Automatic Segmentation and Components Classification of Optic Pathway Gliomas in MRI

Tumor computed tomography (CT) image segmentation can provide a basis for the determination of tumor location and type. Therefore, it is of great significance to study the automatic segmentation method of tumor CT images. To address the problem of poor segmentation effect of traditional automatic tumor CT images segmentation methods, we propose an automatic segmentation method for tumor CT images using deep convolutional neural networks (DCNNs). First, the CT tumor image is simplified. According to the features of the target region and the background region, the distribution features of the tumor region in the CT images are obtained by convolution calculation, and the feature extraction is completed by feature fusion. Second, based on the feature extraction results, a deep supervised network is constructed to determine the image depth, which lays a solid foundation for accurate segmentation of tumor regions. Finally, DCNN was used to construct automatic segmentation for tumor CT images, which achieves the automatic segmentation of tumor CT images by mode calculation. The results show that the segmented tumor region is close to the actual region and the maximum pixel loss coefficient is 0.07, the maximum segmentation sensitivity is 7865[Formula: see text]kbps/s, the pixel segmentation specific coefficient and the segmentation edge distance are kept at a low level, which has a certain application value in the field of tumor CT images.

Develop and evaluate a deep learning-based automatic meningioma segmentation method for preoperative meningioma differentiation using radiomic features. A retrospective multicentre inclusion of MR examinations (T1/T2-weighted and contrast-enhanced T1-weighted imaging) was conducted. Data from centre 1 were allocated to training (n = 307, age = 50.94 ± 11.51) and internal testing (n = 238, age = 50.70 ± 12.72) cohorts, and data from centre 2 external testing cohort (n = 64, age = 48.45 ± 13.59). A modified attention U-Net was trained for meningioma segmentation. Segmentation accuracy was evaluated by five quantitative metrics. The agreement between radiomic features from manual and automatic segmentations was assessed using intra class correlation coefficient (ICC). After univariate and minimum-redundancy-maximum-relevance feature selection, L1-regularized logistic regression models for differentiating between low-grade (I) and high-grade (II and III) meningiomas were separately constructed using manual and automatic segmentations; their performances were evaluated using ROC analysis. Dice of meningioma segmentation for the internal testing cohort were 0.94 ± 0.04 and 0.91 ± 0.05 for tumour volumes in contrast-enhanced T1-weighted and T2-weighted images, respectively; those for the external testing cohort were 0.90 ± 0.07 and 0.88 ± 0.07. Features extracted using manual and automatic segmentations agreed well, for both the internal (ICC = 0.94, interquartile range: 0.88-0.97) and external (ICC = 0.90, interquartile range: 0.78-70.96) testing cohorts. AUC of radiomic model with automatic segmentation was comparable with that of the model with manual segmentation for both the internal (0.95 vs. 0.93, p = 0.176) and external (0.88 vs. 0.91, p = 0.419) testing cohorts. The developed deep learning-based segmentation method enables automatic and accurate extraction of meningioma from multiparametric MR images and can help deploy radiomics for preoperative meningioma differentiation in clinical practice. • A deep learning-based method was developed for automatic segmentation of meningioma from multiparametric MR images. • The automatic segmentation method enabled accurate extraction of meningiomas and yielded radiomic features that were highly consistent with those that were obtained using manual segmentation. • High-grade meningiomas were preoperatively differentiated from low-grade meningiomas using a radiomic model constructed on features from automatic segmentation.

