Liver Segmentation on CT and MR Using Laplacian Mesh Optimization

S2DA-Net: Spatial and spectral-learning double-branch aggregation network for liver tumor segmentation in CT images

Accurate liver tumor segmentation is crucial for aiding radiologists in hepatocellular carcinoma evaluation and surgical planning. While convolutional neural networks (CNNs) have been successful in medical image segmentation, they face challenges in capturing long-term dependencies among pixels. On the other hand, Transformer-based models demand a high number of parameters and involve significant computational costs. To address these issues, we propose the Spatial and Spectral-learning Double-branched Aggregation Network (S2DA-Net) for liver tumor segmentation. S2DA-Net consists of a double-branched encoder and a decoder with a Group Multi-Head Cross-Attention Aggregation (GMCA) module, Two branches in the encoder consist of a Fourier Spectral-learning Multi-scale Fusion (FSMF) branch and a Multi-axis Aggregation Hadamard Attention (MAHA) branch. The FSMF branch employs a Fourier-based network to learn amplitude and phase information, capturing richer features and detailed information without introducing an excessive number of parameters. The FSMF branch utilizes a Fourier-based network to capture amplitude and phase information, enriching features without introducing excessive parameters. The MAHA branch incorporates spatial information, enhancing discriminative features while minimizing computational costs. In the decoding path, a GMCA module extracts local information and establishes long-term dependencies, improving localization capabilities by amalgamating features from diverse branches. Experimental results on the public LiTS2017 liver tumor datasets show that the proposed segmentation model achieves significant improvements compared to the state-of-the-art methods, obtaining dice per case (DPC) 69.4 % and global dice (DG) 80.0 % for liver tumor segmentation on the LiTS2017 dataset. Meanwhile, the pre-trained model based on the LiTS2017 datasets obtain, DPC 73.4 % and an DG 82.2 % on the 3DIRCADb dataset.

Improving automatic segmentation of liver tumor images using a deep learning model

Liver tumors are one of the most aggressive malignancies in the human body. Computer-aided technology and liver interventional surgery are effective in the prediction, identification and management of liver neoplasms. One of the important processes is to accurately grasp the morphological structure of the liver and liver blood vessels. However, accurate identification and segmentation of hepatic blood vessels in CT images poses a formidable challenge. Manually locating and segmenting liver vessels in CT images is time-consuming and impractical. There is an imperative clinical requirement for a precise and effective algorithm to segment liver vessels. In response to this demand, the current paper advocates a liver vessel segmentation approach that employs an enhanced 3D fully convolutional neural network V-Net. The network model improves the basic network structure according to the characteristics of liver vessels. First, a pyramidal convolution block is introduced between the encoder and decoder of the network to improve the network localization ability. Then, multi-resolution deep supervision is introduced in the network, resulting in more robust segmentation. Finally, by fusing feature maps of different resolutions, the overall segmentation result is predicted. Evaluation experiments on public datasets demonstrate that our improved scheme can increase the segmentation ability of existing network models for liver vessels. Compared with the existing work, the experimental outcomes demonstrate that the technique presented in this manuscript has attained superior performance on the Dice Coefficient index, which can promote the treatment of liver tumors.

EPolar-UNet: An edge-attending polar UNet for automatic medical image segmentation with small datasets

BACKGROUND

Medical image segmentation is one of the most key steps in computer-aided clinical diagnosis, geometric characterization, measurement, image registration, and so forth. Convolutional neural networks especially UNet and its variants have been successfully used in many medical image segmentation tasks. However, the results are limited by the deficiency in extracting high resolution edge information because of the design of the skip connections in UNet and the need for large available datasets.

PURPOSE

In this paper, we proposed an edge-attending polar UNet (EPolar-UNet), which was trained on the polar coordinate system instead of classic Cartesian coordinate system with an edge-attending construction in skip connection path.

METHODS

EPolar-UNet extracted the location information from an eight-stacked hourglass network as the pole for polar transformation and extracted the boundary cues from an edge-attending UNet, which consisted of a deconvolution layer and a subtraction operation.

RESULTS

We evaluated the performance of EPolar-UNet across three imaging modalities for different segmentation tasks: CVC-ClinicDB dataset for polyp, ISIC-2018 dataset for skin lesion, and our private ultrasound dataset for liver tumor segmentation. Our proposed model outperformed state-of-the-art models on all three datasets and needed only 30%-60% of training data compared with the benchmark UNet model to achieve similar performances for medical image segmentation tasks.

CONCLUSIONS

We proposed an end-to-end EPolar-UNet for automatic medical image segmentation and showed good performance on small datasets, which was critical in the field of medical image segmentation.

