and radiotherapy for lung or abdominal tumours, especially those near the chest or abdominal wall

Machine Intelligence for Advanced Medical Data Analysis: Manifold Learning Approach

In the current work, linear and non-linear manifold learning techniques, specifically Principle Component Analysis (PCA) and Laplacian Eigenmaps, are studied in detail. Their applications in medical image and shape analysis are investigated. In the first contribution, a manifold learning-based multi-modal image registration technique is developed, which results in a unified intensity system through intensity transformation between the reference and sensed images. The transformation eliminates intensity variations in multi-modal medical scans and hence facilitates employing well-studied mono-modal registration techniques. The method can be used for registering multi-modal images with full and partial data. Next, a manifold learning-based scale invariant global shape descriptor is introduced. The proposed descriptor benefits from the capability of Laplacian Eigenmap in dealing with high dimensional data by introducing an exponential weighting scheme. It eliminates the limitations tied to the well-known cotangent weighting scheme, namely dependency on triangular mesh representation and high intra-class quality of 3D models. In the end, a novel descriptive model for diagnostic classification of pulmonary nodules is presented. The descriptive model benefits from structural differences between benign and malignant nodules for automatic and accurate prediction of a candidate nodule. It extracts concise and discriminative features automatically from the 3D surface structure of a nodule using spectral features studied in the previous work combined with a point cloud-based deep learning network. Extensive experiments have been conducted and have shown that the proposed algorithms based on manifold learning outperform several state-of-the-art methods. Advanced computational techniques with a combination of manifold learning and deep networks can play a vital role in effective healthcare delivery by providing a framework for several fundamental tasks in image and shape processing, namely, registration, classification, and detection of features of interest

Fractal and textural analysis of nuclear chromatin structural complexity in postnatal development and aging

Prethodne studije su utvrdile da tokom starenja veliki broj bioloških struktura kao što su tkiva i organi gubi svoju kompleksnost i da takav gubitak vodi smanjenoj sposobnosti adaptacije na fiziološki stres. Međutim, za sada nema podataka da li se slične strukturne promene dešavaju na individualnim ćelijama i njihovom genetskom materijalu. Strukturna kompleksnost se može kvantifikovati na nekoliko načina. Skorašnje studije su utvrdile da hromatin, kao i mnoge druge biološke strukture u svojoj morfologiji ispoljavaju karakteristike fraktala. Koncept fraktala se u osnovi bazira na principu samosličnosti, odnosno na činjenici da manji delovi nekog fizičkog ili biološkog sistema nalikuju sistemu kao celini. Kompleksnost fraktalnih struktura se može meriti određivanjem fraktalne dimenzije i lakunarnosti kao dva najznačajnija parametra fraktalne analize. Kao dodatak fraktalnoj analizi, danas se često koristi i teksturalna analiza uz pomoć koje se mogu odrediti parametri teksturalne heterogenosti i neuređenosti biološke strukture kao što je entropija. U našoj studiji, na mišijem eksperimentalnom modelu, ispitivane su starosne promene u strukturnoj kompleksnosti nukleusnog hromatina na ukupno 10 ćelijskih populacija u timusu, slezini, bubregu i jetri. Takođe su opisane promene u kompleksnosti nukleusne strukture na kulturi ćelija nakon indukcije DNK oštećenja UV zračenjem...Previous studies have found that during aging a large number of biological structures such as tissues and organs loses its complexity and that such loss leads to reduced ability to adapt to physiological stress. However, so far there is no information on whether similar structural changes occur in individual cells and their genetic material. Structural complexity can be quantified in several ways. Recent studies have determined that the chromatin, as well as many other biological structures exhibit fractal characteristics in their morphology. The concept of fractals is based on the principle of self - similarity, or the fact that the lower parts of a physical or biological system resemble the system as a whole. The complexity of fractal structures Can be measured by determining the fractal dimension and lacunarity as the two most important parameters of fractal analysis. In addition to the fractal analysis, textural analysis as a method is also frequently used. Textural analysis can determine the parameters of textural heterogeneity and disorganization (i.e.entropy)of biological structures. In our study, on the mouse experimental model, we studied age - related changes in chromate in structural complexity in the total of 10 cell populations in the thymus, spleen, kidney and liver. Also, we described changes in the complexity of the nuclear structure in a cell culture after the induction of DNA damage by UV radiation..