Optimal surface segmentation in volumetric images--a graph-theoretic approach

Real-Time Automatic Segmentation of Optical Coherence Tomography Volume Data of the Macular Region

Optical coherence tomography (OCT) is a high speed, high resolution and non-invasive imaging modality that enables the capturing of the 3D structure of the retina. The fast and automatic analysis of 3D volume OCT data is crucial taking into account the increased amount of patient-specific 3D imaging data. In this work, we have developed an automatic algorithm, OCTRIMA 3D (OCT Retinal IMage Analysis 3D), that could segment OCT volume data in the macular region fast and accurately. The proposed method is implemented using the shortest-path based graph search, which detects the retinal boundaries by searching the shortest-path between two end nodes using Dijkstra’s algorithm. Additional techniques, such as inter-frame flattening, inter-frame search region refinement, masking and biasing were introduced to exploit the spatial dependency between adjacent frames for the reduction of the processing time. Our segmentation algorithm was evaluated by comparing with the manual labelings and three state of the art graph-based segmentation methods. The processing time for the whole OCT volume of 496×644×51 voxels (captured by Spectralis SD-OCT) was 26.15 seconds which is at least a 2-8-fold increase in speed compared to other, similar reference algorithms used in the comparisons. The average unsigned error was about 1 pixel (∼ 4 microns), which was also lower compared to the reference algorithms. We believe that OCTRIMA 3D is a leap forward towards achieving reliable, real-time analysis of 3D OCT retinal data.

Automated compromised right lung segmentation method using a robust atlas-based active volume model with sparse shape composition prior in CT

To resolve challenges in image segmentation in oncologic patients with severely compromised lung, we propose an automated right lung segmentation framework that uses a robust, atlas-based active volume model with a sparse shape composition prior. The robust atlas is achieved by combining the atlas with the output of sparse shape composition. Thoracic computed tomography images (n=38) from patients with lung tumors were collected. The right lung in each scan was manually segmented to build a reference training dataset against which the performance of the automated segmentation method was assessed. The quantitative results of this proposed segmentation method with sparse shape composition achieved mean Dice similarity coefficient (DSC) of (0.72, 0.81) with 95% CI, mean accuracy (ACC) of (0.97, 0.98) with 95% CI, and mean relative error (RE) of (0.46, 0.74) with 95% CI. Both qualitative and quantitative comparisons suggest that this proposed method can achieve better segmentation accuracy with less variance than other atlas-based segmentation methods in the compromised lung segmentation.

Automatic detection of subretinal fluid and sub-retinal pigment epithelium fluid in optical coherence tomography images

Age-related macular degeneration (AMD) is the leading cause of blindness in developed countries. Subretinal fluid (SRF) and sub-retinal pigment epithelium (sub-RPE) fluid are signs of AMD and can be detected in optical coherence tomography images. However, manual detection and segmentation of SRFs and sub-RPE fluids are laborious and time consuming. In this paper, a novel pipeline is proposed for automatic detection of SRFs and sub-RPE fluids. First, top and bottom layers of retina are segmented using a graph cut method. Then, a Split Bregman-based segmentation method is used to segment dark regions between layers. These segmented regions are considered as potential fluid candidates, on which a set of features are generated. After that, a random forest classifier is trained to distinguish between the true fluid regions from the falsely detected fluid regions. This method shows reasonable performance in a leave-one-out evaluation using a dataset from 21 patients.

3-D Stent Detection in Intravascular OCT Using a Bayesian Network and Graph Search

Worldwide, many hundreds of thousands of stents are implanted each year to revascularize occlusions in coronary arteries. Intravascular optical coherence tomography is an important emerging imaging technique, which has the resolution and contrast necessary to quantitatively analyze stent deployment and tissue coverage following stent implantation. Automation is needed, as current, it takes up to 16 h to manually analyze hundreds of images and thousands of stent struts from a single pullback. For automated strut detection, we used image formation physics and machine learning via a Bayesian network, and 3-D knowledge of stent structure via graph search. Graph search was done on en face projections using minimum spanning tree algorithms. Depths of all struts in a pullback were simultaneously determined using graph cut. To assess the method, we employed the largest validation data set used so far, involving more than 8000 clinical images from 103 pullbacks from 72 patients. Automated strut detection achieved a 0.91±0.04 recall, and 0.84±0.08 precision. Performance was robust in images of varying quality. This method can improve the workflow for analysis of stent clinical trial data, and can potentially be used in the clinic to facilitate real-time stent analysis and visualization, aiding stent implantation.

A technique for semiautomatic segmentation of echogenic structures in 3D ultrasound, applied to infant hip dysplasia

PURPOSE

Automatic segmentation of anatomical structures and lesions from medical ultrasound images is a formidable challenge in medical imaging due to image noise, blur and artifacts. In this paper we present a segmentation technique with features highly suited to use in noisy 3D ultrasound volumes and demonstrate its use in modeling bone, specifically the acetabulum in infant hips. Quantification of the acetabular shape is crucial in diagnosing developmental dysplasia of the hip (DDH), a common condition associated with hip dislocation and premature osteoarthritis if not treated. The well-established Graf technique for DDH diagnosis has been criticized for high inter-observer and inter-scan variability. In our earlier work we have introduced a more reliable instability metric based on 3D ultrasound data. Visualizing and interpreting the acetabular shape from noisy 3D ultrasound volumes has been one of the major roadblocks in using 3D ultrasound as diagnostic tool for DDH. For this study we developed a semiautomated segmentation technique to rapidly generate 3D acetabular surface models and classified the acetabulum based on acetabular contact angle (ACA) derived from the models. We tested the feasibility and reliability of the technique compared with manual segmentation.

METHODS

The proposed segmentation algorithm is based on graph search. We formulate segmentation of the acetabulum as an optimal path finding problem on an undirected weighted graph. Slice contours are defined as the optimal path passing through a set of user-defined seed points in the graph, and it can be found using dynamic programming techniques (in this case Dijkstra's algorithm). Slice contours are then interpolated over the 3D volume to generate the surface model. A three-dimensional ACA was calculated using normal vectors of the surface model.

RESULTS

The algorithm was tested over an extensive dataset of 51 infant ultrasound hip volumes obtained from 42 subjects with normal to dysplastic hips. The contours generated by the segmentation algorithm closely matched with those obtained from manual segmentation. The average RMS errors between the semiautomated and manual segmentation for the 51 volumes were 0.28 mm/1.1 voxel (with 2 node points) and 0.24 mm/0.9 voxel (with 3 node points). The semiautomatic algorithm gave visually acceptable results on images with moderate levels of noise and was able to trace the boundary of the acetabulum even in the presence of significant shadowing. Semiautomatic contouring was also faster than manual segmentation at 37 versus 56 s per scan. It also improved the repeatability of the ACA calculation with inter-observer and intra-observer variability of 1.4 ± 0.9 degree and 1.4 ± 1.0 degree.

