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

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Deep Learning-based Prescription of Cardiac MRI Planes.

PurposeTo develop and evaluate a system to prescribe imaging planes for cardiac MRI based on deep learning (DL)-based localization of key anatomic landmarks.Materials and methodsAnnotated landmarks on 892 long-axis (LAX) and 493 short-axis (SAX) cine steady-state free precession series from cardiac MR images were retrospectively collected between February 2012 and June 2017. U-Net-based heatmap regression was used for localization of cardiac landmarks, which were used to compute cardiac MRI planes. Performance was evaluated by comparing localization distances and plane angle differences between DL predictions and ground truth. The plane angulations from DL were compared with those prescribed by the technologist at the original time of acquisition. Data were split into 80% for training and 20% for testing, and results confirmed with fivefold cross-validation.ResultsOn LAX images, DL localized the apex within mean 12.56 mm ± 19.11 (standard deviation) and the mitral valve (MV) within 7.68 mm ± 6.91. On SAX images, DL localized the aortic valve within 5.78 mm ± 5.68, MV within 5.90 mm ± 5.24, pulmonary valve within 6.55 mm ± 6.39, and tricuspid valve within 6.39 mm ± 5.89. On the basis of these localizations, average angle bias and mean error of DL-predicted imaging planes relative to ground truth annotations were as follows: SAX, -1.27° ± 6.81 and 4.93° ± 4.86; four chambers, 0.38° ± 6.45 and 5.16° ± 3.80; three chambers, 0.13° ± 12.70 and 9.02° ± 8.83; and two chamber, 0.25° ± 9.08 and 6.53° ± 6.28, respectively.ConclusionDL-based anatomic localization is a feasible strategy for planning cardiac MRI planes. This approach can produce imaging planes comparable to those defined by ground truth landmarks.© RSNA, 2019 Supplemental material is available for this article

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

(no abstract