Recent advances in computerized imaging and its vital roles in liver disease diagnosis, preoperative planning, and interventional liver surgery: A review

The earliest and most accurate detection of the pathological manifestations of hepatic diseases ensures effective treatments and thus positive prognostic outcomes. In clinical settings, screening and determining the extent of a pathology are prominent factors in preparing remedial agents and administering appropriate therapeutic procedures. Moreover, in a patient undergoing liver resection, a realistic preoperative simulation of the subject-specific anatomy and physiology also plays a vital part in conducting initial assessments, making surgical decisions during the procedure, and anticipating postoperative results. Conventionally, various medical imaging modalities, e.g., computed tomography, magnetic resonance imaging, and positron emission tomography, have been employed to assist in these tasks. In fact, several standardized procedures, such as lesion detection and liver segmentation, are also incorporated into prominent commercial software packages. Thus far, most integrated software as a medical device typically involves tedious interactions from the physician, such as manual delineation and empirical adjustments, as per a given patient. With the rapid progress in digital health approaches, especially medical image analysis, a wide range of computer algorithms have been proposed to facilitate those procedures. They include pattern recognition of a liver, its periphery, and lesion, as well as pre- and postoperative simulations. Prior to clinical adoption, however, software must conform to regulatory requirements set by the governing agency, for instance, valid clinical association and analytical and clinical validation. Therefore, this paper provides a detailed account and discussion of the state-of-the-art methods for liver image analyses, visualization, and simulation in the literature. Emphasis is placed upon their concepts, algorithmic classifications, merits, limitations, clinical considerations, and future research trends.

A novel one-to-multiple unsupervised domain adaptation framework for abdominal organ segmentation

Abdominal multi-organ segmentation in multi-sequence magnetic resonance images (MRI) is of great significance in many clinical scenarios, e.g., MRI-oriented pre-operative treatment planning. Labeling multiple organs on a single MR sequence is a time-consuming and labor-intensive task, let alone manual labeling on multiple MR sequences. Training a model by one sequence and generalizing it to other domains is one way to reduce the burden of manual annotation, but the existence of domain gap often leads to poor generalization performance of such methods. Image translation-based unsupervised domain adaptation (UDA) is a common way to address this domain gap issue. However, existing methods focus less on keeping anatomical consistency and are limited by one-to-one domain adaptation, leading to low efficiency for adapting a model to multiple target domains. This work proposes a unified framework called OMUDA for one-to-multiple unsupervised domain-adaptive segmentation, where disentanglement between content and style is used to efficiently translate a source domain image into multiple target domains. Moreover, generator refactoring and style constraint are conducted in OMUDA for better maintaining cross-modality structural consistency and reducing domain aliasing. The average Dice Similarity Coefficients (DSCs) of OMUDA for multiple sequences and organs on the in-house test set, the AMOS22 dataset and the CHAOS dataset are 85.51%, 82.66% and 91.38%, respectively, which are slightly lower than those of CycleGAN(85.66% and 83.40%) in the first two data sets and slightly higher than CycleGAN(91.36%) in the last dataset. But compared with CycleGAN, OMUDA reduces floating-point calculations by about 87 percent in the training phase and about 30 percent in the inference stage respectively. The quantitative results in both segmentation performance and training efficiency demonstrate the usability of OMUDA in some practical scenes, such as the initial phase of product development.

A Coarse-to-Fine Fusion Network for Small Liver Tumor Detection and Segmentation: A Real-World Study

Liver tumor semantic segmentation is a crucial task in medical image analysis that requires multiple MRI modalities. This paper proposes a novel coarse-to-fine fusion segmentation approach to detect and segment small liver tumors of various sizes. To enhance the segmentation accuracy of small liver tumors, the method incorporates a detection module and a CSR (convolution-SE-residual) module, which includes a convolution block, an SE (squeeze and excitation) module, and a residual module for fine segmentation. The proposed method demonstrates superior performance compared to conventional single-stage end-to-end networks. A private liver MRI dataset comprising 218 patients with a total of 3605 tumors, including 3273 tumors smaller than 3.0 cm, were collected for the proposed method. There are five types of liver tumors identified in this dataset: hepatocellular carcinoma (HCC); metastases of the liver; cholangiocarcinoma (ICC); hepatic cyst; and liver hemangioma. The results indicate that the proposed method outperforms the single segmentation networks 3D UNet and nnU-Net as well as the fusion networks of 3D UNet and nnU-Net with nnDetection. The proposed architecture was evaluated on a test set of 44 images, with an average Dice similarity coefficient (DSC) and recall of 86.9% and 86.7%, respectively, which is a 1% improvement compared to the comparison method. More importantly, compared to existing methods, our proposed approach demonstrates state-of-the-art performance in segmenting small objects with sizes smaller than 10 mm, achieving a Dice score of 85.3% and a malignancy detection rate of 87.5%.