CONCLUSION

The semiautomatic segmentation technique proposed in this work offers a fast and reliable method to delineate the contours of the acetabulum from 3D ultrasound volumes of the hip. Since the technique does not rely upon contour evolution, it is less susceptible than other methods to the frequent missing or incomplete boundaries and noise artifacts common in ultrasound images. ACA derived from the segmented 3D surface was able to accurately classify the acetabulum under the categories normal, borderline and dysplastic. The semiautomatic technique makes it easier to segment the volume and reduces the inter-observer and intra-observer variation in ACA calculation compared with manual segmentation. The method can be applied to any structure with an echogenic boundary on ultrasound (such as a ventricle, blood vessel, organ or tumor), or even to structures with a bright border on computed tomography or magnetic resonance imaging.

Computer Vision Techniques for Transcatheter Intervention

Minimally invasive transcatheter technologies have demonstrated substantial promise for the diagnosis and the treatment of cardiovascular diseases. For example, transcatheter aortic valve implantation is an alternative to aortic valve replacement for the treatment of severe aortic stenosis, and transcatheter atrial fibrillation ablation is widely used for the treatment and the cure of atrial fibrillation. In addition, catheter-based intravascular ultrasound and optical coherence tomography imaging of coronary arteries provides important information about the coronary lumen, wall, and plaque characteristics. Qualitative and quantitative analysis of these cross-sectional image data will be beneficial to the evaluation and the treatment of coronary artery diseases such as atherosclerosis. In all the phases (preoperative, intraoperative, and postoperative) during the transcatheter intervention procedure, computer vision techniques (e.g., image segmentation and motion tracking) have been largely applied in the field to accomplish tasks like annulus measurement, valve selection, catheter placement control, and vessel centerline extraction. This provides beneficial guidance for the clinicians in surgical planning, disease diagnosis, and treatment assessment. In this paper, we present a systematical review on these state-of-the-art methods. We aim to give a comprehensive overview for researchers in the area of computer vision on the subject of transcatheter intervention. Research in medical computing is multi-disciplinary due to its nature, and hence, it is important to understand the application domain, clinical background, and imaging modality, so that methods and quantitative measurements derived from analyzing the imaging data are appropriate and meaningful. We thus provide an overview on the background information of the transcatheter intervention procedures, as well as a review of the computer vision techniques and methodologies applied in this area.

Applying an Open-Source Segmentation Algorithm to Different OCT Devices in Multiple Sclerosis Patients and Healthy Controls: Implications for Clinical Trials

Background. The lack of segmentation algorithms operative across optical coherence tomography (OCT) platforms hinders utility of retinal layer measures in MS trials. Objective. To determine cross-sectional and longitudinal agreement of retinal layer thicknesses derived from an open-source, fully-automated, segmentation algorithm, applied to two spectral-domain OCT devices. Methods. Cirrus HD-OCT and Spectralis OCT macular scans from 68 MS patients and 22 healthy controls were segmented. A longitudinal cohort comprising 51 subjects (mean follow-up: 1.4 ± 0.9 years) was also examined. Bland-Altman analyses and interscanner agreement indices were utilized to assess agreement between scanners. Results. Low mean differences (-2.16 to 0.26 μm) and narrow limits of agreement (LOA) were noted for ganglion cell and inner and outer nuclear layer thicknesses cross-sectionally. Longitudinally we found low mean differences (-0.195 to 0.21 μm) for changes in all layers, with wider LOA. Comparisons of rate of change in layer thicknesses over time revealed consistent results between the platforms. Conclusions. Retinal thickness measures for the majority of the retinal layers agree well cross-sectionally and longitudinally between the two scanners at the cohort level, with greater variability at the individual level. This open-source segmentation algorithm enables combining data from different OCT platforms, broadening utilization of OCT as an outcome measure in MS trials.

Anatomy packing with hierarchical segments: an algorithm for segmentation of pulmonary nodules in CT images

BACKGROUND

This paper proposes a semantic segmentation algorithm that provides the spatial distribution patterns of pulmonary ground-glass nodules with solid portions in computed tomography (CT) images.

METHODS

The proposed segmentation algorithm, anatomy packing with hierarchical segments (APHS), performs pulmonary nodule segmentation and quantification in CT images. In particular, the APHS algorithm consists of two essential processes: hierarchical segmentation tree construction and anatomy packing. It constructs the hierarchical segmentation tree based on region attributes and local contour cues along the region boundaries. Each node of the tree corresponds to the soft boundary associated with a family of nested segmentations through different scales applied by a hierarchical segmentation operator that is used to decompose the image in a structurally coherent manner. The anatomy packing process detects and localizes individual object instances by optimizing a hierarchical conditional random field model. Ninety-two histopathologically confirmed pulmonary nodules were used to evaluate the performance of the proposed APHS algorithm. Further, a comparative study was conducted with two conventional multi-label image segmentation algorithms based on four assessment metrics: the modified Williams index, percentage statistic, overlapping ratio, and difference ratio.

RESULTS

Under the same framework, the proposed APHS algorithm was applied to two clinical applications: multi-label segmentation of nodules with a solid portion and surrounding tissues and pulmonary nodule segmentation. The results obtained indicate that the APHS-generated boundaries are comparable to manual delineations with a modified Williams index of 1.013. Further, the resulting segmentation of the APHS algorithm is also better than that achieved by two conventional multi-label image segmentation algorithms.

CONCLUSIONS

The proposed two-level hierarchical segmentation algorithm effectively labelled the pulmonary nodule and its surrounding anatomic structures in lung CT images. This suggests that the generated multi-label structures can potentially serve as the basis for developing related clinical applications.

Automated choroid segmentation based on gradual intensity distance in HD-OCT images

The choroid is an important structure of the eye and plays a vital role in the pathology of retinal diseases. This paper presents an automated choroid segmentation method for high-definition optical coherence tomography (HD-OCT) images, including Bruch's membrane (BM) segmentation and choroidal-scleral interface (CSI) segmentation. An improved retinal nerve fiber layer (RNFL) complex removal algorithm is presented to segment BM by considering the structure characteristics of retinal layers. By analyzing the characteristics of CSI boundaries, we present a novel algorithm to generate a gradual intensity distance image. Then an improved 2-D graph search method with curve smooth constraints is used to obtain the CSI segmentation. Experimental results with 212 HD-OCT images from 110 eyes in 66 patients demonstrate that the proposed method can achieve high segmentation accuracy. The mean choroid thickness difference and overlap ratio between our proposed method and outlines drawn by experts was 6.72µm and 85.04%, respectively.

