A multiatlas segmentation using graph cuts with applications to liver segmentation in CT scans

Effect Evaluation of Perioperative Fast-Track Surgery Nursing for Tibial Fracture Patients with Computerized Tomography Images under Intelligent Algorithm

This study aimed to study the application value of computerized tomography (CT) images under the graph cut algorithm in the effect evaluation of perioperative fast-track surgery (FTS) nursing in tibial fracture. In this study, 80 tibial fracture patients in the perioperative period were selected as the research objects. These objects were randomly divided into two groups according to the examination method. In group A, routine CT examination was performed; in group B, CT examination under the graph cut algorithm was applied. The imaging results showed that there were still 16 cases with collapse of group A and 34 cases with collapse of group B; the difference was statistically significant (P < 0.05). As for 16 cases with collapse in both groups, the average collapse shown in group A was about 2.79 ± 1.31 mm, while that in group B was 5.51 ± 1.88 mm, with a statistically significant difference (P < 0.05). The average broadening in the images of group A was 3.17 ± 1.41 mm and that of group B was 5.72 ± 1.83 mm, suggesting that the difference was statistically significant (P < 0.05). The broadening distance of 3-4 mm was mainly shown in the images of group A and that of 5-8 mm was shown in group B, with a statistical difference (P < 0.05). In terms of the total score, there were 26, 44, 8, and 2 cases that were assessed as excellent, good, common, and bad, respectively, in group A, while 44 cases were assessed as good and 36 cases were assessed as common in group B, which were significantly different (P < 0.05). In summary, the graph cut algorithm not only had a good segmentation effect and segmentation efficiency but also could improve the evaluation of CT images for perioperative FTS nursing effect in patients with tibial fracture.

Efficient Liver Segmentation from Computed Tomography Images Using Deep Learning

Segmentation of a liver in computed tomography (CT) images is an important step toward quantitative biomarkers for a computer-aided decision support system and precise medical diagnosis. To overcome the difficulties that come across the liver segmentation that are affected by fuzzy boundaries, stacked autoencoder (SAE) is applied to learn the most discriminative features of the liver among other tissues in abdominal images. In this paper, we propose a patch-based deep learning method for the segmentation of a liver from CT images using SAE. Unlike the traditional machine learning methods, instead of anticipating pixel by pixel learning, our algorithm utilizes the patches to learn the representations and identify the liver area. We preprocessed the whole dataset to get the enhanced images and converted each image into many overlapping patches. These patches are given as input to SAE for unsupervised feature learning. Finally, the learned features with labels of the images are fine tuned, and the classification is performed to develop the probability map in a supervised way. Experimental results demonstrate that our proposed algorithm shows satisfactory results on test images. Our method achieved a 96.47% dice similarity coefficient (DSC), which is better than other methods in the same domain.

Automatic Multi-Atlas Liver Segmentation and Couinaud Classification from CT Volumes

Primary Live Cancer (PLC) is the sixth most common cancer worldwide and its occurrence predominates in patients with chronic liver diseases and other risk factors like hepatitis B and C. Treatment of PLC and malignant liver tumors depend both in tumor characteristics and the functional status of the organ, thus must be individualized for each patient. Liver segmentation and classification according to Couinaud's classification is essential for computer-aided diagnosis and treatment planning, however, manual segmentation of the liver volume slice by slice can be a time-consuming and challenging task and it is highly dependent on the experience of the user. We propose an alternative automatic segmentation method that allows accuracy and time consumption amelioration. The procedure pursues a multi-atlas based classification for Couinaud segmentation. Our algorithm was implemented on 20 subjects from the IRCAD 3D data base in order to segment and classify the liver volume in its Couinaud segments, obtaining an average DICE coefficient of 0.94.Clinical Relevance- The final purpose of this work is to provide an automatic multi-atlas liver segmentation and Couinaud classification by means of CT image analysis.