Practical utility of liver segmentation methods in clinical surgeries and interventions

Clinical imaging (e.g., magnetic resonance imaging and computed tomography) is a crucial adjunct for clinicians, aiding in the diagnosis of diseases and planning of appropriate interventions. This is especially true in malignant conditions such as hepatocellular carcinoma (HCC), where image segmentation (such as accurate delineation of liver and tumor) is the preliminary step taken by the clinicians to optimize diagnosis, staging, and treatment planning and intervention (e.g., transplantation, surgical resection, radiotherapy, PVE, embolization, etc). Thus, segmentation methods could potentially impact the diagnosis and treatment outcomes. This paper comprehensively reviews the literature (during the year 2012–2021) for relevant segmentation methods and proposes a broad categorization based on their clinical utility (i.e., surgical and radiological interventions) in HCC. The categorization is based on the parameters such as precision, accuracy, and automation.

Liver surgery for colorectal metastasis: New paths and new goals with the help of artificial intelligence

Colorectal cancer is one of the most common neoplasia with an high risk to metastatic spread. Improving medical and surgical treatment is moving along with improving the precision of diagnosis and patient's assessment, the latter two aided more and more with the use of artificial intelligence (AI). The management of colorectal liver metastasis is multidisciplinary, and surgery is the main option. After the diagnosis, a surgical assessment of the patient is fundamental. Reaching a R0 resection with a proper remnant liver volume can be done using new techniques involving also artificial intelligence. Considering the recent application of artificial intelligence as a valid substitute for liver biopsy in chronic liver diseases, several authors tried to apply similar techniques to pre-operative imaging of liver metastasis. Radiomics showed good results in identifying structural changes in a unhealthy liver and in evaluating the prognosis after a liver resection. Recently deep learning has been successfully applied in estimating the remnant liver volume before surgery. Moreover AI techniques can help surgeons to perform an early diagnosis of neoplastic relapse or a better differentiation between a colorectal metastasis and a benign lesion. AI could be applied also in the histopathological diagnostic tool. Although AI implementation is still partially automatized, it appears faster and more precise than the usual diagnostic tools and, in the short future, could become the new gold standard in liver surgery.

3D FULLY CONVOLUTIONAL NETWORK FOR THORAX MULTI-ORGANS SEMANTIC SEGMENTATION

Automatically delineating Organs-at-Risks (OARs) on computed tomography (CT) has the benefit of both reducing the time and improving the quality of radiotherapy (RT) planning. A 3D convolutional deep learning framework for multi-organs segmentation is proposed in this work; moreover, for the small volume OARs, a robust 3D squeeze-and-excitation (SE) feature extraction mechanism and a new Dice loss function are incorporated in the traditional 3D U-Net. We collected 60 thorax CT images set with annotations and expanded to 260 patients by the augmented method of randomly rotating [Formula: see text]6 degrees with a 1/3 probability and adding Gaussian noise. The objective is to segment five important organs: esophagus, spinal cord, heart, and bilateral lungs. Compared with 3D U-Net, 3D-2D U-Net proposed in our work increases the Dice similarity coefficient by 5% on average for the heart and bilateral lungs, and 3D Small Volume U-Net can further increase the Dice similarity coefficient to above 80% for the spinal cord. The experiment results demonstrate that the proposed model can improve the delineation accuracy of OARs from CT images.

Hybrid-attention densely connected U-Net with GAP for extracting livers from CT volumes

PURPOSE

Liver segmentation is an important step in the clinical treatment of liver cancer, and accurate and automatic liver segmentation methods are extremely important. U-Net has been used as the benchmark for many medical segmentation networks, but it cannot fully utilize low-resolution information and global contextual information. To solve these problems, we propose a new network architecture named the hybrid-attention densely connected U-Net (HDU-Net).

METHODS

The proposed HDU-Net has three main changes relative to U-Net, as follows: (1) It uses a densely connected structure and dilated convolution to achieve feature reuse and avoid information loss. (2) A global average pooling block is proposed to further augment the receptive field and improve the segmentation accuracy of the network for small or disconnected liver regions. (3) By combining the spatial attention and channel attention mechanisms, a hybrid attention structure is proposed to replace the skip connection component to filter and integrate low-resolution information.

RESULTS

Experiments conducted on the LITS2017, 3Dircadb and Sliver07 datasets show that the proposed model can segment the liver accurately and effectively. Dice scores reach 96.5%, 96.18%, and 97.57% on these datasets, respectively, constituting results that are superior to many previously proposed methods.

CONCLUSIONS

The experimental liver segmentation results have demonstrated that our proposed network provides improved segmentation performance in comparison with other networks. The experimental results without postprocessing confirmed that our network solves the oversegmentation and undersegmentation problems to some extent. The proposed model is effective, robust, and efficient in terms of liver segmentation without requiring extensive training time or a very large dataset.