Automated 3-D retinal layer segmentation of macular optical coherence tomography images with serous pigment epithelial detachments

Automated retinal layer segmentation of optical coherence tomography (OCT) images has been successful for normal eyes but becomes challenging for eyes with retinal diseases if the retinal morphology experiences critical changes. We propose a method to automatically segment the retinal layers in 3-D OCT data with serous retinal pigment epithelial detachments (PED), which is a prominent feature of many chorioretinal disease processes. The proposed framework consists of the following steps: fast denoising and B-scan alignment, multi-resolution graph search based surface detection, PED region detection and surface correction above the PED region. The proposed technique was evaluated on a dataset with OCT images from 20 subjects diagnosed with PED. The experimental results showed the following. 1) The overall mean unsigned border positioning error for layer segmentation is 7.87±3.36 μm , and is comparable to the mean inter-observer variability ( 7.81±2.56 μm). 2) The true positive volume fraction (TPVF), false positive volume fraction (FPVF) and positive predicative value (PPV) for PED volume segmentation are 87.1%, 0.37%, and 81.2%, respectively. 3) The average running time is 220 s for OCT data of 512 × 64 × 480 voxels.

Prostate boundary segment extraction using cascaded shape regression and optimal surface detection

In this paper, we proposed a new method (CSR+OSD) for the extraction of irregular open prostate boundaries in noisy extracorporeal ultrasound image. First, cascaded shape regression (CSR) is used to locate the position of prostate boundary in the images. In CSR, a sequence of random fern predictors are trained in a boosted regression manner, using shape-indexed features to achieve invariance against position variations of prostate boundaries. Afterwards, we adopt optimal surface detection (OSD) to refine the prostate boundary segments across 3D sections globally and efficiently. The proposed method is tested on 162 ECUS images acquired from 8 patients with benign prostate hyperplasia. The method yields a Root Mean Square Distance of 2.11±1.72 mm and a Mean Absolute Distance of 1.61±1.26 mm, which are lower than those of JFilament, an open active contour algorithm and Chan-Vese region based level set model, respectively.

Longitudinal graph-based segmentation of macular OCT using fundus alignment

Segmentation of retinal layers in optical coherence tomography (OCT) has become an important diagnostic tool for a variety of ocular and neurological diseases. Currently all OCT segmentation algorithms analyze data independently, ignoring previous scans, which can lead to spurious measurements due to algorithm variability and failure to identify subtle changes in retinal layers. In this paper, we present a graph-based segmentation framework to provide consistent longitudinal segmentation results. Regularization over time is accomplished by adding weighted edges between corresponding voxels at each visit. We align the scans to a common subject space before connecting the graphs by registering the data using both the retinal vasculature and retinal thickness generated from a low resolution segmentation. This initial segmentation also allows the higher dimensional temporal problem to be solved more efficiently by reducing the graph size. Validation is performed on longitudinal data from 24 subjects, where we explore the variability between our longitudinal graph method and a cross-sectional graph approach. Our results demonstrate that the longitudinal component improves segmentation consistency, particularly in areas where the boundaries are difficult to visualize due to poor scan quality.

Automatic segmentation of lymph vessel wall using optimal surface graph cut and hidden Markov Models

We present a novel method to segment the lymph vessel wall in confocal microscopy images using Optimal Surface Segmentation (OSS) and hidden Markov Models (HMM). OSS is used to preform a pre-segmentation on the images, to act as the initial state for the HMM. We utilize a steerable filter to determine edge based filters for both of these segmentations, and use these features to build Gaussian probability distributions for both the vessel walls and the background. From this we infer the emission probability for the HMM, and the transmission probability is learned using a Baum-Welch algorithm. We transform the segmentation problem into one of cost minimization, with each node in the graph corresponding to one state, and the weight for each node being defined using its emission probability. We define the inter-relations between neighboring nodes using the transmission probability. Having constructed the problem, it is solved using the Viterbi algorithm, allowing the vessel to be reconstructed. The optimal solution can be found in polynomial time. We present qualitative and quantitative analysis to show the performance of the proposed method.

Three-dimensional segmentation and reconstruction of the retinal vasculature from spectral-domain optical coherence tomography

We reconstruct the three-dimensional shape and location of the retinal vascular network from commercial spectral-domain (SD) optical coherence tomography (OCT) data. The two-dimensional location of retinal vascular network on the eye fundus is obtained through support vector machines classification of properly defined fundus images from OCT data, taking advantage of the fact that on standard SD-OCT, the incident light beam is absorbed by hemoglobin, creating a shadow on the OCT signal below each perfused vessel. The depth-wise location of the vessel is obtained as the beginning of the shadow. The classification of crossovers and bifurcations within the vascular network is also addressed. We illustrate the feasibility of the method in terms of vessel caliber estimation and the accuracy of bifurcations and crossovers classification.

RFA-cut: Semi-automatic segmentation of radiofrequency ablation zones with and without needles via optimal s-t-cuts

In this contribution, we present a semi-automatic segmentation algorithm for radiofrequency ablation (RFA) zones via optimal s-t-cuts. Our interactive graph-based approach builds upon a polyhedron to construct the graph and was specifically designed for computed tomography (CT) acquisitions from patients that had RFA treatments of Hepatocellular Carcinomas (HCC). For evaluation, we used twelve post-interventional CT datasets from the clinical routine and as evaluation metric we utilized the Dice Similarity Coefficient (DSC), which is commonly accepted for judging computer aided medical segmentation tasks. Compared with pure manual slice-by-slice expert segmentations from interventional radiologists, we were able to achieve a DSC of about eighty percent, which is sufficient for our clinical needs. Moreover, our approach was able to handle images containing (DSC=75.9%) and not containing (78.1%) the RFA needles still in place. Additionally, we found no statistically significant difference (p<;0.423) between the segmentation results of the subgroups for a Mann-Whitney test. Finally, to the best of our knowledge, this is the first time a segmentation approach for CT scans including the RFA needles is reported and we show why another state-of-the-art segmentation method fails for these cases. Intraoperative scans including an RFA probe are very critical in the clinical practice and need a very careful segmentation and inspection to avoid under-treatment, which may result in tumor recurrence (up to 40%). If the decision can be made during the intervention, an additional ablation can be performed without removing the entire needle. This decreases the patient stress and associated risks and costs of a separate intervention at a later date. Ultimately, the segmented ablation zone containing the RFA needle can be used for a precise ablation simulation as the real needle position is known.

