Prostate Segmentation Research Articles

PO-0990: A Clinical Decision Support Tool Based on Active Appearance Modelling for Prostate Segmentation

PO-0990: A Clinical Decision Support Tool Based on Active Appearance Modelling for Prostate Segmentation

A semiautomatic algorithm for three-dimensional segmentation of the prostate on CT images using shape and local texture characteristics.

Prostate segmentation in computed tomography (CT) images is useful for planning and guidance of the diagnostic and therapeutic procedures. However, the low soft-tissue contrast of CT images makes the manual prostate segmentation a time-consuming task with high inter-observer variation. We developed a semi-automatic, three-dimensional (3D) prostate segmentation algorithm using shape and texture analysis and have evaluated the method against manual reference segmentations. In a training data set we defined an inter-subject correspondence between surface points in the spherical coordinate system. We applied this correspondence to model the globular and smoothly curved shape of the prostate with 86, well-distributed surface points using a point distribution model that captures prostate shape variation. We also studied the local texture difference between prostate and non-prostate tissues close to the prostate surface. For segmentation, we used the learned shape and texture characteristics of the prostate in CT images and we used a set of user inputs for prostate localization. We trained our algorithm using 23 CT images and tested it on 10 images. We evaluated the results compared with those of two experts' manual reference segmentations using different error metrics. The average measured Dice similarity coefficient (DSC) and mean absolute distance (MAD) were 88 ± 2% and 1.9 ± 0.5 mm, respectively. The averaged inter-expert difference measured on the same dataset was 91 ± 4% (DSC) and 1.3 ± 0.6 mm (MAD). With no prior intra-patient information, the proposed algorithm showed a fast, robust and accurate performance for 3D CT segmentation.

Automatic Prostate Cancer Segmentation Using Kinetic Analysis in Dynamic Contrast-Enhanced MRI

Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) provides functional information on the microcirculation in tissues by analyzing the enhancement kinetics which can be used as biomarkers for prostate lesions detection and characterization. The purpose of this study is to investigate spatiotemporal patterns of tumors by extracting semi-quantitative as well as wavelet-based features, both extracted from pixel-based time-signal intensity curves to segment prostate lesions on prostate DCE-MRI. Quantitative dynamic contrast-enhanced MRI data were acquired on 22 patients. Optimal features selected by forward selection are used for the segmentation of prostate lesions by applying fuzzy c-means (FCM) clustering. The images were reviewed by an expert radiologist and manual segmentation performed as the ground truth. Empirical results indicate that fuzzy c-mean classifier can achieve better results in terms of sensitivity, specificity when semi-quantitative features were considered versus wavelet kinetic features for lesion segmentation (Sensitivity of 87.58% and 75.62%, respectively) and (Specificity of 89.85% and 68.89 %, respectively). The proposed segmentation algorithm in this work can potentially be implemented for automatic prostate lesion detection in a computer aided diagnosis scheme and combined with morphologic features to increase diagnostic credibility.

PSNet: prostate segmentation on MRI based on a convolutional neural network.

Automatic segmentation of the prostate on magnetic resonance images (MRI) has many applications in prostate cancer diagnosis and therapy. We proposed a deep fully convolutional neural network (CNN) to segment the prostate automatically. Our deep CNN model is trained end-to-end in a single learning stage, which uses prostate MRI and the corresponding ground truths as inputs. The learned CNN model can be used to make an inference for pixel-wise segmentation. Experiments were performed on three data sets, which contain prostate MRI of 140 patients. The proposed CNN model of prostate segmentation (PSNet) obtained a mean Dice similarity coefficient of [Formula: see text] as compared to the manually labeled ground truth. Experimental results show that the proposed model could yield satisfactory segmentation of the prostate on MRI.