A method for corneal nerves automatic segmentation and morphometric analysis

We present a robust, automated, model-based segmentation method for kidney MR Images. We used dynamic programming and a minimal path approach to detect the optimal path within a weighted graph between two end points. We used an energy function to combine distance and gradient information to guide the marching curve and thus evaluate the best path and span a broken edge. We developed an algorithm to automate the placement of initial end points. Dynamic programming was used to automatically optimize and update end points in the procedure for searching curves. A deformable 3D model was generated using principle component analysis (PCA) and it was used as the prior knowledge for the selection of initial end points and for the evaluation of the best path. We used our minimal path method with surface models to segment mouse kidneys slice-by-slice. The method has been tested for kidney MR images of 44 mice. To quantitatively assess the automatic segmentation method, we compared the automatic segmentation results with manual segmentation. The average and standard deviation of the overlap ratios is 0.93 + 0.05. The distance error between the automatic and manual segmentation is 0.85 plusmn 0.41 pixel. The 3D automatic minimal path segmentation method is fast, accurate, and robust. It provides a useful tool for quantification and characterization of kidney MR images.

Event Abstract Back to Event Study of cerebral asymmetry in schizophrenia based on an novel automatic cerebral hemisphere segmentation method for MRI Lu Zhao1*, Ulla Ruotsalainen1, Jussi Hirvonen2, Jarmo Hietala3 and Jussi Tohka1 1 Tampere University of Technology, Finland 2 Turku PET Centre, Finland 3 University of Turku, Finland In this work, we statistically analyzed the cerebral volume asymmetry for schizophrenic and healthy populations by employing a novel and completely automatic cerebral hemisphere segmentation method for MRI. The segmentation method is based on the information of partial volume effect (PVE) and the partial differential equations based shape bottlenecks (PDE-SB) algorithm [1]. PVE is an inevitable problem of MRI, but it is rarely taken into account by the existing automatic MR brain image segmentation techniques. The PDE-SB algorithm can detect the bottlenecks connecting two parts of a complex object by simulating a steady state of the information transmission process between the two parts with partial differential equations. Our method consists of two major stages: compartmental brain decomposition [2] and cerebral hemisphere segmentation [3]. Firstly, a partial volume estimation approach [4] is used to obtain the partial volume voxel classification [into grey matter (GM), white matter (WM), cerebrospinal fluid (CSF), CSF/GM, GM/WM and CSF/background] and estimate the amount of each tissue type in each brain voxel. Then the WM+GM/WM region is split into compartmental seeds corresponding to cerebrum, cerebellum and brainstem utilizing the PDE-SB algorithm. The brain volume is compartmentally decomposed by reconstructing the original shapes of the three compartments from the compartmental seeds according to the compartmental boundary knowledge defined with partial volume information. The cerebrum portion is extracted from the decomposed brain volume, and the cerebral hemispheres are segmented with the PDE-SB algorithm and the partial volume estimation results. In this work, this method was applied to a set of clinical T1-weighted MR images of 18 schizophrenic (11 males, 7 females) and 19 healthy (12 males, 7 females) subjects. All subjects were right-handed, and the schizophrenic patients were never medicated. With the obtained PVE information and cerebral hemisphere segmentation, the asymmetry index (AI) was calculated for cerebrum, cerebral GM and cerebral WM. AI was defined as (VR-VL)/[1/2(VR+VL)]×100, where VR and VL were the volume sizes of the right and left hemispheres respectively. The permutation test was conducted to evaluate the statistical significance of the difference of acquired AIs between schizophrenic and healthy populations. Here, the null hypothesis was defined as that AIs of schizophrenic and healthy populations had identical probability distribution, and the significance level was selected as 0.05. According to the statistical analysis results, the cerebral GM volume asymmetry of female schizophrenic population had significantly different probability distribution from the female healthy population's (p=0.002). There were no significant difference between schizophrenic and healthy populations with regard to volume asymmetry in the other cases (p>0.05). Conference: Neuroinformatics 2008, Stockholm, Sweden, 7 Sep - 9 Sep, 2008. Presentation Type: Poster Presentation Topic: Neuroimaging Citation: Zhao L, Ruotsalainen U, Hirvonen J, Hietala J and Tohka J (2008). Study of cerebral asymmetry in schizophrenia based on an novel automatic cerebral hemisphere segmentation method for MRI. Front. Neuroinform. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.069 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 28 Jul 2008; Published Online: 28 Jul 2008. * Correspondence: Lu Zhao, Tampere University of Technology, Tampere, Finland, lu.zhao@tut.fi Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Lu Zhao Ulla Ruotsalainen Jussi Hirvonen Jarmo Hietala Jussi Tohka Google Lu Zhao Ulla Ruotsalainen Jussi Hirvonen Jarmo Hietala Jussi Tohka Google Scholar Lu Zhao Ulla Ruotsalainen Jussi Hirvonen Jarmo Hietala Jussi Tohka PubMed Lu Zhao Ulla Ruotsalainen Jussi Hirvonen Jarmo Hietala Jussi Tohka Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Application of an automatic segmentation method for evaluating cardiac structure doses received by breast radiotherapy patients