Multi-surface and multi-field co-segmentation of 3-D retinal optical coherence tomography

When segmenting intraretinal layers from multiple optical coherence tomography (OCT) images forming a mosaic or a set of repeated scans, it is attractive to exploit the additional information from the overlapping areas rather than discarding it as redundant, especially in low contrast and noisy images. However, it is currently not clear how to effectively combine the multiple information sources available in the areas of overlap. In this paper, we propose a novel graph-theoretic method for multi-surface multi-field co-segmentation of intraretinal layers, assuring consistent segmentation of the fields across the overlapped areas. After 2-D en-face alignment, all the fields are segmented simultaneously, imposing a priori soft interfield-intrasurface constraints for each pair of overlapping fields. The constraints penalize deviations from the expected surface height differences, taken to be the depth-axis shifts that produce the maximum cross-correlation of pairwise-overlapped areas. The method's accuracy and reproducibility are evaluated qualitatively and quantitatively on 212 OCT images (20 nine-field, 32 single-field acquisitions) from 26 patients with glaucoma. Qualitatively, the obtained thickness maps show no stitching artifacts, compared to pronounced stitches when the fields are segmented independently. Quantitatively, two ophthalmologists manually traced four intraretinal layers on 10 patients, and the average error ( 4.58 ±1.46 μm) was comparable to the average difference between the observers ( 5.86±1.72 μm). Furthermore, we show the benefit of the proposed approach in co-segmenting longitudinal scans. As opposed to segmenting layers in each of the fields independently, the proposed co-segmentation method obtains consistent segmentations across the overlapped areas, producing accurate, reproducible, and artifact-free results.

Hybrid approaches for interactive image segmentation using the live markers paradigm

Interactive image segmentation methods normally rely on cues about the foreground imposed by the user as region constraints (markers/brush strokes) or boundary constraints (anchor points). These paradigms often have complementary strengths and weaknesses, which can be addressed to improve the interactive experience by reducing the user’s effort. We propose a novel hybrid paradigm based on a new form of interaction called live markers, where optimum boundary-tracking segments are turned into internal and external markers for region-based delineation to effectively extract the object. We present four techniques within this paradigm: 1) LiveMarkers; 2) RiverCut; 3) LiveCut; and 4) RiverMarkers. The homonym LiveMarkers couples boundary-tracking via live-wire-on-the-fly (LWOF) with optimum seed competition by the image foresting transform (IFT-SC). The IFT-SC can cope with complex object silhouettes, but presents a leaking problem on weaker parts of the boundary that is solved by the effective live markers produced by LWOF. Conversely, in RiverCut, the long boundary segments computed by Riverbed around complex shapes provide markers for Graph Cuts by the Min-Cut/Max-Flow algorithm (GCMF) to complete segmentation on poorly defined sections of the object’s border. LiveCut and RiverMarkers further demonstrate that live markers can improve segmentation even when the combined approaches are not complementary (e.g., GCMFs shrinking bias is also dramatically prevented when using it with LWOF). Moreover, since delineation is always region based, our methodology subsumes both paradigms, representing a new way of extending boundary tracking to the 3D image domain, while speeding up the addition of markers close to the object’s boundary-a necessary but time consuming task when done manually. We justify our claims through an extensive experimental evaluation on natural and medical images data sets, using recently proposed robot users for boundary-tracking methods.

Thoracic cavity segmentation algorithm using multiorgan extraction and surface fitting in volumetric CT

PURPOSE

To develop and validate a semiautomatic segmentation method for thoracic cavity volumetry and mediastinum fat quantification of patients with chronic obstructive pulmonary disease.

METHODS

The thoracic cavity region was separated by segmenting multiorgans, namely, the rib, lung, heart, and diaphragm. To encompass various lung disease-induced variations, the inner thoracic wall and diaphragm were modeled by using a three-dimensional surface-fitting method. To improve the accuracy of the diaphragm surface model, the heart and its surrounding tissue were segmented by a two-stage level set method using a shape prior. To assess the accuracy of the proposed algorithm, the algorithm results of 50 patients were compared to the manual segmentation results of two experts with more than 5 years of experience (these manual results were confirmed by an expert thoracic radiologist). The proposed method was also compared to three state-of-the-art segmentation methods. The metrics used to evaluate segmentation accuracy were volumetric overlap ratio (VOR), false positive ratio on VOR (FPRV), false negative ratio on VOR (FNRV), average symmetric absolute surface distance (ASASD), average symmetric squared surface distance (ASSSD), and maximum symmetric surface distance (MSSD).

RESULTS

In terms of thoracic cavity volumetry, the mean ± SD VOR, FPRV, and FNRV of the proposed method were (98.17 ± 0.84)%, (0.49 ± 0.23)%, and (1.34 ± 0.83)%, respectively. The ASASD, ASSSD, and MSSD for the thoracic wall were 0.28 ± 0.12, 1.28 ± 0.53, and 23.91 ± 7.64 mm, respectively. The ASASD, ASSSD, and MSSD for the diaphragm surface were 1.73 ± 0.91, 3.92 ± 1.68, and 27.80 ± 10.63 mm, respectively. The proposed method performed significantly better than the other three methods in terms of VOR, ASASD, and ASSSD.

CONCLUSIONS

The proposed semiautomatic thoracic cavity segmentation method, which extracts multiple organs (namely, the rib, thoracic wall, diaphragm, and heart), performed with high accuracy and may be useful for clinical purposes.

Subvoxel accurate graph search using non-Euclidean graph space

Graph search is attractive for the quantitative analysis of volumetric medical images, and especially for layered tissues, because it allows globally optimal solutions in low-order polynomial time. However, because nodes of graphs typically encode evenly distributed voxels of the volume with arcs connecting orthogonally sampled voxels in Euclidean space, segmentation cannot achieve greater precision than a single unit, i.e. the distance between two adjoining nodes, and partial volume effects are ignored. We generalize the graph to non-Euclidean space by allowing non-equidistant spacing between nodes, so that subvoxel accurate segmentation is achievable. Because the number of nodes and edges in the graph remains the same, running time and memory use are similar, while all the advantages of graph search, including global optimality and computational efficiency, are retained. A deformation field calculated from the volume data adaptively changes regional node density so that node density varies with the inverse of the expected cost. We validated our approach using optical coherence tomography (OCT) images of the retina and 3-D MR of the arterial wall, and achieved statistically significant increased accuracy. Our approach allows improved accuracy in volume data acquired with the same hardware, and also, preserved accuracy with lower resolution, more cost-effective, image acquisition equipment. The method is not limited to any specific imaging modality and readily extensible to higher dimensions.

Exact surface registration of retinal surfaces from 3-D optical coherence tomography images

Nonrigid registration of optical coherence tomography (OCT) images is an important problem in studying eye diseases, evaluating the effect of pharmaceuticals in treating vision loss, and performing group-wise cross-sectional analysis. High dimensional nonrigid registration algorithms required for cross-sectional and longitudinal analysis are still being developed for accurate registration of OCT image volumes, with the speckle noise in images presenting a challenge for registration. Development of algorithms for segmentation of OCT images to generate surface models of retinal layers has advanced considerably and several algorithms are now available that can segment retinal OCT images into constituent retinal surfaces. Important morphometric measurements can be extracted if accurate surface registration algorithm for registering retinal surfaces onto corresponding template surfaces were available. In this paper, we present a novel method to perform multiple and simultaneous retinal surface registration, targeted to registering surfaces extracted from ocular volumetric OCT images. This enables a point-to-point correspondence (homology) between template and subject surfaces, allowing for a direct, vertex-wise comparison of morphometric measurements across subject groups. We demonstrate that this approach can be used to localize and analyze regional changes in choroidal and nerve fiber layer thickness among healthy and glaucomatous subjects, allowing for cross-sectional population wise analysis. We also demonstrate the method's ability to track longitudinal changes in optic nerve head morphometry, allowing for within-individual tracking of morphometric changes. This method can also, in the future, be used as a precursor to 3-D OCT image registration to better initialize nonrigid image registration algorithms closer to the desired solution.