Exploiting Interslice Correlation for MRI Prostate Image Segmentation, from Recursive Neural Networks Aspect

Segmentation of the prostate from Magnetic Resonance Imaging (MRI) plays an important role in prostate cancer diagnosis. However, the lack of clear boundary and significant variation of prostate shapes and appearances make the automatic segmentation very challenging. In the past several years, approaches based on deep learning technology have made significant progress on prostate segmentation. However, those approaches mainly paid attention to features and contexts within each single slice of a 3D volume. As a result, this kind of approaches faces many difficulties when segmenting the base and apex of the prostate due to the limited slice boundary information. To tackle this problem, in this paper, we propose a deep neural network with bidirectional convolutional recurrent layers for MRI prostate image segmentation. In addition to utilizing the intraslice contexts and features, the proposed model also treats prostate slices as a data sequence and utilizes the interslice contexts to assist segmentation. The experimental results show that the proposed approach achieved significant segmentation improvement compared to other reported methods.

Automatic Magnetic Resonance Image Prostate Segmentation Based on Adaptive Feature Learning Probability Boosting Tree Initialization and CNN-ASM Refinement

This paper proposes a method based on the active shape model (ASM) to segment the prostate in magnetic resonance (MR) images. Due to the great variability in appearance among different boundaries of the prostate and among subjects, the traditional ASM is weak in MR image prostate segmentation. To address these limitations, we investigated a novel ASM-based method by incorporating deep feature learning into our previous liver segmentation framework. First, an adaptive feature learning probability boosting tree (AFL-PBT) based on both simple handcrafted features and deep learned features was developed for prostate pre-segmentation and for further shape model initialization. The proposed AFL-PBT classifier also provided a boundary searching band, which made the ASM less sensitive to model initialization. Then, the convolutional neutral network (CNN) deep learning method was used to train a boundary model, which separated voxels into three types: near, inside, and outside the boundary. A three-level ASM based on the CNN boundary model was employed for the final segmentation refinement. On MICCAI PROMISE12 test data sets, the proposed method yielded a mean Dice score of 84% with a standard deviation of 4%. The experimental results demonstrated that the proposed method outperformed other ASM-based prostate MRI segmentation methods and achieved a level of accuracy comparable to that of state-of-the-art methods.

A Survey of Prostate Segmentation Techniques in Different Imaging Modalities

Background: Prostate cancer (PCa) is a leading dreadful cancer amid aged men in the United States. During past few decades, a number of studies have been carried out in both medical field and imaging technology for PCa detection and diagnosis. Techniques: Imaging technology-based diagnosis includes TRUS, MRI and CT at the macroscopic level and histological images at the microscopic level. Discussion: To assist novice researchers for a better understanding of prostate segmentation techniques, this article mainly presents the survey of various delineation techniques for prostate pertaining to different modalities i.e. TRUS, MRI and CT, which is an important auxiliary phase in PCa diagnosis. This paper also highlights various PCa grading approaches based on histology imaging with certain gaps that need to address for timely and precise diagnostic recommendations to suppress mortality rates globally. Quantitative/qualitative evaluation and analysis of the existing state-of-the-art segmentation techniques along with their strength and limitations as described in literature is also presented. Conclusion: Prostate delineation is still an open challenge and with progression of technology for identification, medication and follow up of prostate diseases, new prerequisites have to be realized. Keywords: PCa, TRUS, MRI, CT, histology, prostate delineation.

Learning normalized inputs for iterative estimation in medical image segmentation.

In this paper, we introduce a simple, yet powerful pipeline for medical image segmentation that combines Fully Convolutional Networks (FCNs) with Fully Convolutional Residual Networks (FC-ResNets). We propose and examine a design that takes particular advantage of recent advances in the understanding of both Convolutional Neural Networks as well as ResNets. Our approach focuses upon the importance of a trainable pre-processing when using FC-ResNets and we show that a low-capacity FCN model can serve as a pre-processor to normalize medical input data. In our image segmentation pipeline, we use FCNs to obtain normalized images, which are then iteratively refined by means of a FC-ResNet to generate a segmentation prediction. As in other fully convolutional approaches, our pipeline can be used off-the-shelf on different image modalities. We show that using this pipeline, we exhibit state-of-the-art performance on the challenging Electron Microscopy benchmark, when compared to other 2D methods. We improve segmentation results on CT images of liver lesions, when contrasting with standard FCN methods. Moreover, when applying our 2D pipeline on a challenging 3D MRI prostate segmentation challenge we reach results that are competitive even when compared to 3D methods. The obtained results illustrate the strong potential and versatility of the pipeline by achieving accurate segmentations on a variety of image modalities and different anatomical regions.