Hyper-fusion network for semi-automatic segmentation of skin lesions.

Magnetic resonance imaging (MRI) has potential benefits in understanding fetal and placental complications in pregnancy. An accurate segmentation of the uterine cavity and placenta can help facilitate fast and automated analyses of placenta accreta spectrum and other pregnancy complications. In this study, we trained a deep neural network for fully automatic segmentation of the uterine cavity and placenta from MR images of pregnant women with and without placental abnormalities. The two datasets were axial MRI data of 241 pregnant women, among whom, 101 patients also had sagittal MRI data. Our trained model was able to perform fully automatic 3D segmentation of MR image volumes and achieved an average Dice similarity coefficient (DSC) of 92% for uterine cavity and of 82% for placenta on the sagittal dataset and an average DSC of 87% for uterine cavity and of 82% for placenta on the axial dataset. Use of our automatic segmentation method is the first step in designing an analytics tool for to assess the risk of pregnant women with placenta accreta spectrum.

Automatic and reliable prostate segmentation is an essential prerequisite for assisting the diagnosis and treatment, such as guiding biopsy procedure and radiation therapy. Notwithstanding, automatic segmentation is challenging due to the lack of clear prostate boundaries owing to similar appearance of prostate and surrounding tissues and the wide variation in size and shape among different patients. Therefore, this paper proposes an automatic method for prostate segmentation on 3D MRI scans using a content-sensitive superpixels technique, deep convolutional neural networks with residual connections (ResCNN), and the particle swarm optimization (PSO) algorithm. The proposed method has been evaluated on the Prostate 3T and PROMISE12 databases, presenting a Dice similarity coefficient of 86.68 %, Jaccard index of 76.58%, relative volume difference of 3.92%, volumetric similarity of 96.69 %, sensitivity of 88.36 %, specificity of 93.43%, accuracy of 91.97% and an area under ROC curve of 90.90 %. Experimental results demonstrate the high performance-potential of the proposed method comparable to those previously published.

The automatic analysis of retinal blood vessels plays an important role in the computer-aided diagnosis. In this paper, we introduce a probabilistic tracking-based method for automatic vessel segmentation in retinal images. We take into account vessel edge detection on the whole retinal image and handle different vessel structures. During the tracking process, a Bayesian method with maximum a posteriori (MAP) as criterion is used to detect vessel edge points. Experimental evaluations of the tracking algorithm are performed on real retinal images from three publicly available databases: STARE (Hoover et al., 2000), DRIVE (Staal et al., 2004), and REVIEW (Al-Diri et al., 2008 and 2009). We got high accuracy in vessel segmentation, width measurements, and vessel structure identification. The sensitivity and specificity on STARE are 0.7248 and 0.9666, respectively. On DRIVE, the sensitivity is 0.6522 and the specificity is up to 0.9710.