Automated 3D Segmentation of Intraretinal Surfaces in SD-OCT Volumes in Normal and Diabetic Mice

PURPOSE

To describe an adaptation of an existing graph-theoretic method (initially developed for human optical coherence tomography [OCT] images) for the three-dimensional (3D) automated segmentation of 10 intraretinal surfaces in mice scans, and assess the accuracy of the method and the reproducibility of thickness measurements.

METHODS

Ten intraretinal surfaces were segmented in repeat spectral domain (SD)-OCT volumetric images acquired from normal (n = 8) and diabetic (n = 10) mice. The accuracy of the method was assessed by computing the border position errors of the automated segmentation with respect to manual tracings obtained from two experts. The reproducibility was statistically assessed for four retinal layers within eight predefined regions using the mean and SD of the differences in retinal thickness measured in the repeat scans, the coefficient of variation (CV) and the intraclass correlation coefficients (ICC; with 95% confidence intervals [CIs]).

RESULTS

The overall mean unsigned border position error for the 10 surfaces computed over 97 B-scans (10 scans, 10 normal mice) was 3.16 ± 0.91 μm. The overall mean differences in retinal thicknesses computed from the normal and diabetic mice were 1.86 ± 0.95 and 2.15 ± 0.86 μm, respectively. The CV of the retinal thicknesses for all the measured layers ranged from 1.04% to 5%. The ICCs for the total retinal thickness in the normal and diabetic mice were 0.78 [0.10, 0.92] and 0.83 [0.31, 0.96], respectively.

CONCLUSION

The presented method (publicly available as part of the Iowa Reference Algorithms) has acceptable accuracy and reproducibility and is expected to be useful in the quantitative study of intraretinal layers in mice.

TRANSLATIONAL RELEVANCE

The presented method, initially developed for human OCT, has been adapted for mice, with the potential to be adapted for other animals as well. Quantitative in vivo assessment of the retina in mice allows changes to be measured longitudinally, decreasing the need for them.

Depth-encoded all-fiber swept source polarization sensitive OCT

Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of conventional OCT and can assess depth-resolved tissue birefringence in addition to intensity. Most existing PS-OCT systems are relatively complex and their clinical translation remains difficult. We present a simple and robust all-fiber PS-OCT system based on swept source technology and polarization depth-encoding. Polarization multiplexing was achieved using a polarization maintaining fiber. Polarization sensitive signals were detected using fiber based polarization beam splitters and polarization controllers were used to remove the polarization ambiguity. A simplified post-processing algorithm was proposed for speckle noise reduction relaxing the demand for phase stability. We demonstrated systems design for both ophthalmic and catheter-based PS-OCT. For ophthalmic imaging, we used an optical clock frequency doubling method to extend the imaging range of a commercially available short cavity light source to improve polarization depth-encoding. For catheter based imaging, we demonstrated 200 kHz PS-OCT imaging using a MEMS-tunable vertical cavity surface emitting laser (VCSEL) and a high speed micromotor imaging catheter. The system was demonstrated in human retina, finger and lip imaging, as well as ex vivo swine esophagus and cardiovascular imaging. The all-fiber PS-OCT is easier to implement and maintain compared to previous PS-OCT systems and can be more easily translated to clinical applications due to its robust design.

Spatio-temporal video segmentation with shape growth or shrinkage constraint

We propose a new method for joint segmentation of monotonously growing or shrinking shapes in a time sequence of noisy images. The task of segmenting the image time series is expressed as an optimization problem using the spatio-temporal graph of pixels, in which we are able to impose the constraint of shape growth or of shrinkage by introducing monodirectional infinite links connecting pixels at the same spatial locations in successive image frames. The globally optimal solution is computed with a graph cut. The performance of the proposed method is validated on three applications: segmentation of melting sea ice floes and of growing burned areas from time series of 2D satellite images, and segmentation of a growing brain tumor from sequences of 3D medical scans. In the latter application, we impose an additional intersequences inclusion constraint by adding directed infinite links between pixels of dependent image structures.

Local optimization based segmentation of spatially-recurring, multi-region objects with part configuration constraints

Incorporating prior knowledge into image segmentation algorithms has proven useful for obtaining more accurate and plausible results. Two important constraints, containment and exclusion of regions, have gained attention in recent years mainly due to their descriptive power. In this paper, we augment the level set framework with the ability to handle these two intuitive geometric relationships, containment and exclusion, along with a distance constraint between boundaries of multi-region objects. Level set's important property of automatically handling topological changes of evolving contours/surfaces enables us to segment spatially-recurring objects (e.g., multiple instances of multi-region cells in a large microscopy image) while satisfying the two aforementioned constraints. In addition, the level set approach gives us a very simple and natural way to compute the distance between contours/surfaces and impose constraints on it. The downside, however, is a local optimization framework in which the final segmentation solution depends on the initialization. In fact, here, we sacrifice the optimizability (local instead of global solution) in exchange for lower space complexity (less memory usage) and faster runtime (especially for large microscopic images) as well as no grid artifacts. Nevertheless, the result from validating our method on several biomedical applications showed the utility and advantages of this augmented level set framework (even with rough initialization that is distant from the desired boundaries). We also compared our framework with its counterpart methods in the discrete domain and reported the pros and cons of each of these methods in terms of metrication error and efficiency in memory usage and runtime.

Volumetric quantification of airway wall in CT via collision-free active surface model: application to asthma assessment

Emerging idea in asthma phenotyping, incorporating local morphometric information on the airway wall thickness would be able to better account for the process of airway remodeling as indicator of pathology or therapeutic impact. It is thus important that such information be provided uniformly along the airway tree, not on a sparse (cross-section) sampling basis. The volumetric segmentation of the airway wall from CT data is the issue addressed in this paper by exploiting a patient-specific surface active model. An original aspect taken into account in the proposed deformable model is the management of auto-collisions for this complex morphology. The analysis of several solutions ended up with the design of a motion vector field specific to the patient geometry to guide the deformation. The segmentation result, presented as two embedded inner/outer surfaces of the wall, allows the quantification of the tissue thickness based on a locally-defined measure sensitive to even small surface irregularities. The method is validated with respect to several ground truth simulations of pulmonary CT data with different airway geometries and acquisition protocols showing accuracy within the CT resolution range. Results from an ongoing clinical study on moderate and severe asthma are presented and discussed.