Survey on Liver Tumour Resection Planning System: Steps, Techniques, and Parameters

Preoperative planning for liver surgical treatments is an essential planning tool that aids in reducing the risks of surgical resection. Based on the computed tomography (CT) images, the resection can be planned before the actual tumour resection surgery. The computer-aided system provides an overview of the spatial relationships of the liver organ and its internal structures, tumours, and vasculature. It also allows for an accurate calculation of the remaining liver volume after resection. The aim of this paper was to review the main stages of the computer-aided system that helps to evaluate the risk of resection during liver cancer surgical treatments. The computer-aided system assists with surgical planning by enabling physicians to get volumetric measurements and visualise the liver, tumours, and surrounding vasculature. In this paper, it is concluded that for accurate planning of tumour resections, the liver organ and its internal structures should be segmented to understand the clear spatial relationship between them, thus allowing for a safer resection. This paper presents the main proposed segmentation techniques for each stage in the computer-aided system, namely the liver organ, tumours, and vessels. From the reviewed methods, it has been found that instead of relying on a single specific technique, a combination of a group of techniques would give more accurate segmentation results. The extracted masks from the segmentation algorithms are fused together to give the surgeons the 3D visualisation tool to study the spatial relationships of the liver and to calculate the required resection planning parameters.

Multi-slice low-rank tensor decomposition based multi-atlas segmentation: Application to automatic pathological liver CT segmentation

Liver segmentation from abdominal CT images is an essential step for liver cancer computer-aided diagnosis and surgical planning. However, both the accuracy and robustness of existing liver segmentation methods cannot meet the requirements of clinical applications. In particular, for the common clinical cases where the liver tissue contains major pathology, current segmentation methods show poor performance. In this paper, we propose a novel low-rank tensor decomposition (LRTD) based multi-atlas segmentation (MAS) framework that achieves accurate and robust pathological liver segmentation of CT images. Firstly, we propose a multi-slice LRTD scheme to recover the underlying low-rank structure embedded in 3D medical images. It performs the LRTD on small image segments consisting of multiple consecutive image slices. Then, we present an LRTD-based atlas construction method to generate tumor-free liver atlases that mitigates the performance degradation of liver segmentation due to the presence of tumors. Finally, we introduce an LRTD-based MAS algorithm to derive patient-specific liver atlases for each test image, and to achieve accurate pairwise image registration and label propagation. Extensive experiments on three public databases of pathological liver cases validate the effectiveness of the proposed method. Both qualitative and quantitative results demonstrate that, in the presence of major pathology, the proposed method is more accurate and robust than state-of-the-art methods.

A State-of-the-Art Review for Gastric Histopathology Image Analysis Approaches and Future Development

Gastric cancer is a common and deadly cancer in the world. The gold standard for the detection of gastric cancer is the histological examination by pathologists, where Gastric Histopathological Image Analysis (GHIA) contributes significant diagnostic information. The histopathological images of gastric cancer contain sufficient characterization information, which plays a crucial role in the diagnosis and treatment of gastric cancer. In order to improve the accuracy and objectivity of GHIA, Computer-Aided Diagnosis (CAD) has been widely used in histological image analysis of gastric cancer. In this review, the CAD technique on pathological images of gastric cancer is summarized. Firstly, the paper summarizes the image preprocessing methods, then introduces the methods of feature extraction, and then generalizes the existing segmentation and classification techniques. Finally, these techniques are systematically introduced and analyzed for the convenience of future researchers.

Automatic Multiorgan Segmentation via Multiscale Registration and Graph Cut

We propose an automatic multiorgan segmentation method for 3-D radiological images of different anatomical contents and modalities. The approach is based on a simultaneous multilabel graph cut optimization of location, appearance, and spatial configuration criteria of target structures. Organ location is defined by target-specific probabilistic atlases (PA) constructed from a training dataset using a fast (2+1)D SURF-based multiscale registration method involving a simple four-parameter transformation. PAs are also used to derive target-specific organ appearance models represented as intensity histograms. The spatial configuration prior is derived from shortest-path constraints defined on the adjacency graph of structures. Thorough evaluations on Visceral project benchmarks and training dataset, as well as comparisons with the state-of-the-art confirm that our approach is comparable to and often outperforms similar approaches in multiorgan segmentation, thus proving that the combination of multiple suboptimal but complementary information sources can yield very good performance.

