Patch-based segmentation with spatial context for medical image analysis

Accurate segmentations in medical imaging form a crucial role in many applications from pa- tient diagnosis to population studies. As the amount of data generated from medical images increases, the ability to perform this task without human intervention becomes ever more de- sirable. One approach, known broadly as atlas-based segmentation, is to propagate labels from images which have already been manually labelled by clinical experts. Methods using this ap- proach have been shown to be e ective in many applications, demonstrating great potential for automatic labelling of large datasets. However, these methods usually require the use of image registration and are dependent on the outcome of the registration. Any registrations errors that occur are also propagated to the segmentation process and are likely to have an adverse e ect on segmentation accuracy. Recently, patch-based methods have been shown to allow a relaxation of the required image alignment, whilst achieving similar results. In general, these methods label each voxel of a target image by comparing the image patch centred on the voxel with neighbouring patches from an atlas library and assigning the most likely label according to the closest matches. The main contributions of this thesis focuses around this approach in providing accurate segmentation results whilst minimising the dependency on registration quality. In particular, this thesis proposes a novel kNN patch-based segmentation framework, which utilises both intensity and spatial information, and explore the use of spatial context in a diverse range of applications. The proposed methods extend the potential for patch-based segmentation to tolerate registration errors by rede ning the \locality" for patch selection and comparison, whilst also allowing similar looking patches from di erent anatomical structures to be di erentiated. The methods are evaluated on a wide variety of image datasets, ranging from the brain to the knees, demonstrating its potential with results which are competitive to state-of-the-art techniques.Open Acces

Computational Anatomy for Multi-Organ Analysis in Medical Imaging: A Review

The medical image analysis field has traditionally been focused on the development of organ-, and disease-specific methods. Recently, the interest in the development of more 20 comprehensive computational anatomical models has grown, leading to the creation of multi-organ models. Multi-organ approaches, unlike traditional organ-specific strategies, incorporate inter-organ relations into the model, thus leading to a more accurate representation of the complex human anatomy. Inter-organ relations are not only spatial, but also functional and physiological. Over the years, the strategies 25 proposed to efficiently model multi-organ structures have evolved from the simple global modeling, to more sophisticated approaches such as sequential, hierarchical, or machine learning-based models. In this paper, we present a review of the state of the art on multi-organ analysis and associated computation anatomy methodology. The manuscript follows a methodology-based classification of the different techniques 30 available for the analysis of multi-organs and multi-anatomical structures, from techniques using point distribution models to the most recent deep learning-based approaches. With more than 300 papers included in this review, we reflect on the trends and challenges of the field of computational anatomy, the particularities of each anatomical region, and the potential of multi-organ analysis to increase the impact of 35 medical imaging applications on the future of healthcare.Comment: Paper under revie

Automatic Abdominal Organ Segmentation from CT images

In the recent years a great deal of research work has been devoted to the development of semi-automatic and automatic techniques for the analysis of abdominal CT images. Some of the current interests are the automatic diagnosis of liver, spleen, and kidney pathologies and the 3D volume rendering of the abdominal organs. The first and fundamental step in all these studies is the automatic organs segmentation, that is still an open problem. In this paper we propose our fully automatic system that employs a hierarchical gray level based framework to segment heart, bones (i.e. ribs and spine), liver and its blood vessels, kidneys, and spleen. The overall system has been evaluated on the data of 100 patients, obtaining a good assessment both by visual inspection by three experts, and by comparing the computed results to the boundaries manually traced by experts

Automatic segmentation of the spine by means of a probabilistic atlas with a special focus on ribs suppression