3D Registration of mpMRI for Assessment of Prostate Cancer Focal Therapy

This study aimed to assess a novel method of three-dimensional (3D) co-registration of prostate magnetic resonance imaging (MRI) examinations performed before and after prostate cancer focal therapy. We developed a software platform for automatic 3D deformable co-registration of prostate MRI at different time points and applied this method to 10 patients who underwent focal ablative therapy. MRI examinations were performed preoperatively, as well as 1 week and 6 months post treatment. Rigid registration served as reference for assessing co-registration accuracy and precision. Segmentation of preoperative and postoperative prostate revealed a significant postoperative volume decrease of the gland that averaged 6.49 cc (P = .017). Applying deformable transformation based on mutual information from 120 pairs of MRI slices, we refined by 2.9 mm (max. 6.25 mm) the alignment of the ablation zone, segmented from contrast-enhanced images on the 1-week postoperative examination, to the 6-month postoperative T2-weighted images. This represented a 500% improvement over the rigid approach (P = .001), corrected by volume. The dissimilarity by Dice index of the mapped ablation zone using deformable transformation vs rigid control was significantly (P = .04) higher at the ablation site than in the whole gland. Our findings illustrate our method's ability to correct for deformation at the ablation site. The preliminary analysis suggests that deformable transformation computed from mutual information of preoperative and follow-up MRI is accurate in co-registration of MRI examinations performed before and after focal therapy. The ability to localize the previously ablated tissue in 3D space may improve targeting for image-guided follow-up biopsy within focal therapy protocols.

Atlas registration and ensemble deep convolutional neural network-based prostate segmentation using magnetic resonance imaging

Automatic segmentation of prostate in magnetic resonance (MR) images has been more and more applied to the diagnosis of prostate disease and various clinical applications. However, due to the inhomogeneous and varying anatomical appearance around prostate boundary, the segmentation of prostate MR images faces great challenges. Since deep learning shows superior performance in computer vision, we propose a coarse-to-fine segmentation strategy by using deep neural networks to tackle the segmentation problem of the endorectal coil prostate images and non-endorectal coil prostate images separately. First, we present a registration-based coarse segmentation to the pre-processed prostate MR images to get the potential boundary region. Second, we train deep neural networks as pixel-based classifier to predict whether the pixel in the potential boundary region is prostate pixel or not. To improve the discriminability of the algorithm, we further introduce ensemble learning for fine segmentation. Finally, a boundary refinement is used to eliminate the outlier and smooth the boundary. The proposed method has been extensively evaluated on the PROMIS12 challenge dataset and PROSTATEx17 challenge dataset. Experimental results show superior segmentation performance (0.910 ± 0.036 in dice ratio, 1.583 ± 0.441 in average boundary distance and 4.579 ± 1.791 in Hausdorff distance), which demonstrates the effectiveness of the proposed algorithm.

A combined learning algorithm for prostate segmentation on 3D CT images.

Segmentation of the prostate on CT images has many applications in the diagnosis and treatment of prostate cancer. Because of the low soft-tissue contrast on CT images, prostate segmentation is a challenging task. A learning-based segmentation method is proposed for the prostate on three-dimensional (3D) CT images. We combine population-based and patient-based learning methods for segmenting the prostate on CT images. Population data can provide useful information to guide the segmentation processing. Because of inter-patient variations, patient-specific information is particularly useful to improve the segmentation accuracy for an individual patient. In this study, we combine a population learning method and a patient-specific learning method to improve the robustness of prostate segmentation on CT images. We train a population model based on the data from a group of prostate patients. We also train a patient-specific model based on the data of the individual patient and incorporate the information as marked by the user interaction into the segmentation processing. We calculate the similarity between the two models to obtain applicable population and patient-specific knowledge to compute the likelihood of a pixel belonging to the prostate tissue. A new adaptive threshold method is developed to convert the likelihood image into a binary image of the prostate, and thus complete the segmentation of the gland on CT images. The proposed learning-based segmentation algorithm was validated using 3D CT volumes of 92 patients. All of the CT image volumes were manually segmented independently three times by two, clinically experienced radiologists and the manual segmentation results served as the gold standard for evaluation. The experimental results show that the segmentation method achieved a Dice similarity coefficient of 87.18 ± 2.99%, compared to the manual segmentation. By combining the population learning and patient-specific learning methods, the proposed method is effective for segmenting the prostate on 3D CT images. The prostate CT segmentation method can be used in various applications including volume measurement and treatment planning of the prostate.