Bioluminescence tomography with structural information estimated via statistical mouse atlas registration

Due to an ill-posed and underestimated characteristic of bioluminescence tomography (BLT) reconstruction, a priori anatomical information obtained from computed tomography (CT) or magnetic resonance imaging (MRI), is usually incorporated to improve the reconstruction accuracy. The organs need to be segmented, which is time-consuming and challenging, especially for the low-contrast CT images. In this paper, we present a BLT reconstruction method based on a statistical mouse atlas to improve the efficiency of heterogeneous model generation and the accuracy of target localization. The low-contrast CT image of the mouse was first registered to the statistical mouse atlas model with the constraints of mouse surface and high-contrast organs (bone and lung). Then the other organs, such as the liver and kidney, were determined automatically through the statistical mouse atlas model. The estimated organs were then discretized into tetrahedral meshes for BLT reconstruction. The linearized Bregman method was used to solve the sparse inverse problem of BLT by minimizing the regularization function (L1 norm plus L2 norm with smooth factor). Both numerical simulations and in vivo experiments were conducted, and the results demonstrate that even though the localization of the estimated organs may not be exactly accurate, the proposed method is feasible to reconstruct the bioluminescent source effectively and accurately with the estimated organs. This method would greatly benefit the bioluminescent light source localization for hybrid BLT/CT systems.

Topographic analysis of eyelid position using digital image processing software

PURPOSE

To propose a novel analysis technique for objective quantification of topographic eyelid position with an algorithmatically calculated scheme and to determine its feasibility.

METHODS

One hundred normal eyelids from 100 patients were segmented using a graph cut algorithm, and 11 shape features of eyelids were semi-automatically quantified using in-house software. To evaluate the intra- and inter-examiner reliability of this software, intra-class correlation coefficients (ICCs) were used. To evaluate the diagnostic value of this scheme, the correlations between semi-automatic and manual measurements of margin reflex distance 1 (MRD1) and margin reflex distance 2 (MRD2) were analysed using a Bland-Altman analysis. To determine the degree of agreement according to manual MRD length, the relationship between the variance of semi-automatic measurements and the manual measurements was evaluated using linear regression.

RESULTS

Intra- and inter-examiner reliability were excellent, with ICCs ranging from 0.913 to 0.980 in 11 shape features including MRD1, MRD2, palpebral fissure, lid perimeter, upper and lower lid lengths, roundness, total area, and medial, central, and lateral areas. The correlations between semi-automatic and manual MRDs were also excellent, with better correlation in MRD1 than in MRD2 (R = 0.893 and 0.823, respectively). In addition, significant positive relationships were observed between the variance and the length of MRD1 and 2; the longer the MRD length, the more the variance.

CONCLUSION

The proposed novel optimized integrative scheme, which is shown to have high repeatability and reproducibility, is useful for topographic analysis of eyelid position.

Combined endeavor of Neutrosophic Set and Chan-Vese model to extract accurate liver image from CT scan