[EN] Purpose: The development of automatic and reliable algorithms for the detection and segmentation of the vertebrae are of great importance prior to any diagnostic task. However, an important problem found to accurately segment the vertebrae is the presence of the ribs in the thoracic region. To overcome this problem, a probabilistic atlas of the spine has been developed dealing with the proximity of other structures, with a special focus on ribs suppression. Methods: The data sets used consist of Computed Tomography images corresponding to 21 patients suffering from spinal metastases. Two methods have been combined to obtain the final result: firstly, an initial segmentation is performed using a fully automatic level-set method; secondly, to refine the initial segmentation, a 3D volume indicating the probability of each voxel of belonging to the spine has been developed. In this way, a probability map is generated and deformed to be adapted to each testing case. Results: To validate the improvement obtained after applying the atlas, the Dice coefficient (DSC), the Hausdorff distance (HD), and the mean surface-to-surface distance (MSD) were used. The results showed up an average of 10 mm of improvement accuracy in terms of HD, obtaining an overall final average of 15.51 2.74 mm. Also, a global value of 91.01 3.18% in terms of DSC and a MSD of 0.66 0.25 mm were obtained. The major improvement using the atlas was achieved in the thoracic region, as ribs were almost perfectly suppressed. Conclusion: The study demonstrated that the atlas is able to detect and appropriately eliminate the ribs while improving the segmentation accuracy.The authors thank the financial support of the Spanish Ministerio de Economia y Competitividad (MINECO) and FEDER funds under Grants TEC2012-33778 and BFU2015-64380-C2-2-R (D.M.) and DPI2013-4572-R (J.D., E.D.)Ruiz-España, S.; Domingo, J.; Díaz-Parra, A.; Dura, E.; D'ocon-Alcaniz, V.; Arana, E.; Moratal, D. (2017). Automatic segmentation of the spine by means of a probabilistic atlas with a special focus on ribs suppression. Medical Physics. 44(9):4695-4707. https://doi.org/10.1002/mp.12431S46954707449Harris, R. I., & Macnab, I. (1954). STRUCTURAL CHANGES IN THE LUMBAR INTERVERTEBRAL DISCS. The Journal of Bone and Joint Surgery. British volume, 36-B(2), 304-322. doi:10.1302/0301-620x.36b2.304Oliveira, M. F. de, Rotta, J. M., & Botelho, R. V. (2015). Survival analysis in patients with metastatic spinal disease: the influence of surgery, histology, clinical and neurologic status. Arquivos de Neuro-Psiquiatria, 73(4), 330-335. doi:10.1590/0004-282x20150003Chou, R. (2011). Diagnostic Imaging for Low Back Pain: Advice for High-Value Health Care From the American College of Physicians. Annals of Internal Medicine, 154(3), 181. doi:10.7326/0003-4819-154-3-201102010-00008Brayda-Bruno, M., Tibiletti, M., Ito, K., Fairbank, J., Galbusera, F., Zerbi, A., … Sivan, S. S. (2013). Advances in the diagnosis of degenerated lumbar discs and their possible clinical application. European Spine Journal, 23(S3), 315-323. doi:10.1007/s00586-013-2960-9Quattrocchi, C. C., Santini, D., Dell’Aia, P., Piciucchi, S., Leoncini, E., Vincenzi, B., … Zobel, B. B. (2007). A prospective analysis of CT density measurements of bone metastases after treatment with zoledronic acid. Skeletal Radiology, 36(12), 1121-1127. doi:10.1007/s00256-007-0388-1Doi, K. (2007). Computer-aided diagnosis in medical imaging: Historical review, current status and future potential. Computerized Medical Imaging and Graphics, 31(4-5), 198-211. doi:10.1016/j.compmedimag.2007.02.002Ruiz-España, S., Arana, E., & Moratal, D. (2015). Semiautomatic computer-aided classification of degenerative lumbar spine disease in magnetic resonance imaging. Computers in Biology and Medicine, 62, 196-205. doi:10.1016/j.compbiomed.2015.04.028Alomari, R. S., Ghosh, S., Koh, J., & Chaudhary, V. (2014). Vertebral Column Localization, Labeling, and Segmentation. Lecture Notes in Computational Vision and Biomechanics, 193-229. doi:10.1007/978-3-319-12508-4_7Hamarneh, G., & Li, X. (2009). Watershed segmentation using prior shape and appearance knowledge. Image and Vision Computing, 27(1-2), 59-68. doi:10.1016/j.imavis.2006.10.009Ghebreab, S., & Smeulders, A. W. (2004). Combining Strings and Necklaces for Interactive Three-Dimensional Segmentation of Spinal Images Using an Integral Deformable Spine Model. IEEE Transactions on Biomedical Engineering, 51(10), 1821-1829. doi:10.1109/tbme.2004.831540Mastmeyer, A., Engelke, K., Fuchs, C., & Kalender, W. A. (2006). A hierarchical 3D segmentation method