Refinement-cut: user-guided segmentation algorithm for translational science

In this contribution, a semi-automatic segmentation algorithm for (medical) image analysis is presented. More precise, the approach belongs to the category of interactive contouring algorithms, which provide real-time feedback of the segmentation result. However, even with interactive real-time contouring approaches there are always cases where the user cannot find a satisfying segmentation, e.g. due to homogeneous appearances between the object and the background, or noise inside the object. For these difficult cases the algorithm still needs additional user support. However, this additional user support should be intuitive and rapid integrated into the segmentation process, without breaking the interactive real-time segmentation feedback. I propose a solution where the user can support the algorithm by an easy and fast placement of one or more seed points to guide the algorithm to a satisfying segmentation result also in difficult cases. These additional seed(s) restrict(s) the calculation of the segmentation for the algorithm, but at the same time, still enable to continue with the interactive real-time feedback segmentation. For a practical and genuine application in translational science, the approach has been tested on medical data from the clinical routine in 2D and 3D.

Comparison of retinal layer intensity profiles from different OCT devices

BACKGROUND AND OBJECTIVE

The purpose of this study is to use automated multiple retinal layer segmentation to compare retinal layer intensity profiles between different spectral-domain optical coherence tomography (SD-OCT) devices with and without normalization.

PATIENTS AND METHODS

A graph-based multistage segmentation approach was used to identify 11 boundaries in horizontal SD-OCT B-scans passing through the foveal center. Four acquisition protocols from two different SD-OCT devices were applied on 34 eyes from 17 healthy participants. The mean intensity of the 11 layers was compared within each device and between the two devices. In addition, the intensity of the various layers was normalized against the vitreous and retinal pigment epithelium band, and the normalized intensity profiles were also compared.

RESULTS

Within each OCT device, the mean intensity of the 11 retinal layers did not show significant difference (P values of paired t test ranging between 0.15 and 0.30). For the two different devices, before normalization, the mean intensity of the 11 retinal layers differed significantly (P = .02 to .03). After normalization, the mean intensity no longer differed significantly (P = .26 to .51). Linear regression demonstrated an average R(2) of 0.94 (P < .001) before normalization and 0.98 (P < .001) after normalization between the two devices.

CONCLUSION

The morphology of the intensity profiles was found to be similar within each SD-OCT device. Comparing intensity profiles from the two different devices, significant differences in unnormalized layer intensity were observed. Following normalization, the differences between OCT devices were no longer significant.

Cube-cut: vertebral body segmentation in MRI-data through cubic-shaped divergences

In this article, we present a graph-based method using a cubic template for volumetric segmentation of vertebrae in magnetic resonance imaging (MRI) acquisitions. The user can define the degree of deviation from a regular cube via a smoothness value Δ. The Cube-Cut algorithm generates a directed graph with two terminal nodes (s-t-network), where the nodes of the graph correspond to a cubic-shaped subset of the image’s voxels. The weightings of the graph’s terminal edges, which connect every node with a virtual source s or a virtual sink t, represent the affinity of a voxel to the vertebra (source) and to the background (sink). Furthermore, a set of infinite weighted and non-terminal edges implements the smoothness term. After graph construction, a minimal s-t-cut is calculated within polynomial computation time, which splits the nodes into two disjoint units. Subsequently, the segmentation result is determined out of the source-set. A quantitative evaluation of a C++ implementation of the algorithm resulted in an average Dice Similarity Coefficient (DSC) of 81.33% and a running time of less than a minute.

3D geometric split-merge segmentation of brain MRI datasets

In this paper, a novel method for MRI volume segmentation based on region adaptive splitting and merging is proposed. The method, called Adaptive Geometric Split Merge (AGSM) segmentation, aims at finding complex geometrical shapes that consist of homogeneous geometrical 3D regions. In each volume splitting step, several splitting strategies are examined and the most appropriate is activated. A way to find the maximal homogeneity axis of the volume is also introduced. Along this axis, the volume splitting technique divides the entire volume in a number of large homogeneous 3D regions, while at the same time, it defines more clearly small homogeneous regions within the volume in such a way that they have greater probabilities of survival at the subsequent merging step. Region merging criteria are proposed to this end. The presented segmentation method has been applied to brain MRI medical datasets to provide segmentation results when each voxel is composed of one tissue type (hard segmentation). The volume splitting procedure does not require training data, while it demonstrates improved segmentation performance in noisy brain MRI datasets, when compared to the state of the art methods.

An adaptive grid for graph-based segmentation in retinal OCT

Graph-based methods for retinal layer segmentation have proven to be popular due to their efficiency and accuracy. These methods build a graph with nodes at each voxel location and use edges connecting nodes to encode the hard constraints of each layer's thickness and smoothness. In this work, we explore deforming the regular voxel grid to allow adjacent vertices in the graph to more closely follow the natural curvature of the retina. This deformed grid is constructed by fixing node locations based on a regression model of each layer's thickness relative to the overall retina thickness, thus we generate a subject specific grid. Graph vertices are not at voxel locations, which allows for control over the resolution that the graph represents. By incorporating soft constraints between adjacent nodes, segmentation on this grid will favor smoothly varying surfaces consistent with the shape of the retina. Our final segmentation method then follows our previous work. Boundary probabilities are estimated using a random forest classifier followed by an optimal graph search algorithm on the new adaptive grid to produce a final segmentation. Our method is shown to produce a more consistent segmentation with an overall accuracy of 3.38 μm across all boundaries.

Fat water decomposition using globally optimal surface estimation (GOOSE) algorithm

PURPOSE

This article focuses on developing a novel noniterative fat water decomposition algorithm more robust to fat water swaps and related ambiguities.

METHODS

Field map estimation is reformulated as a constrained surface estimation problem to exploit the spatial smoothness of the field, thus minimizing the ambiguities in the recovery. Specifically, the differences in the field map-induced frequency shift between adjacent voxels are constrained to be in a finite range. The discretization of the above problem yields a graph optimization scheme, where each node of the graph is only connected with few other nodes. Thanks to the low graph connectivity, the problem is solved efficiently using a noniterative graph cut algorithm. The global minimum of the constrained optimization problem is guaranteed. The performance of the algorithm is compared with that of state-of-the-art schemes. Quantitative comparisons are also made against reference data.

RESULTS

The proposed algorithm is observed to yield more robust fat water estimates with fewer fat water swaps and better quantitative results than other state-of-the-art algorithms in a range of challenging applications.

CONCLUSION

The proposed algorithm is capable of considerably reducing the swaps in challenging fat water decomposition problems. The experiments demonstrate the benefit of using explicit smoothness constraints in field map estimation and solving the problem using a globally convergent graph-cut optimization algorithm.