Antinuclear antibodies (ANAs) testing is the main serological diagnosis screening test for autoimmune diseases. ANAs testing is conducted principally by the indirect immunofluorescence (IIF) on human epithelial cell-substrate (HEp-2) protocol. However, due to its high variability and human subjectivity, there is an insistent need to develop an efficient method for automatic image segmentation and classification. This article develops an automatic segmentation and classification framework based on artificial intelligence (AI) on the ANA images. The Otsu thresholding method and watershed segmentation algorithm are adopted to segment IIF images of cells. Moreover, multiple texture features such as scale-invariant feature transform (SIFT), local binary pattern (LBP), cooccurrence among adjacent LBPs (CoALBP), and rotation invariant cooccurrence among adjacent LBPs (RIC-LBP) are utilized. Firstly, this article adopts traditional machine learning methods such as support vector machine (SVM), k-nearest neighbor algorithm (KNN), and random forest (RF) and then uses ensemble classifier (ECLF) combined with soft voting rules to merge these machine learning methods for classification. The deep learning method InceptionResNetV2 is also utilized to train on the classification of cell images. Eventually, the best accuracy of 0.9269 on the Changsha dataset and 0.9635 on the ICPR 2016 dataset for the traditional methods is obtained by a combination of SIFT and RIC-LBP with the ECLF classifier, and the best accuracy obtained by the InceptionResNetV2 is 0.9465 and 0.9836 separately, which outperforms other schemes.

In this paper, an improved fuzzy connectedness (FC) method was proposed for automatic three-dimensional (3D) liver vessel segmentation in computed tomography (CT) images. The vessel-enhanced image (i.e., vesselness image) was incorporated into the fuzzy affinity function of FC, rather than the intensity image used by traditional FC. An improved vesselness filter was proposed by incorporating adaptive sigmoid filtering and a background-suppressing item. The fuzzy scene of FC was automatically initialized by using the Otsu segmentation algorithm and one single seed generated adaptively, while traditional FC required multiple seeds. The improved FC method was evaluated on 40 cases of clinical CT volumetric images from the 3Dircadb (n=20) and Sliver07 (n=20) datasets. Experimental results showed that the proposed liver vessel segmentation strategy could achieve better segmentation performance than traditional FC, region growing, and threshold level set. Average accuracy, sensitivity, specificity, and Dice coefficient of the improved FC method were, respectively, (96.4 ± 1.1)%, (73.7 ± 7.6)%, (97.4 ± 1.3)%, and (67.3 ± 5.7)% for the 3Dircadb dataset and (96.8 ± 0.6)%, (89.1 ± 6.8)%, (97.6 ± 1.1)%, and (71.4 ± 7.6)% for the Sliver07 dataset. It was concluded that the improved FC may be used as a new method for automatic 3D segmentation of liver vessel from CT images.

The study presented in this paper tests the hypothesis that the combination of a global similarity transformation and local free form deformations can be used for the accurate segmentation of internal structures in MR images of the brain. To quantitatively evaluate our approach, the entire brain, the cerebellum and the head of the caudate have been segmented manually on one of the volumes and mapped back onto all the other volumes using the computed transformations. The contours so obtained have been compared to contours drawn manually around the structures of interest in each individual brain. Manual delineation was repeated to test intra-rater variability. Contours were quantitatively compared using a similarity index defined as 2 times the area encircled by both contours divided by the sum of the areas encircled by each contour. This index ranges from 0 to 1 with zero indicating zero overlap and one indicating a perfect agreement between two contours. It is sensitive to both displacement and differences in shape and it is thus preferable to a simple area comparison. Results indicate that the method we proposed can be used to segment accurately and fully automatically large and small structures in high resolution 3D images of the brain. The average similarity indices between the manual and automatic segmentations are 0.96, 0.97, and 0.845 for the whole head, the cerebellum, and the head of the caudate respectively. These numbers are 0.97, 0.97, and 0.88 when two manual delineations are compared. Statistical analysis reveals that the differences in mean similarity indices between the two manual delineations and between the manual delineations and the automatic segmentation method are statistically significant for the whole head and the caudate but not for the cerebellum. It is shown, however, that similarity indices in the range of 0.85 correspond to contours that are virtually undistinguishable.