and the definition of vertebral body coordinate systems for QCT of the lumbar spine. Medical Image Analysis, 10(4), 560-577. doi:10.1016/j.media.2006.05.005Rasoulian, A., Rohling, R., & Abolmaesumi, P. (2013). Lumbar Spine Segmentation Using a Statistical Multi-Vertebrae Anatomical Shape+Pose Model. IEEE Transactions on Medical Imaging, 32(10), 1890-1900. doi:10.1109/tmi.2013.2268424Ma, J., & Lu, L. (2013). Hierarchical segmentation and identification of thoracic vertebra using learning-based edge detection and coarse-to-fine deformable model. Computer Vision and Image Understanding, 117(9), 1072-1083. doi:10.1016/j.cviu.2012.11.016Kim, Y., & Kim, D. (2009). A fully automatic vertebra segmentation method using 3D deformable fences. Computerized Medical Imaging and Graphics, 33(5), 343-352. doi:10.1016/j.compmedimag.2009.02.006Klinder, T., Ostermann, J., Ehm, M., Franz, A., Kneser, R., & Lorenz, C. (2009). Automated model-based vertebra detection, identification, and segmentation in CT images. Medical Image Analysis, 13(3), 471-482. doi:10.1016/j.media.2009.02.004Štern, D., Likar, B., Pernuš, F., & Vrtovec, T. (2011). Parametric modelling and segmentation of vertebral bodies in 3D CT and MR spine images. Physics in Medicine and Biology, 56(23), 7505-7522. doi:10.1088/0031-9155/56/23/011Korez, R., Ibragimov, B., Likar, B., Pernus, F., & Vrtovec, T. (2015). A Framework for Automated Spine and Vertebrae Interpolation-Based Detection and Model-Based Segmentation. IEEE Transactions on Medical Imaging, 34(8), 1649-1662. doi:10.1109/tmi.2015.2389334Castro-Mateos, I., Pozo, J. M., Pereanez, M., Lekadir, K., Lazary, A., & Frangi, A. F. (2015). Statistical Interspace Models (SIMs): Application to Robust 3D Spine Segmentation. IEEE Transactions on Medical Imaging, 34(8), 1663-1675. doi:10.1109/tmi.2015.2443912Pereanez, M., Lekadir, K., Castro-Mateos, I., Pozo, J. M., Lazary, A., & Frangi, A. F. (2015). Accurate Segmentation of Vertebral Bodies and Processes Using Statistical Shape Decomposition and Conditional Models. IEEE Transactions on Medical Imaging, 34(8), 1627-1639. doi:10.1109/tmi.2015.2396774Michael Kelm, B., Wels, M., Kevin Zhou, S., Seifert, S., Suehling, M., Zheng, Y., & Comaniciu, D. (2013). Spine detection in CT and MR using iterated marginal space learning. Medical Image Analysis, 17(8), 1283-1292. doi:10.1016/j.media.2012.09.007Yan Kang, Engelke, K., & Kalender, W. A. (2003). A new accurate and precise 3-D segmentation method for skeletal structures in volumetric CT data. IEEE Transactions on Medical Imaging, 22(5), 586-598. doi:10.1109/tmi.2003.812265Huang, J., Jian, F., Wu, H., & Li, H. (2013). An improved level set method for vertebra CT image segmentation. BioMedical Engineering OnLine, 12(1), 48. doi:10.1186/1475-925x-12-48Lim, P. H., Bagci, U., & Bai, L. (2013). Introducing Willmore Flow Into Level Set Segmentation of Spinal Vertebrae. IEEE Transactions on Biomedical Engineering, 60(1), 115-122. doi:10.1109/tbme.2012.2225833Forsberg, D., Lundström, C., Andersson, M., & Knutsson, H. (2013). Model-based registration for assessment of spinal deformities in idiopathic scoliosis. Physics in Medicine and Biology, 59(2), 311-326. doi:10.1088/0031-9155/59/2/311Yao, J., Burns, J. E., Forsberg, D., Seitel, A., Rasoulian, A., Abolmaesumi, P., … Li, S. (2016). A multi-center milestone study of clinical vertebral CT segmentation. Computerized Medical Imaging and Graphics, 49, 16-28. doi:10.1016/j.compmedimag.2015.12.006Shi, C., Wang, J., & Cheng, Y. (2015). Sparse Representation-Based Deformation Model for Atlas-Based Segmentation of Liver CT Images. Image and Graphics, 410-419. doi:10.1007/978-3-319-21969-1_36Domingo, J., Dura, E., Ayala, G., & Ruiz-España, S. (2015). Means of 2D and 3D Shapes and Their Application in Anatomical Atlas Building. Lecture Notes in Computer Science, 522-533. doi:10.1007/978-3-319-23192-1_44Hyunjin Park, Bland, P. H., & Meyer, C. R. (2003). Construction of an abdominal probabilistic atlas and its application in segmentation. IEEE Transactions on Medical Imaging, 22(4), 483-492. doi:10.1109/tmi.2003.809139Cabezas, M., Oliver, A., Lladó, X., Freixenet, J., & Bach Cuadra, M. (2011). A review of atlas-based segmentation for magnetic resonance brain images. Computer Methods and Programs in Biomedicine, 104(3), e158-e177. doi:10.1016/j.cmpb.2011.07.015Fortunati, V., Verhaart, R. F., van der Lijn, F., Niessen, W. J., Veenland, J. F., Paulides, M. M., & van Walsum, T. (2013). Tissue segmentation of head and neck CT images for treatment planning: A multiatlas approach combined with intensity modeling. Medical Physics, 