A hybrid approach based on deep learning and level set formulation for liver segmentation in CT images

Accurate liver segmentation is essential for radiation therapy planning of hepatocellular carcinoma and absorbed dose calculation. However, liver segmentation is a challenging task due to the anatomical variability in both shape and size and the low contrast between liver and its surrounding organs. Thus we propose a convolutional neural network (CNN) for automated liver segmentation. In our method, fractional differential enhancement is firstly applied for preprocessing. Subsequently, an initial liver segmentation is obtained by using a CNN. Finally, accurate liver segmentation is achieved by the evolution of an active contour model. Experimental results show that the proposed method outperforms existing methods. One hundred fifty CT scans are evaluated for the experiment. For liver segmentation, Dice of 95.8%, true positive rate of 95.1%, positive predictive value of 93.2%, and volume difference of 7% are calculated. In addition, the values of these evaluation measures show that the proposed method is able to provide a precise and robust segmentation estimate, which can also assist the manual liver segmentation task.

Deep Neural Network With Consistency Regularization of Multi-Output Channels for Improved Tumor Detection and Delineation

Deep learning is becoming an indispensable tool for imaging applications, such as image segmentation, classification, and detection. In this work, we reformulate a standard deep learning problem into a new neural network architecture with multi-output channels, which reflects different facets of the objective, and apply the deep neural network to improve the performance of image segmentation. By adding one or more interrelated auxiliary-output channels, we impose an effective consistency regularization for the main task of pixelated classification (i.e., image segmentation). Specifically, multi-output-channel consistency regularization is realized by residual learning via additive paths that connect main-output channel and auxiliary-output channels in the network. The method is evaluated on the detection and delineation of lung and liver tumors with public data. The results clearly show that multi-output-channel consistency implemented by residual learning improves the standard deep neural network. The proposed framework is quite broad and should find widespread applications in various deep learning problems.

An automated liver segmentation in liver iron concentration map using fuzzy c-means clustering combined with anatomical landmark data

Background

To estimate median liver iron concentration (LIC) calculated from magnetic resonance imaging, excluded vessels of the liver parenchyma region were defined manually. Previous works proposed the automated method for excluding vessels from the liver region. However, only user-defined liver region remained a manual process. Therefore, this work aimed to develop an automated liver region segmentation technique to automate the whole process of median LIC calculation.

Methods

553 MR examinations from 471 thalassemia major patients were used in this study. LIC maps (in mg/g dry weight) were calculated and used as the input of segmentation procedures. Anatomical landmark data were detected and used to restrict ROI. After that, the liver region was segmented using fuzzy c-means clustering and reduced segmentation errors by morphological processes. According to the clinical application, erosion with a suitable size of the structuring element was applied to reduce the segmented liver region to avoid uncertainty around the edge of the liver. The segmentation results were evaluated by comparing with manual segmentation performed by a board-certified radiologist.

Results

The proposed method was able to produce a good grade output in approximately 81% of all data. Approximately 11% of all data required an easy modification step. The rest of the output, approximately 8%, was an unsuccessful grade and required manual intervention by a user. For the evaluation matrices, percent dice similarity coefficient (%DSC) was in the range 86–92, percent Jaccard index (%JC) was 78–86, and Hausdorff distance (H) was 14–28 mm, respectively. In this study, percent false positive (%FP) and percent false negative (%FN) were applied to evaluate under- and over-segmentation that other evaluation matrices could not handle. The average of operation times could be reduced from 10 s per case using traditional method, to 1.5 s per case using our proposed method.

Conclusion

The experimental results showed that the proposed method provided an effective automated liver segmentation technique, which can be applied clinically for automated median LIC calculation in thalassemia major patients.

Symmetric Reconstruction of Functional Liver Segments and Cross-Individual Correspondence of Hepatectomy

Accurate localization and analyses of functional liver segments are crucial in devising various surgical procedures, including hepatectomy. To this end, they require the extraction of a liver from computed tomography, and then the identification of resection correspondence between individuals. The first part is usually impeded by inherent deficiencies, as present in medical images, and vast anatomical variations across subjects. While the model-based approach is found viable to tackle both issues, it is often undermined by an inadequate number of labeled samples, to capture all plausible variations. To address segmentation problems by balancing between accuracy, resource consumption, and data availability, this paper presents an efficient method for liver segmentation based on a graph-cut algorithm. One of its main novelties is the incorporation of a feature preserving a metric for boundary separation. Intuitive anatomical constraints are imposed to ensure valid extraction. The second part involves the symmetric conformal parameterization of the extracted liver surface onto a genus-0 domain. Provided with a few landmarks specified on two livers, we demonstrated that, by using a modified Beltrami differential, not only could they be non-rigidly registered, but also the hepatectomy on one liver could be envisioned on another. The merits of the proposed scheme were elucidated by both visual and numerical assessments on a standard MICCAI SLIVER07 dataset.