Automatic magnetic resonance prostate segmentation by deep learning with holistically nested networks.

Accurate automatic segmentation of the prostate in magnetic resonance images (MRI) is a challenging task due to the high variability of prostate anatomic structure. Artifacts such as noise and similar signal intensity of tissues around the prostate boundary inhibit traditional segmentation methods from achieving high accuracy. We investigate both patch-based and holistic (image-to-image) deep-learning methods for segmentation of the prostate. First, we introduce a patch-based convolutional network that aims to refine the prostate contour which provides an initialization. Second, we propose a method for end-to-end prostate segmentation by integrating holistically nested edge detection with fully convolutional networks. Holistically nested networks (HNN) automatically learn a hierarchical representation that can improve prostate boundary detection. Quantitative evaluation is performed on the MRI scans of 250 patients in fivefold cross-validation. The proposed enhanced HNN model achieves a mean ± standard deviation. A Dice similarity coefficient (DSC) of [Formula: see text] and a mean Jaccard similarity coefficient (IoU) of [Formula: see text] are used to calculate without trimming any end slices. The proposed holistic model significantly ([Formula: see text]) outperforms a patch-based AlexNet model by 9% in DSC and 13% in IoU. Overall, the method achieves state-of-the-art performance as compared with other MRI prostate segmentation methods in the literature.

Designing image segmentation studies: Statistical power, sample size and reference standard quality.

Segmentation algorithms are typically evaluated by comparison to an accepted reference standard. The cost of generating accurate reference standards for medical image segmentation can be substantial. Since the study cost and the likelihood of detecting a clinically meaningful difference in accuracy both depend on the size and on the quality of the study reference standard, balancing these trade-offs supports the efficient use of research resources. In this work, we derive a statistical power calculation that enables researchers to estimate the appropriate sample size to detect clinically meaningful differences in segmentation accuracy (i.e. the proportion of voxels matching the reference standard) between two algorithms. Furthermore, we derive a formula to relate reference standard errors to their effect on the sample sizes of studies using lower-quality (but potentially more affordable and practically available) reference standards. The accuracy of the derived sample size formula was estimated through Monte Carlo simulation, demonstrating, with 95% confidence, a predicted statistical power within 4% of simulated values across a range of model parameters. This corresponds to sample size errors of less than 4 subjects and errors in the detectable accuracy difference less than 0.6%. The applicability of the formula to real-world data was assessed using bootstrap resampling simulations for pairs of algorithms from the PROMISE12 prostate MR segmentation challenge data set. The model predicted the simulated power for the majority of algorithm pairs within 4% for simulated experiments using a high-quality reference standard and within 6% for simulated experiments using a low-quality reference standard. A case study, also based on the PROMISE12 data, illustrates using the formulae to evaluate whether to use a lower-quality reference standard in a prostate segmentation study.

Segmentation of prostate contours for automated diagnosis using ultrasound images: A survey

Prostate cancer is the most common cancer that affects elderly men. The conventional non-imaging screening test for prostate cancer like prostate antigen (PSA) and digital rectal examination (DRE) tests generally lack specificity. Ultrasound is the most commonly available, inexpensive, non-invasive, and radiation-free imaging modality among all the screening imaging modalities available for prostate cancer diagnosis. The precise segmentation of prostate contours in ultrasound images is crucial in applications such as the exact placement of needles during biopsies, computing the prostate gland volume, and to localize the prostate cancer. Moreover, the low-dose-rate (LDR) brachytherapy treatment in which radioactive seeds are implanted in the prostate region requires accurate contouring of the prostate gland in ultrasound images. Therefore, it is very important to segment the prostrate region accurately for the diagnosis and treatment. This paper aims to present the analysis of existing approaches used for the segmentation of prostate in transrectal ultrasound (TRUS) images. In this survey, different segmentation methods used to extract the prostrate using criteria such as mean absolute distance, Hausdorff distance and time are discussed in detail and compared.