40(7), 071905. doi:10.1118/1.4810971Zhuang, X., Bai, W., Song, J., Zhan, S., Qian, X., Shi, W., … Rueckert, D. (2015). Multiatlas whole heart segmentation of CT data using conditional entropy for atlas ranking and selection. Medical Physics, 42(7), 3822-3833. doi:10.1118/1.4921366Zhou, J., Yan, Z., Lasio, G., Huang, J., Zhang, B., Sharma, N., … D’Souza, W. (2015). Automated compromised right lung segmentation method using a robust atlas-based active volume model with sparse shape composition prior in CT. Computerized Medical Imaging and Graphics, 46, 47-55. doi:10.1016/j.compmedimag.2015.07.003Linguraru, M. G., Sandberg, J. K., Li, Z., Shah, F., & Summers, R. M. (2010). Automated segmentation and quantification of liver and spleen from CT images using normalized probabilistic atlases and enhancement estimation. Medical Physics, 37(2), 771-783. doi:10.1118/1.3284530Xu, Y., Xu, C., Kuang, X., Wang, H., Chang, E. I.-C., Huang, W., & Fan, Y. (2016). 3D-SIFT-Flow for atlas-based CT liver image segmentation. Medical Physics, 43(5), 2229-2241. doi:10.1118/1.4945021Michopoulou, S. K., Costaridou, L., Panagiotopoulos, E., Speller, R., Panayiotakis, G., & Todd-Pokropek, A. (2009). Atlas-Based Segmentation of Degenerated Lumbar Intervertebral Discs From MR Images of the Spine. IEEE Transactions on Biomedical Engineering, 56(9), 2225-2231. doi:10.1109/tbme.2009.2019765Taso, M., Le Troter, A., Sdika, M., Ranjeva, J.-P., Guye, M., Bernard, M., & Callot, V. (2013). Construction of an in vivo human spinal cord atlas based on high-resolution MR images at cervical and thoracic levels: preliminary results. Magnetic Resonance Materials in Physics, Biology and Medicine, 27(3), 257-267. doi:10.1007/s10334-013-0403-6Lévy, S., Benhamou, M., Naaman, C., Rainville, P., Callot, V., & Cohen-Adad, J. (2015). White matter atlas of the human spinal cord with estimation of partial volume effect. NeuroImage, 119, 262-271. doi:10.1016/j.neuroimage.2015.06.040Hardisty, M., Gordon, L., Agarwal, P., Skrinskas, T., & Whyne, C. (2007). Quantitative characterization of metastatic disease in the spine. Part I. Semiautomated segmentation using atlas-based deformable registration and the level set method. Medical Physics, 34(8), 3127-3134. doi:10.1118/1.2746498Forsberg, D. (2015). Atlas-Based Registration for Accurate Segmentation of Thoracic and Lumbar Vertebrae in CT Data. Lecture Notes in Computational Vision and Biomechanics, 49-59. doi:10.1007/978-3-319-14148-0_5Ibañez MV Schroeder W Cates L Insight software Consortium. The ITK Software Guide 2016 http://www.itk.org/ItkSoftwareGuide.pdfLoader C R package: Local regression, likelihood and density estimation. CRAN repository 2013 2016 http://cran.r-project.org/web/packages/locfitPARK, H., HERO, A., BLAND, P., KESSLER, M., SEO, J., & MEYER, C. (2010). Construction of Abdominal Probabilistic Atlases and Their Value in Segmentation of Normal Organs in Abdominal CT Scans. IEICE Transactions on Information and Systems, E93-D(8), 2291-2301. doi:10.1587/transinf.e93.d.2291Pohl, K. M., Fisher, J., Bouix, S., Shenton, M., McCarley, R. W., Grimson, W. E. L., … Wells, W. M. (2007). Using the logarithm of odds to define a vector space on probabilistic atlases. Medical Image Analysis, 11(5), 465-477. doi:10.1016/j.media.2007.06.003Baddeley, A., & Molchanov, I. (1998). Journal of Mathematical Imaging and Vision, 8(1), 79-92. doi:10.1023/a:1008214317492De Bruijne, M., van Ginneken, B., Viergever, M. A., & Niessen, W. J. (2003). Adapting Active Shape Models for 3D Segmentation of Tubular Structures in Medical Images. Information Processing in Medical Imaging, 136-147. doi:10.1007/978-3-540-45087-0_12Zhang, K., Zhang, L., Song, H., & Zhou, W. (2010). Active contours with selective local or global segmentation: A new formulation and level set method. Image and Vision Computing, 28(4), 668-676. doi:10.1016/j.imavis.2009.10.009Kalpathy-Cramer, J., Awan, M., Bedrick, S., Rasch, C. R. N., Rosenthal, D. I., & Fuller, C. D. (2013). Development of a Software for Quantitative Evaluation Radiotherapy Target and Organ-at-Risk Segmentation Comparison. Journal of Digital Imaging, 27(1), 108-119. doi:10.1007/s10278-013-9633-4Huttenlocher, D. P., Klanderman, G. A., & Rucklidge, W. J. (1993). Comparing images using the Hausdorff distance. IEEE Transactions on Pattern Analysis and Machine Intelligence, 15(9), 850-863. doi:10.1109/34.232073Aspert, N., Santa-Cruz, D., & Ebrahimi, T. (s. f.). MESH: measuring errors between surfaces using the Hausdorff distance. Proceedings. IEEE International Conference on Multimedia and Expo. doi:10.1109/icme.2002.103587