Many different diseases can occur in the liver, including infections such as hepatitis, cirrhosis, cancer and over effect of medication or toxins. The foremost stage for computer-aided diagnosis of liver is the identification of liver region. Liver segmentation algorithms extract liver image from scan images which helps in virtual surgery simulation, speedup the diagnosis, accurate investigation and surgery planning. The existing liver segmentation algorithms try to extort exact liver image from abdominal Computed Tomography (CT) scan images. It is an open problem because of ambiguous boundaries, large variation in intensity distribution, variability of liver geometry from patient to patient and presence of noise. A novel approach is proposed to meet challenges in extracting the exact liver image from abdominal CT scan images. The proposed approach consists of three phases: (1) Pre-processing (2) CT scan image transformation to Neutrosophic Set (NS) and (3) Post-processing. In pre-processing, the noise is removed by median filter. The "new structure" is designed to transform a CT scan image into neutrosophic domain which is expressed using three membership subset: True subset (T), False subset (F) and Indeterminacy subset (I). This transform approximately extracts the liver image structure. In post processing phase, morphological operation is performed on indeterminacy subset (I) and apply Chan-Vese (C-V) model with detection of initial contour within liver without user intervention. This resulted in liver boundary identification with high accuracy. Experiments show that, the proposed method is effective, robust and comparable with existing algorithm for liver segmentation of CT scan images.

3D-SIFT-Flow for atlas-based CT liver image segmentation

PURPOSE

In this paper, the authors proposed a new 3D registration algorithm, 3D-scale invariant feature transform (SIFT)-Flow, for multiatlas-based liver segmentation in computed tomography (CT) images.

METHODS

In the registration work, the authors developed a new registration method that takes advantage of dense correspondence using the informative and robust SIFT feature. The authors computed the dense SIFT features for the source image and the target image and designed an objective function to obtain the correspondence between these two images. Labeling of the source image was then mapped to the target image according to the former correspondence, resulting in accurate segmentation. In the fusion work, the 2D-based nonparametric label transfer method was extended to 3D for fusing the registered 3D atlases.

RESULTS

Compared with existing registration algorithms, 3D-SIFT-Flow has its particular advantage in matching anatomical structures (such as the liver) that observe large variation/deformation. The authors observed consistent improvement over widely adopted state-of-the-art registration methods such as ELASTIX, ANTS, and multiatlas fusion methods such as joint label fusion. Experimental results of liver segmentation on the MICCAI 2007 Grand Challenge are encouraging, e.g., Dice overlap ratio 96.27% ± 0.96% by our method compared with the previous state-of-the-art result of 94.90% ± 2.86%.

CONCLUSIONS

Experimental results show that 3D-SIFT-Flow is robust for segmenting the liver from CT images, which has large tissue deformation and blurry boundary, and 3D label transfer is effective and efficient for improving the registration accuracy.

3D liver segmentation using multiple region appearances and graph cuts

PURPOSE

Efficient and accurate 3D liver segmentations from contrast-enhanced computed tomography (CT) images play an important role in therapeutic strategies for hepatic diseases. However, inhomogeneous appearances, ambiguous boundaries, and large variance in shape often make it a challenging task. The existence of liver abnormalities poses further difficulty. Despite the significant intensity difference, liver tumors should be segmented as part of the liver. This study aims to address these challenges, especially when the target livers contain subregions with distinct appearances.

METHODS

The authors propose a novel multiregion-appearance based approach with graph cuts to delineate the liver surface. For livers with multiple subregions, a geodesic distance based appearance selection scheme is introduced to utilize proper appearance constraint for each subregion. A special case of the proposed method, which uses only one appearance constraint to segment the liver, is also presented. The segmentation process is modeled with energy functions incorporating both boundary and region information. Rather than a simple fixed combination, an adaptive balancing weight is introduced and learned from training sets. The proposed method only calls initialization inside the liver surface. No additional constraints from user interaction are utilized.

RESULTS

The proposed method was validated on 50 3D CT images from three datasets, i.e., Medical Image Computing and Computer Assisted Intervention (MICCAI) training and testing set, and local dataset. On MICCAI testing set, the proposed method achieved a total score of 83.4 ± 3.1, outperforming nonexpert manual segmentation (average score of 75.0). When applying their method to MICCAI training set and local dataset, it yielded a mean Dice similarity coefficient (DSC) of 97.7% ± 0.5% and 97.5% ± 0.4%, respectively. These results demonstrated the accuracy of the method when applied to different computed tomography (CT) datasets. In addition, user operator variability experiments showed its good reproducibility.