Semi-automatic liver segmentation based on probabilistic models and anatomical constraints

Segmenting a liver and its peripherals from abdominal computed tomography is a crucial step toward computer aided diagnosis and therapeutic intervention. Despite the recent advances in computing methods, faithfully segmenting the liver has remained a challenging task, due to indefinite boundary, intensity inhomogeneity, and anatomical variations across subjects. In this paper, a semi-automatic segmentation method based on multivariable normal distribution of liver tissues and graph-cut sub-division is presented. Although it is not fully automated, the method minimally involves human interactions. Specifically, it consists of three main stages. Firstly, a subject specific probabilistic model was built from an interior patch, surrounding a seed point specified by the user. Secondly, an iterative assignment of pixel labels was applied to gradually update the probabilistic map of the tissues based on spatio-contextual information. Finally, the graph-cut model was optimized to extract the 3D liver from the image. During post-processing, overly segmented nodal regions due to fuzzy tissue separation were removed, maintaining its correct anatomy by using robust bottleneck detection with adjacent contour constraint. The proposed system was implemented and validated on the MICCAI SLIVER07 dataset. The experimental results were benchmarked against the state-of-the-art methods, based on major clinically relevant metrics. Both visual and numerical assessments reported herein indicated that the proposed system could improve the accuracy and reliability of asymptomatic liver segmentation.

A 3D Deep Neural Network for Liver Volumetry in 3T Contrast-Enhanced MRI

PURPOSE

 To create a fully automated, reliable, and fast segmentation tool for Gd-EOB-DTPA-enhanced MRI scans using deep learning.

MATERIALS AND METHODS

 Datasets of Gd-EOB-DTPA-enhanced liver MR images of 100 patients were assembled. Ground truth segmentation of the hepatobiliary phase images was performed manually. Automatic image segmentation was achieved with a deep convolutional neural network.

RESULTS

 Our neural network achieves an intraclass correlation coefficient (ICC) of 0.987, a Sørensen-Dice coefficient of 96.7 ± 1.9 % (mean ± std), an overlap of 92 ± 3.5 %, and a Hausdorff distance of 24.9 ± 14.7 mm compared with two expert readers who corresponded to an ICC of 0.973, a Sørensen-Dice coefficient of 95.2 ± 2.8 %, and an overlap of 90.9 ± 4.9 %. A second human reader achieved a Sørensen-Dice coefficient of 95 % on a subset of the test set.

CONCLUSION

 Our study introduces a fully automated liver volumetry scheme for Gd-EOB-DTPA-enhanced MR imaging. The neural network achieves competitive concordance with the ground truth regarding ICC, Sørensen-Dice, and overlap compared with manual segmentation. The neural network performs the task in just 60 seconds.

KEY POINTS

  · The proposed neural network helps to segment the liver accurately, providing detailed information about patient-specific liver anatomy and volume.. · With the help of a deep learning-based neural network, fully automatic segmentation of the liver on MRI scans can be performed in seconds.. · A fully automatic segmentation scheme makes liver segmentation on MRI a valuable tool for treatment planning..

CITATION FORMAT

· Winther H, Hundt C, Ringe KI et al. A 3D Deep Neural Network for Liver Volumetry in 3T Contrast-Enhanced MRI. Fortschr Röntgenstr 2021; 193: 305 - 314.

Effective segmentation and classification of tumor on liver MRI and CT images using multi-kernel K-means clustering

Our proposed research technique intends to provide an effective liver magnetic resonance imaging (MRI) and computed tomography (CT) scan image classification which would play a significant role in medical dataset especially in feature selection and classification. There are a number of existing research works classifying the liver tumor disease. Early detection of liver tumor will help the patients to get cured rapidly. Our proposed research focuses on the classification of medical images with respect to the classification technique artificial neural network (ANN) to classify an image as normal or abnormal. In the pre-processing step, the input image is selected from the database and adaptive median filtering is used for noise removal. For better enhancement, histogram equalization (HE) is done in the noise-removed images. In the pre-processed images, the texture feature such as gray-level co-occurrence matrix (GLCM) and statistical features are extracted. From the extensive feature set, optimal features are selected using the optimal kernel K-means (OKK-means) clustering algorithm along with the oppositional firefly algorithm (OFA). The proposed method obtained 97.5% accuracy in the classification when compared to the existing method.

Computed Tomography-Based Preoperative Simulation System for Pedicle Screw Fixation in Spinal Surgery

BACKGROUND

A preoperative planning system facilitates improving surgical outcomes that depend on the experience of the surgeons, thanks to real-time interaction between the system and surgeons. It visualizes intermediate surgical planning results to help surgeons discuss the planning. The purpose of this study was to demonstrate the use of a newly-developed preoperative planning system for surgeons less experienced in pedicle-screw fixation in spinal surgery, especially on patients with anatomical variations.