Automatic segmentation of the retinal vasculature is a first step in computer-assisted diagnosis and treatment planning. The extraction of retinal vessels in pediatric retinal images is challenging because of comparatively wide arterioles with a light streak running longitudinally along the vessel's center, the central vessel reflex. A new method for automatic segmentation was developed and tested. A supervised method for retinal vessel segmentation in the images of multi-ethnic school children was developed based on ensemble classifier of bootstrapped decision trees. A collection of dual Gaussian, second derivative of Gaussian and Gabor filters, along with the generalized multiscale line strength measure and morphological transformation is used to generate the feature vector. The feature vector encodes information to handle the normal vessels as well as the vessels with the central reflex. The methodology is evaluated on CHASE_DB1, a relatively new public retinal image database of multi-ethnic school children, which is a subset of retinal images from the Child Heart and Health Study in England (CHASE) dataset. The segmented retinal images from the CHASE_DB1 database produced best case accuracy, sensitivity and specificity of 0.96, 0.74 and 0.98, respectively, and worst case measures of 0.94, 0.67 and 0.98, respectively. A new retinal blood vessel segmentation algorithm was developed and tested with a shared database. The observed accuracy, speed, robustness and simplicity suggest that the algorithm may be a suitable tool for automated retinal image analysis in large population-based studies.

—Segmenting tumor from MRI images is an essential but time consuming manual duty. Performing an automatic segmentation is a defying task since different forms of tumor tissue exist for diverse patients and in many cases the tumor is similar to the normal tissue. Various studies proposed earlier to handle the issue of precisely segmenting the tumor but they discard the degradations and their effect to the precision of the segmentation. This article provides a more precise segmentation process through the use of appropriate pre-processing algorithms. The authors studied many enhancement and restoration algorithms and selected the NL-means, Laplacian filter and histogram equalization to be used as preprocessing techniques. Experimental results showed that using a suitable preprocessing scheme would produce a better segmentation process. Index Terms — Medical image processing, Tumor segmentation, MRI images, Non-local Means, Histogram equalization, Laplacian filter. I. INTRODUCTION A tumor is a mass of tissue that grows out of control of the normal forces that regulates growth. Brain tumor has a higher mortality rate when compared to more common types of cancer. This underlines the need of accurate prognosis of brain tumor in health care industry [1]. MRI has become a widely-used method of high-quality medical imaging, especially in brain imaging [2]. Image segmentation refers to the process of partitioning a digital image into multiple segments, also known as super pixels. Image segmentation is an important process in computer vision and image processing, which divides an image into a number of disjoint regions such that the pixels have high similarity in order to use its different fields; science, medical, agriculture and industrial fields [3]. Besides, Magnetic Resonance Imaging (MRI) images are known to be corrupted by noise [4], blur [5] and low contrast artifact [6]. Therefore, this article discusses the issue of achieving a better segmentation through the use of proper image restoration and enhancement techniques. Moreover, the accurate and automatic segmentation of a brain tumor on MRI image is of great interest for assessing tumor growth and treatment responses, enhancing computer-assisted surgery, and constructing tumor growth models [7]. For those reasons, an automatic and reliable tumor segmentation method would be a useful tool since the medical image segmentation plays an instrumental role in clinical diagnosis [8]. The rest of the article sections are organized as the following: in section two, a brief elucidation about some related studies is presented as the used literature review. Moreover, detailed explanations about the employed algorithms are delivered in section three as a methodology. Also, the results of the proposed methodology are illustrated in section four as the experimental results. Likewise, a detailed discussion about the use of certain algorithms and its results is deliberated in section five. Finally, a brief closure about this article is provided in section six as a conclusion. II. LITERATURE REVIEW In this section, three recent studies are briefly described. The first study was presented by [9] which proposed a texture based analysis to identify irregularity in the brain and automatic segmentation using seeded region growing segmentation. The method of tumor detection based on the texture of the MRI is proposed to segment the abnormality from the regular adjacent, although small quantities misclassified, but the segmentation result is precise. Moreover, [10] suggested a strong technique for automatic detection of tumor for brain MRI images. He also proposed a new morphological technique which is used for the stripped skull region from the brain images. Detecting tumor precisely based on seeded region growing segmentation on an improved single seed point selection algorithm is