Automated Prostate Gland Segmentation Based on an Unsupervised Fuzzy C-Means Clustering Technique Using Multispectral T1w and T2w MR Imaging

Prostate imaging analysis is difficult in diagnosis, therapy, and staging of prostate cancer. In clinical practice, Magnetic Resonance Imaging (MRI) is increasingly used thanks to its morphologic and functional capabilities. However, manual detection and delineation of prostate gland on multispectral MRI data is currently a time-expensive and operator-dependent procedure. Efficient computer-assisted segmentation approaches are not yet able to address these issues, but rather have the potential to do so. In this paper, a novel automatic prostate MR image segmentation method based on the Fuzzy C-Means (FCM) clustering algorithm, which enables multispectral T1-weighted (T1w) and T2-weighted (T2w) MRI anatomical data processing, is proposed. This approach, using an unsupervised Machine Learning technique, helps to segment the prostate gland effectively. A total of 21 patients with suspicion of prostate cancer were enrolled in this study. Volume-based metrics, spatial overlap-based metrics and spatial distance-based metrics were used to quantitatively evaluate the accuracy of the obtained segmentation results with respect to the gold-standard boundaries delineated manually by an expert radiologist. The proposed multispectral segmentation method was compared with the same processing pipeline applied on either T2w or T1w MR images alone. The multispectral approach considerably outperforms the monoparametric ones, achieving an average Dice Similarity Coefficient 90.77 ± 1.75, with respect to 81.90 ± 6.49 and 82.55 ± 4.93 by processing T2w and T1w imaging alone, respectively. Combining T2w and T1w MR image structural information significantly enhances prostate gland segmentation by exploiting the uniform gray appearance of the prostate on T1w MRI.

Accuracy Validation of an Automated Method for Prostate Segmentation in Magnetic Resonance Imaging.

Three dimensional (3D) manual segmentation of the prostate on magnetic resonance imaging (MRI) is a laborious and time-consuming task that is subject to inter-observer variability. In this study, we developed a fully automatic segmentation algorithm for T2-weighted endorectal prostate MRI and evaluated its accuracy within different regions of interest using a set of complementary error metrics. Our dataset contained 42 T2-weighted endorectal MRI from prostate cancer patients. The prostate was manually segmented by one observer on all of the images and by two other observers on a subset of 10 images. The algorithm first coarsely localizes the prostate in the image using a template matching technique. Then, it defines the prostate surface using learned shape and appearance information from a set of training images. To evaluate the algorithm, we assessed the error metric values in the context of measured inter-observer variability and compared performance to that of our previously published semi-automatic approach. The automatic algorithm needed an average execution time of ∼60s to segment the prostate in 3D. When compared to a single-observer reference standard, the automatic algorithm has an average mean absolute distance of 2.8mm, Dice similarity coefficient of 82%, recall of 82%, precision of 84%, and volume difference of 0.5cm3 in the mid-gland. Concordant with other studies, accuracy was highest in the mid-gland and lower in the apex and base. Loss of accuracy with respect to the semi-automatic algorithm was less than the measured inter-observer variability in manual segmentation for the same task.

Segmentation of the prostate on magnetic resonance images using an ellipsoidal shape prior constraint algorithm

We propose a novel strategy for multi-atlas-based image segmentation of the prostate on magnetic resonance (MR) images using an ellipsoidal shape prior constraint algorithm. An ellipsoidal shape prior constraint was incorporated into the process of multi-atlas based segmentation to restrict the regions of interest on the prostate images and avoid the interference by the surrounding tissues and organs in atlas selection. In the subsequent process of atlas fusion, the ellipsoidal shape prior constraint calibrated and compensated for the shape prior obtained by the registration technique to avoid incorrect segmentation caused by registration errors. Evaluation of this proposed method on prostate images from 50 subjects showed that this algorithm was effective and yielded a mean Dice similarity coefficients of 0.8812, suggesting its high accuracy and robustness to segment the prostate on MR images.