METHODS

The marching cubes algorithm, a typical surface extraction technique, was applied to computed tomography (CT) images of vertebrae to enable three-dimensional (3D) reconstruction of a spinal mesh. Real-time processing of such data is difficult, as the surface mesh extracted from high-resolution CT data is rough, and the size of the mesh is large. To mitigate these factors, Laplacian smoothing was applied, followed by application of a quadric error metric-based mesh simplification to reduce the mesh size for the level-of-detail (LOD) image. Taubin smoothing was applied to smooth out the rough surface. On a multiplanar reconstruction (MPR) cross-sectional image or a 3D model view, the insertion position and orientation of the pedicle screw were manipulated using a mouse. The results after insertion were then visualized in each image.

RESULTS

The system was used for pre-planning pedicle-screw fixation in spinal surgery. Using any pointing device such as a mouse, surgeons can manipulate the position and angle of the screws. The pedicle screws were easy to manipulate intuitively on the MPR images, and the accuracy of screw fixation was confirmed on a trajectory view and 3D images. After surgery, CT scans were performed again, and the CT images were checked to ensure that the screws were inserted properly.

CONCLUSION

The preoperative planning system allows surgeons and students who are not familiar with pedicle-screw fixation to safely undertake surgery following preoperative planning. It also provides opportunities for screw-fixation training and simulation.

Modified U-Net (mU-Net) With Incorporation of Object-Dependent High Level Features for Improved Liver and Liver-Tumor Segmentation in CT Images

Segmentation of livers and liver tumors is one of the most important steps in radiation therapy of hepatocellular carcinoma. The segmentation task is often done manually, making it tedious, labor intensive, and subject to intra-/inter- operator variations. While various algorithms for delineating organ-at-risks (OARs) and tumor targets have been proposed, automatic segmentation of livers and liver tumors remains intractable due to their low tissue contrast with respect to the surrounding organs and their deformable shape in CT images. The U-Net has gained increasing popularity recently for image analysis tasks and has shown promising results. Conventional U-Net architectures, however, suffer from three major drawbacks. First, skip connections allow for the duplicated transfer of low resolution information in feature maps to improve efficiency in learning, but this often leads to blurring of extracted image features. Secondly, high level features extracted by the network often do not contain enough high resolution edge information of the input, leading to greater uncertainty where high resolution edge dominantly affects the network's decisions such as liver and liver-tumor segmentation. Thirdly, it is generally difficult to optimize the number of pooling operations in order to extract high level global features, since the number of pooling operations used depends on the object size. To cope with these problems, we added a residual path with deconvolution and activation operations to the skip connection of the U-Net to avoid duplication of low resolution information of features. In the case of small object inputs, features in the skip connection are not incorporated with features in the residual path. Furthermore, the proposed architecture has additional convolution layers in the skip connection in order to extract high level global features of small object inputs as well as high level features of high resolution edge information of large object inputs. Efficacy of the modified U-Net (mU-Net) was demonstrated using the public dataset of Liver tumor segmentation (LiTS) challenge 2017. For liver-tumor segmentation, Dice similarity coefficient (DSC) of 89.72 %, volume of error (VOE) of 21.93 %, and relative volume difference (RVD) of - 0.49 % were obtained. For liver segmentation, DSC of 98.51 %, VOE of 3.07 %, and RVD of 0.26 % were calculated. For the public 3D Image Reconstruction for Comparison of Algorithm Database (3Dircadb), DSCs were 96.01 % for the liver and 68.14 % for liver-tumor segmentations, respectively. The proposed mU-Net outperformed existing state-of-art networks.

Liver segmentation and metastases detection in MR images using convolutional neural networks

Primary tumors have a high likelihood of developing metastases in the liver, and early detection of these metastases is crucial for patient outcome. We propose a method based on convolutional neural networks to detect liver metastases. First, the liver is automatically segmented using the six phases of abdominal dynamic contrast-enhanced (DCE) MR images. Next, DCE-MR and diffusion weighted MR images are used for metastases detection within the liver mask. The liver segmentations have a median Dice similarity coefficient of 0.95 compared with manual annotations. The metastases detection method has a sensitivity of 99.8% with a median of two false positives per image. The combination of the two MR sequences in a dual pathway network is proven valuable for the detection of liver metastases. In conclusion, a high quality liver segmentation can be obtained in which we can successfully detect liver metastases.

