504 research outputs found
Keypoint Transfer for Fast Whole-Body Segmentation
We introduce an approach for image segmentation based on sparse
correspondences between keypoints in testing and training images. Keypoints
represent automatically identified distinctive image locations, where each
keypoint correspondence suggests a transformation between images. We use these
correspondences to transfer label maps of entire organs from the training
images to the test image. The keypoint transfer algorithm includes three steps:
(i) keypoint matching, (ii) voting-based keypoint labeling, and (iii)
keypoint-based probabilistic transfer of organ segmentations. We report
segmentation results for abdominal organs in whole-body CT and MRI, as well as
in contrast-enhanced CT and MRI. Our method offers a speed-up of about three
orders of magnitude in comparison to common multi-atlas segmentation, while
achieving an accuracy that compares favorably. Moreover, keypoint transfer does
not require the registration to an atlas or a training phase. Finally, the
method allows for the segmentation of scans with highly variable field-of-view.Comment: Accepted for publication at IEEE Transactions on Medical Imagin
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 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.; DĂaz-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. 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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. 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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
Cloud-Based Benchmarking of Medical Image Analysis
Medical imagin
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