Atlas construction and spatial normalisation to facilitate radiation-induced late effects research in childhood cancer

Reducing radiation-induced side effects is one of the most important challenges in paediatric cancer treatment. Recently, there has been growing interest in using spatial normalisation to enable voxel-based analysis of radiation-induced toxicities in a variety of patient groups. The need to consider three-dimensional distribution of doses, rather than dose-volume histograms, is desirable but not yet explored in paediatric populations. In this paper, we investigate the feasibility of atlas construction and spatial normalisation in paediatric radiotherapy. We used planning computed tomography (CT) scans from twenty paediatric patients historically treated with craniospinal irradiation to generate a template CT that is suitable for spatial normalisation. This childhood cancer population representative template was constructed using groupwise image registration. An independent set of 53 subjects from a variety of childhood malignancies was then used to assess the quality of the propagation of new subjects to this common reference space using deformable image registration (i.e., spatial normalisation). The method was evaluated in terms of overall image similarity metrics, contour similarity and preservation of dose-volume properties. After spatial normalisation, we report a dice similarity coefficient of 0.95±0.05, 0.85±0.04, 0.96±0.01, 0.91±0.03, 0.83±0.06 and 0.65±0.16 for brain and spinal canal, ocular globes, lungs, liver, kidneys and bladder. We then demonstrated the potential advantages of an atlas-based approach to study the risk of second malignant neoplasms after radiotherapy. Our findings indicate satisfactory mapping between a heterogeneous group of patients and the template CT. The poorest performance was for organs in the abdominal and pelvic region, likely due to respiratory and physiological motion and to the highly deformable nature of abdominal organs. More specialised algorithms should be explored in the future to improve mapping in these regions. This study is the first step toward voxel-based analysis in radiation-induced toxicities following paediatric radiotherapy

AUTOMATIC LIVER SEGMENTATION FROM CT SCANS USING INTENSITY ANALYSIS AND LEVEL-SET ACTIVE CONTOURS

Liver segmentation from CT scans is still a challenging task due to the liver characteristics in terms of shape and intensity variability. In this work, we propose an automatic segmentation method of the liver from CT data sets. The framework consists of three main steps: liver shape model localization, liver intensity range estimation and localized active contouring. We proposed an adaptive multiple thresholding technique to estimate the range of the liver intensities. First, multiple thresholding is used to extract the dense tissue from the whole CT scan. A localization step is then used to find the approximate location of the liver in the CT scan, to localize a constructed mean liver shape model. A liver intensity-range estimation step is then applied within the localized shape model ROI. The localized shape model and the estimated liver intensity range are used to build the initial mask. A level set based active contour algorithm is used to deform the initial mask to the liver boundaries in the CT scan. The proposed method was evaluated on two public data sets: SLIVER07 and 3D-IRCAD. The experiments showed that the proposed method is able to segment to liver in all CT scans in the two data sets accurately