A robust multi-variability model based liver segmentation algorithm for CT-scan and MRI modalities

Developing methods to segment the liver in medical images, study and analyze it remains a significant challenge. The shape of the liver can vary considerably from one patient to another, and adjacent organs are visualized in medical images with similar intensities, making the boundaries of the liver ambiguous. Consequently, automatic or semi-automatic segmentation of liver is a difficult task. Moreover, scanning systems and magnetic resonance imaging have different settings and parameters. Thus the images obtained differ from one machine to another. In this article, we propose an automatic model-based segmentation that allows building a faithful 3-D representation of the liver, with a mean Dice value equal to 90.3% on CT and MRI datasets. We compare our algorithm with a semi-automatic method and with other approaches according to the state of the art. Our method works with different data sources, we use a large quantity of CT and MRI images from machines in various hospitals and multiple DICOM images available from public challenges. Finally, for evaluation of liver segmentation approaches in state of the art, robustness is not adequacy addressed with a precise definition. Another originality of this article is the introduction of a novel measure of robustness, which takes into account the liver variability at different scales.

Deep Learning for Automated Segmentation of Liver Lesions at CT in Patients with Colorectal Cancer Liver Metastases

Purpose

To evaluate the performance, agreement, and efficiency of a fully convolutional network (FCN) for liver lesion detection and segmentation at CT examinations in patients with colorectal liver metastases (CLMs).

Materials and Methods

This retrospective study evaluated an automated method using an FCN that was trained, validated, and tested with 115, 15, and 26 contrast material-enhanced CT examinations containing 261, 22, and 105 lesions, respectively. Manual detection and segmentation by a radiologist was the reference standard. Performance of fully automated and user-corrected segmentations was compared with that of manual segmentations. The interuser agreement and interaction time of manual and user-corrected segmentations were assessed. Analyses included sensitivity and positive predictive value of detection, segmentation accuracy, Cohen κ, Bland-Altman analyses, and analysis of variance.

Results

In the test cohort, for lesion size smaller than 10 mm (n = 30), 10-20 mm (n = 35), and larger than 20 mm (n = 40), the detection sensitivity of the automated method was 10%, 71%, and 85%; positive predictive value was 25%, 83%, and 94%; Dice similarity coefficient was 0.14, 0.53, and 0.68; maximum symmetric surface distance was 5.2, 6.0, and 10.4 mm; and average symmetric surface distance was 2.7, 1.7, and 2.8 mm, respectively. For manual and user-corrected segmentation, κ values were 0.42 (95% confidence interval: 0.24, 0.63) and 0.52 (95% confidence interval: 0.36, 0.72); normalized interreader agreement for lesion volume was -0.10 ± 0.07 (95% confidence interval) and -0.10 ± 0.08; and mean interaction time was 7.7 minutes ± 2.4 (standard deviation) and 4.8 minutes ± 2.1 (P < .001), respectively.

Conclusion

Automated detection and segmentation of CLM by using deep learning with convolutional neural networks, when manually corrected, improved efficiency but did not substantially change agreement on volumetric measurements.© RSNA, 2019Supplemental material is available for this article.

Discontinuity Preserving Liver MR Registration with 3D Active Contour Motion Segmentation

OBJECTIVE

The sliding motion of the liver during respiration violates the homogeneous motion smoothness assumption in conventional non-rigid image registration and commonly results in compromised registration accuracy. This paper presents a novel approach, registration with 3D active contour motion segmentation (RAMS), to improve registration accuracy with discontinuity-aware motion regularization.

METHODS

A Markov random field-based discrete optimization with dense displacement sampling and self-similarity context metric is used for registration, while a graph cuts-based 3D active contour approach is applied to segment the sliding interface. In the first registration pass, a mask-free L1 regularization on an image-derived minimum spanning tree is performed to allow motion discontinuity. Based on the motion field estimates, a coarse segmentation finds the motion boundaries. Next, based on MR signal intensity, a fine segmentation aligns the motion boundaries with anatomical boundaries. In the second registration pass, smoothness constraints across the segmented sliding interface are removed by masked regularization on a minimum spanning forest and masked interpolation of the motion field.

RESULTS

For in vivo breath-hold abdominal MRI data, the motion masks calculated by RAMS are highly consistent with manual segmentations in terms of Dice similarity and bidirectional local distance measure. These automatically obtained masks are shown to substantially improve registration accuracy for both the proposed discrete registration as well as conventional continuous non-rigid algorithms.

CONCLUSION/SIGNIFICANCE

The presented results demonstrated the feasibility of automated segmentation of the respiratory sliding motion interface in liver MR images and the effectiveness of using the derived motion masks to preserve motion discontinuity.