Computed tomographic measures of airway morphology in smokers and never-smoking normals

Bronchial wall area percent (WA% = 100 × wall area/total bronchial cross sectional area) is a standard computed tomographic (CT) measure of central airway morphology utilized in smokers with chronic obstructive pulmonary disease (COPD). Although it provides significant clinical correlations, the range of reported WA% is narrow. This suggests limited macroscopic change in response to smoking or that remodeling proportionally affects the airway wall and lumen dimensions such that their ratio is preserved. The objective of this study is to assess central airway wall area (WA), lumen area (Ai), and total bronchial area (Ao) from CT scans of 5,179 smokers and 92 never smoking normal subjects. In smokers, WA, Ai, and Ao were positively correlated with forced expiratory volume in 1 s (FEV1) expressed as a percent of predicted (FEV1%), and the WA% was negatively correlated with FEV1% (P < 0.0001 for all comparisons). Importantly, smokers with lower FEV1% tended to have airways of smaller cross-sectional area with lower WA. The increases in the WA% across GOLD stages of chronic obstructive pulmonary disease (COPD) can therefore not be due to increases in WA. The data suggest two possible origins for the WA% increases: 1) central airway remodeling resulting in overall reductions in airway caliber in excess of the decreased WA or 2) those with COPD had smaller native airways before they began smoking. In both cases, these observations provide an explanation for the limited range of values of WA% across stages of COPD.

Interactive Hierarchical-Flow Segmentation of Scar Tissue From Late-Enhancement Cardiac MR Images

We propose a novel multi-region image segmentation approach to extract myocardial scar tissue from 3-D whole-heart cardiac late-enhancement magnetic resonance images in an interactive manner. For this purpose, we developed a graphical user interface to initialize a fast max-flow-based segmentation algorithm and segment scar accurately with progressive interaction. We propose a partially-ordered Potts (POP) model to multi-region segmentation to properly encode the known spatial consistency of cardiac regions. Its generalization introduces a custom label/region order constraint to Potts model to multi-region segmentation. The combinatorial optimization problem associated with the proposed POP model is solved by means of convex relaxation, for which a novel multi-level continuous max-flow formulation, i.e., the hierarchical continuous max-flow (HMF) model, is proposed and studied. We demonstrate that the proposed HMF model is dual or equivalent to the convex relaxed POP model and introduces a new and efficient hierarchical continuous max-flow based algorithm by modern convex optimization theory. In practice, the introduced hierarchical continuous max-flow based algorithm can be implemented on the parallel GPU to achieve significant acceleration in numerics. Experiments are performed in 50 whole heart 3-D LE datasets, 35 with left-ventricular and 15 with right-ventricular scar. The experimental results are compared to full-width-at-half-maximum and Signal-threshold to reference-mean methods using manual expert myocardial segmentations and operator variabilities and the effect of user interaction are assessed. The results indicate a substantial reduction in image processing time with robust accuracy for detection of myocardial scar. This is achieved without the need for additional region constraints and using a single optimization procedure, substantially reducing the potential for error.

Oriented image foresting transform segmentation by seed competition

Seed-based methods for region-based image segmentation are known to provide satisfactory results for several applications, being usually easy to extend to multidimensional images. However, while boundary-based methods like live wire can easily incorporate a preferred boundary orientation, regionbased methods are usually conceived for undirected graphs, and do not resolve well between boundaries with opposite orientations. This motivated researchers to investigate extensions for some region-based frameworks, seeking to better solve oriented transitions. In this same spirit, we discuss how to incorporate this orientation information in a region-based approach called “IFT segmentation by seed competition” by exploring digraphs. We give direct proof for the optimality of the proposed extensions in terms of energy functions associated with the cuts. To stress these theoretical results, we also present an experimental evaluation that shows the obtained gains in accuracy for some 2D and 3D data sets of medical images.

PROPER ORDERED MESHING OF COMPLEX SHAPES AND OPTIMAL GRAPH CUTS APPLIED TO ATRIAL-WALL SEGMENTATION FROM DE-MRI

Segmentation of the left atrium wall from delayed enhancement MRI is challenging because of inconsistent contrast combined with noise and high variation in atrial shape and size. This paper presents a method for left-atrium wall segmentation by using a novel sophisticated mesh-generation strategy and graph cuts on a proper ordered graph. The mesh is part of a template/model that has an associated set of learned intensity features. When this mesh is overlaid onto a test image, it produces a set of costs on the graph vertices which eventually leads to an optimal segmentation. The novelty also lies in the construction of proper ordered graphs on complex shapes and for choosing among distinct classes of base shapes/meshes for automatic segmentation. We evaluate the proposed segmentation framework quantitatively on simulated and clinical cardiac MRI.

RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI

BACKGROUND

High-field MRI is a popular technique for the study of rodent brains. These datasets, while similar to human brain MRI in many aspects, present unique image processing challenges. We address a very common preprocessing step, skull-stripping, which refers to the segmentation of the brain tissue from the image for further processing. While several methods exist for addressing this problem, they are computationally expensive and often require interactive post-processing by an expert to clean up poorly segmented areas. This further increases total processing time per subject.

NEW METHOD

We propose a novel algorithm, based on grayscale mathematical morphology and LOGISMOS-based graph segmentation, which is rapid, robust and highly accurate.

RESULTS

Comparative results obtained on two challenging in vivo datasets, consisting of 22 T1-weighted rat brain images and 10 T2-weighted mouse brain images illustrate the robustness and excellent performance of the proposed algorithm, in a fraction of the computational time needed by existing algorithms.

COMPARISON WITH EXISTING METHODS

In comparison to current state-of-the-art methods, our approach achieved average Dice similarity coefficient of 0.92 ± 0.02 and average Hausdorff distance of 13.6 ± 5.2 voxels (vs. 0.85 ± 0.20, p<0.05 and 42.6 ± 22.9, p << 0.001) for the rat dataset, and 0.96 ± 0.01 and average Hausdorff distance of 21.6 ± 12.7 voxels (vs. 0.93 ± 0.01, p <<0.001 and 33.7 ± 3.5, p <<0.001) for the mouse dataset. The proposed algorithm took approximately 90s per subject, compared to 10-20 min for the neural-network based method and 30-90 min for the atlas-based method.

CONCLUSIONS

RATS is a robust and computationally efficient method for accurate rodent brain skull-stripping even in challenging data.

A conditional statistical shape model with integrated error estimation of the conditions; application to liver segmentation in non-contrast CT images

This paper presents a novel conditional statistical shape model in which the condition can be relaxed instead of being treated as a hard constraint. The major contribution of this paper is the integration of an error model that estimates the reliability of the observed conditional features and subsequently relaxes the conditional statistical shape model accordingly. A three-step pipeline consisting of (1) conditional feature extraction from a maximum a posteriori estimation, (2) shape prior estimation through the novel level set based conditional statistical shape model with integrated error model and (3) subsequent graph cuts segmentation based on the estimated shape prior is applied to automatic liver segmentation from non-contrast abdominal CT volumes. Comparison with three other state of the art methods shows the superior performance of the proposed algorithm.