CONCLUSIONS

A multiregion-appearance based method is proposed and evaluated to segment liver. This approach does not require prior model construction and so eliminates the burdens associated with model construction and matching. The proposed method provides comparable results with state-of-the-art methods. Validation results suggest that it may be suitable for the clinical use.

Automatic Liver Segmentation on Volumetric CT Images Using Supervoxel-Based Graph Cuts

Accurate segmentation of liver from abdominal CT scans is critical for computer-assisted diagnosis and therapy. Despite many years of research, automatic liver segmentation remains a challenging task. In this paper, a novel method was proposed for automatic delineation of liver on CT volume images using supervoxel-based graph cuts. To extract the liver volume of interest (VOI), the region of abdomen was firstly determined based on maximum intensity projection (MIP) and thresholding methods. Then, the patient-specific liver VOI was extracted from the region of abdomen by using a histogram-based adaptive thresholding method and morphological operations. The supervoxels of the liver VOI were generated using the simple linear iterative clustering (SLIC) method. The foreground/background seeds for graph cuts were generated on the largest liver slice, and the graph cuts algorithm was applied to the VOI supervoxels. Thirty abdominal CT images were used to evaluate the accuracy and efficiency of the proposed algorithm. Experimental results show that the proposed method can detect the liver accurately with significant reduction of processing time, especially when dealing with diseased liver cases.

Multi-atlas registration and adaptive hexahedral voxel discretization for fast bioluminescence tomography

Bioluminescence tomography (BLT) has been a valuable optical molecular imaging technique to non-invasively depict the cellular and molecular processes in living animals with high sensitivity and specificity. Due to the inherent ill-posedness of BLT, a priori information of anatomical structure is usually incorporated into the reconstruction. The structural information is usually provided by computed tomography (CT) or magnetic resonance imaging (MRI). In order to obtain better quantitative results, BLT reconstruction with heterogeneous tissues needs to segment the internal organs and discretize them into meshes with the finite element method (FEM). It is time-consuming and difficult to handle the segmentation and discretization problems. In this paper, we present a fast reconstruction method for BLT based on multi-atlas registration and adaptive voxel discretization to relieve the complicated data processing procedure involved in the hybrid BLT/CT system. A multi-atlas registration method is first adopted to estimate the internal organ distribution of the imaged animal. Then, the animal volume is adaptively discretized into hexahedral voxels, which are fed into FEM for the following BLT reconstruction. The proposed method is validated in both numerical simulation and an in vivo study. The results demonstrate that the proposed method can reconstruct the bioluminescence source efficiently with satisfactory accuracy.

Multi-atlas segmentation of biomedical images: A survey

Multi-atlas segmentation (MAS), first introduced and popularized by the pioneering work of Rohlfing, et al. (2004), Klein, et al. (2005), and Heckemann, et al. (2006), is becoming one of the most widely-used and successful image segmentation techniques in biomedical applications. By manipulating and utilizing the entire dataset of "atlases" (training images that have been previously labeled, e.g., manually by an expert), rather than some model-based average representation, MAS has the flexibility to better capture anatomical variation, thus offering superior segmentation accuracy. This benefit, however, typically comes at a high computational cost. Recent advancements in computer hardware and image processing software have been instrumental in addressing this challenge and facilitated the wide adoption of MAS. Today, MAS has come a long way and the approach includes a wide array of sophisticated algorithms that employ ideas from machine learning, probabilistic modeling, optimization, and computer vision, among other fields. This paper presents a survey of published MAS algorithms and studies that have applied these methods to various biomedical problems. In writing this survey, we have three distinct aims. Our primary goal is to document how MAS was originally conceived, later evolved, and now relates to alternative methods. Second, this paper is intended to be a detailed reference of past research activity in MAS, which now spans over a decade (2003-2014) and entails novel methodological developments and application-specific solutions. Finally, our goal is to also present a perspective on the future of MAS, which, we believe, will be one of the dominant approaches in biomedical image segmentation.