Registration-Based Organ Positioning and Joint Segmentation Method for Liver and Tumor Segmentation

The automated segmentation of liver and tumor from CT images is of great importance in medical diagnoses and clinical treatment. However, accurate and automatic segmentation of liver and tumor is generally complicated due to the complex anatomical structures and low contrast. This paper proposes a registration-based organ positioning (ROP) and joint segmentation method for liver and tumor segmentation from CT images. First, a ROP method is developed to obtain liver's bounding box accurately and efficiently. Second, a joint segmentation method based on fuzzy c-means (FCM) and extreme learning machine (ELM) is designed to perform coarse liver segmentation. Third, the coarse segmentation is regarded as the initial contour of active contour model (ACM) to refine liver boundary by considering the topological information. Finally, tumor segmentation is performed using another ELM. Experiments on two datasets demonstrate the performance advantages of our proposed method compared with other related works.

A Unified Level Set Framework Combining Hybrid Algorithms for Liver and Liver Tumor Segmentation in CT Images

Accurate and reliable segmentation of liver tissue and liver tumor is essential for the follow-up of hepatic diagnosis. In this paper, we present a method for liver segmentation and a method for liver tumor segmentation. The two methods are grounded on a novel unified level set method (LSM), which incorporates both region information and edge information to evolve the contour. This level set framework is more resistant to edge leakage than the single-information driven LSMs for liver segmentation and surpasses many other models for liver tumor segmentation. Specifically, for liver segmentation, a hybrid image preprocessing scheme is used first to convert an input CT image into a binary image. Then with manual setting of a few seed points on the obtained binary image, the following region-growing is performed to extract a rough liver region with no leakage. The unified LSM is proposed at last to refine the segmentation result. For liver tumor segmentation, a local intensity clustering based LSM coupled with hidden Markov random field and expectation-maximization (HMRF-EM) algorithm is applied to construct an enhanced edge indicator for the unified LSM. With this development, expected segmentation results can be obtained via the unified LSM, even for complex tumors. The two methods were evaluated with various datasets containing a local hospital dataset, the public datasets SLIVER07, 3Dircadb, and MIDAS via five measures. The proposed liver segmentation method outperformed other previous semiautomatic methods on the SLIVER07 dataset and required less interaction. The proposed liver tumor segmentation method was also competitive with other state-of-the-art methods in both accuracy and efficiency on the 3Dircadb database. Our methods are evaluated to be accurate and efficient, which allows their adoptions in clinical practice.

Fully automatic liver segmentation combining multi-dimensional graph cut with shape information in 3D CT images

Liver segmentation is an essential procedure in computer-assisted surgery, radiotherapy, and volume measurement. It is still a challenging task to extract liver tissue from 3D CT images owing to nearby organs with similar intensities. In this paper, an automatic approach integrating multi-dimensional features into graph cut refinement is developed and validated. Multi-atlas segmentation is utilized to estimate the coarse shape of liver on the target image. The unsigned distance field based on initial shape is then calculated throughout the whole image, which aims at automatic graph construction during refinement procedure. Finally, multi-dimensional features and shape constraints are embedded into graph cut framework. The optimal liver region can be precisely detected with a minimal cost. The proposed technique is evaluated on 40 CT scans, obtained from two public databases Sliver07 and 3Dircadb1. The dataset Sliver07 is considered as the training set for parameter learning. On the dataset 3Dircadb1, the average of volume overlap is up to 94%. The experiment results indicate that the proposed method has ability to reach the desired boundary of liver and has potential value for clinical application.

Superpixel-based and boundary-sensitive convolutional neural network for automated liver segmentation

Segmentation of liver in abdominal computed tomography (CT) is an important step for radiation therapy planning of hepatocellular carcinoma. Practically, a fully automatic segmentation of liver remains challenging because of low soft tissue contrast between liver and its surrounding organs, and its highly deformable shape. The purpose of this work is to develop a novel superpixel-based and boundary sensitive convolutional neural network (SBBS-CNN) pipeline for automated liver segmentation. The entire CT images were first partitioned into superpixel regions, where nearby pixels with similar CT number were aggregated. Secondly, we converted the conventional binary segmentation into a multinomial classification by labeling the superpixels into three classes: interior liver, liver boundary, and non-liver background. By doing this, the boundary region of the liver was explicitly identified and highlighted for the subsequent classification. Thirdly, we computed an entropy-based saliency map for each CT volume, and leveraged this map to guide the sampling of image patches over the superpixels. In this way, more patches were extracted from informative regions (e.g. the liver boundary with irregular changes) and fewer patches were extracted from homogeneous regions. Finally, deep CNN pipeline was built and trained to predict the probability map of the liver boundary. We tested the proposed algorithm in a cohort of 100 patients. With 10-fold cross validation, the SBBS-CNN achieved mean Dice similarity coefficients of 97.31  ±  0.36% and average symmetric surface distance of 1.77  ±  0.49 mm. Moreover, it showed superior performance in comparison with state-of-art methods, including U-Net, pixel-based CNN, active contour, level-sets and graph-cut algorithms. SBBS-CNN provides an accurate and effective tool for automated liver segmentation. It is also envisioned that the proposed framework is directly applicable in other medical image segmentation scenarios.