Standardized evaluation methodology and reference database for evaluating IVUS image segmentation

This paper describes an evaluation framework that allows a standardized and quantitative comparison of IVUS lumen and media segmentation algorithms. This framework has been introduced at the MICCAI 2011 Computing and Visualization for (Intra)Vascular Imaging (CVII) workshop, comparing the results of eight teams that participated. We describe the available data-base comprising of multi-center, multi-vendor and multi-frequency IVUS datasets, their acquisition, the creation of the reference standard and the evaluation measures. The approaches address segmentation of the lumen, the media, or both borders; semi- or fully-automatic operation; and 2-D vs. 3-D methodology. Three performance measures for quantitative analysis have been proposed. The results of the evaluation indicate that segmentation of the vessel lumen and media is possible with an accuracy that is comparable to manual annotation when semi-automatic methods are used, as well as encouraging results can be obtained also in case of fully-automatic segmentation. The analysis performed in this paper also highlights the challenges in IVUS segmentation that remains to be solved.

Optimal co-segmentation of tumor in PET-CT images with context information

Positron emission tomography (PET)-computed tomography (CT) images have been widely used in clinical practice for radiotherapy treatment planning of the radiotherapy. Many existing segmentation approaches only work for a single imaging modality, which suffer from the low spatial resolution in PET or low contrast in CT. In this work, we propose a novel method for the co-segmentation of the tumor in both PET and CT images, which makes use of advantages from each modality: the functionality information from PET and the anatomical structure information from CT. The approach formulates the segmentation problem as a minimization problem of a Markov random field model, which encodes the information from both modalities. The optimization is solved using a graph-cut based method. Two sub-graphs are constructed for the segmentation of the PET and the CT images, respectively. To achieve consistent results in two modalities, an adaptive context cost is enforced by adding context arcs between the two sub-graphs. An optimal solution can be obtained by solving a single maximum flow problem, which leads to simultaneous segmentation of the tumor volumes in both modalities. The proposed algorithm was validated in robust delineation of lung tumors on 23 PET-CT datasets and two head-and-neck cancer subjects. Both qualitative and quantitative results show significant improvement compared to the graph cut methods solely using PET or CT.

Airway tree segmentation in serial block-face cryomicrotome images of rat lungs

A highly automated method for the segmentation of airways in the serial block-face cryomicrotome images of rat lungs is presented. First, a point inside of the trachea is manually specified. Then, a set of candidate airway centerline points is automatically identified. By utilizing a novel path extraction method, a centerline path between the root of the airway tree and each point in the set of candidate centerline points is obtained. Local disturbances are robustly handled by a novel path extraction approach, which avoids the shortcut problem of standard minimum cost path algorithms. The union of all centerline paths is utilized to generate an initial airway tree structure, and a pruning algorithm is applied to automatically remove erroneous subtrees or branches. Finally, a surface segmentation method is used to obtain the airway lumen. The method was validated on five image volumes of Sprague-Dawley rats. Based on an expert-generated independent standard, an assessment of airway identification and lumen segmentation performance was conducted. The average of airway detection sensitivity was 87.4% with a 95% confidence interval (CI) of (84.9, 88.6)%. A plot of sensitivity as a function of airway radius is provided. The combined estimate of airway detection specificity was 100% with a 95% CI of (99.4, 100)%. The average number and diameter of terminal airway branches was 1179 and 159 μm, respectively. Segmentation results include airways up to 31 generations. The regression intercept and slope of airway radius measurements derived from final segmentations were estimated to be 7.22 μm and 1.005, respectively. The developed approach enables the quantitative studies of physiology and lung diseases in rats, requiring detailed geometric airway models.

Motion-compensated mega-voltage cone beam CT using the deformation derived directly from 2D projection images

This paper presents a novel method for respiratory motion compensated reconstruction for cone beam computed tomography (CBCT). The reconstruction is based on a time sequence of motion vector fields, which is generated by a dynamic geometrical object shape model. The dynamic model is extracted from the 2D projection images of the CBCT. The process of the motion extraction is converted into an optimal 3D multiple interrelated surface detection problem, which can be solved by computing a maximum flow in a 4D directed graph. The method was tested on 12 mega-voltage (MV) CBCT scans from three patients. Two sets of motion-artifact-free 3D volumes, full exhale (FE) and full inhale (FI) phases, were reconstructed for each daily scan. The reconstruction was compared with three other motion-compensated approaches based on quantification accuracy of motion and size. Contrast-to-noise ratio (CNR) was also quantified for image quality. The proposed approach has the best overall performance, with a relative tumor volume quantification error of 3.39 ± 3.64% and 8.57 ± 8.31% for FE and FI phases, respectively. The CNR near the tumor area is 3.85 ± 0.42 (FE) and 3.58 ± 3.33 (FI). These results show the clinical feasibility to use the proposed method to reconstruct motion-artifact-free MVCBCT volumes.

Graph-based IVUS segmentation with efficient computer-aided refinement

A new graph-based approach for segmentation of luminal and external elastic lamina (EEL) surface of coronary vessels in gated 20 MHz intravascular ultrasound (IVUS) image sequences (volumes) is presented. The approach consists of a fully automated segmentation stage ("new automated" or NA) and a user-guided computer-aided refinement ("new refinement" or NR) stage. Both approaches are based on the LOGISMOS approach for simultaneous dual-surface graph-based segmentation. This combination allows the user to efficiently combine general information about IVUS image appearance and case-specific IVUS morphology and therefore deal with frequently occurring issues like calcified plaque-causing signal shadowing-and imaging artifacts. The automated segmentation stage starts with pre-segmenting the lumen to automatically define the lumen centerline, which is used to transform the segmentation task into a LOGISMOS-family graph optimization problem. Following the automated segmentation, the user can inspect the result and correct local or regional segmentation inaccuracies by (iteratively) providing approximate clues regarding the location of the desired surface locations. This expert information is utilized to modify the previously calculated cost functions, locally re-optimizing the underlying modified graph without a need to start the new optimization from scratch. Validation of our method was performed on 41 gated 20 MHz IVUS data sets for which an expert-defined independent standard was available. Resulting from the automated stage of the approach (NA), the mean and standard deviation of the root mean square area errors for the luminal and external elastic lamina surfaces were 1.12 ±0.67 mm (2) and 2.35 ±1.61 mm (2) , respectively. Following the refinement stage (NR), the root mean square area errors significantly decreased to 0.82 ±0.44 mm (2) and 1.17 ±0.65 mm (2) for the same surfaces, respectively ( for both surfaces). The approach is delivering a previously unachievable speed of obtaining clinically relevant segmentations compared to the current approaches of automated segmentation followed by manual editing.