DeepInfer: Open-Source Deep Learning Deployment Toolkit for Image-Guided Therapy.

Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. Instead of using hand-engineered features, deep models attempt to automatically extract hierarchical representations at multiple levels of abstraction from the data. Therefore, deep models are usually considered to be more flexible and robust solutions for image analysis problems compared to conventional computer vision models. They have demonstrated significant improvements in computer-aided diagnosis and automatic medical image analysis applied to such tasks as image segmentation, classification and registration. However, deploying deep learning models often has a steep learning curve and requires detailed knowledge of various software packages. Thus, many deep models have not been integrated into the clinical research workflows causing a gap between the state-of-the-art machine learning in medical applications and evaluation in clinical research procedures. In this paper, we propose "DeepInfer" - an open-source toolkit for developing and deploying deep learning models within the 3D Slicer medical image analysis platform. Utilizing a repository of task-specific models, DeepInfer allows clinical researchers and biomedical engineers to deploy a trained model selected from the public registry, and apply it to new data without the need for software development or configuration. As two practical use cases, we demonstrate the application of DeepInfer in prostate segmentation for targeted MRI-guided biopsy and identification of the target plane in 3D ultrasound for spinal injections.

Fine-Grained Recurrent Neural Networks for Automatic Prostate Segmentation in Ultrasound Images

Boundary incompleteness raises great challenges to automatic prostate segmentation in ultrasound images. Shape prior can provide strong guidance in estimating the missing boundary, but traditional shape models often suffer from hand-crafted descriptors and local information loss in the fitting procedure. In this paper, we attempt to address those issues with a novel framework. The proposed framework can seamlessly integrate feature extraction and shape prior exploring, and estimate the complete boundary with a sequential manner. Our framework is composed of three key modules. Firstly, we serialize the static 2D prostate ultrasound images into dynamic sequences and then predict prostate shapes by sequentially exploring shape priors. Intuitively, we propose to learn the shape prior with the biologically plausible Recurrent Neural Networks (RNNs). This module is corroborated to be effective in dealing with the boundary incompleteness. Secondly, to alleviate the bias caused by different serialization manners, we propose a multi-view fusion strategy to merge shape predictions obtained from different perspectives. Thirdly, we further implant the RNN core into a multiscale Auto-Context scheme to successively refine the details of the shape prediction map. With extensive validation on challenging prostate ultrasound images, our framework bridges severe boundary incompleteness and achieves the best performance in prostate boundary delineation when compared with several advanced methods. Additionally, our approach is general and can be extended to other medical image segmentation tasks, where boundary incompleteness is one of the main challenges.

Volumetric ConvNets with Mixed Residual Connections for Automated Prostate Segmentation from 3D MR Images

Automated prostate segmentation from 3D MR images is very challenging due to large variations of prostate shape and indistinct prostate boundaries. We propose a novel volumetric convolutional neural network (ConvNet) with mixed residual connections to cope with this challenging problem. Compared with previous methods, our volumetric ConvNet has two compelling advantages. First, it is implemented in a 3D manner and can fully exploit the 3D spatial contextual information of input data to perform efficient, precise and volume-to-volume prediction. Second and more important, the novel combination of residual connections (i.e., long and short) can greatly improve the training efficiency and discriminative capability of our network by enhancing the information propagation within the ConvNet both locally and globally. While the forward propagation of location information can improve the segmentation accuracy, the smooth backward propagation of gradient flow can accelerate the convergence speed and enhance the discrimination capability. Extensive experiments on the open MICCAI PROMISE12 challenge dataset corroborated the effectiveness of the proposed volumetric ConvNet with mixed residual connections. Our method ranked the first in the challenge, outperforming other competitors by a large margin with respect to most of evaluation metrics. The proposed volumetric ConvNet is general enough and can be easily extended to other medical image analysis tasks, especially ones with limited training data.