3,762 research outputs found
Relational Reasoning Network (RRN) for Anatomical Landmarking
Accurately identifying anatomical landmarks is a crucial step in deformation
analysis and surgical planning for craniomaxillofacial (CMF) bones. Available
methods require segmentation of the object of interest for precise landmarking.
Unlike those, our purpose in this study is to perform anatomical landmarking
using the inherent relation of CMF bones without explicitly segmenting them. We
propose a new deep network architecture, called relational reasoning network
(RRN), to accurately learn the local and the global relations of the landmarks.
Specifically, we are interested in learning landmarks in CMF region: mandible,
maxilla, and nasal bones. The proposed RRN works in an end-to-end manner,
utilizing learned relations of the landmarks based on dense-block units and
without the need for segmentation. For a given a few landmarks as input, the
proposed system accurately and efficiently localizes the remaining landmarks on
the aforementioned bones. For a comprehensive evaluation of RRN, we used
cone-beam computed tomography (CBCT) scans of 250 patients. The proposed system
identifies the landmark locations very accurately even when there are severe
pathologies or deformations in the bones. The proposed RRN has also revealed
unique relationships among the landmarks that help us infer several reasoning
about informativeness of the landmark points. RRN is invariant to order of
landmarks and it allowed us to discover the optimal configurations (number and
location) for landmarks to be localized within the object of interest
(mandible) or nearby objects (maxilla and nasal). To the best of our knowledge,
this is the first of its kind algorithm finding anatomical relations of the
objects using deep learning.Comment: 10 pages, 6 Figures, 3 Table
Automatic landmark annotation and dense correspondence registration for 3D human facial images
Dense surface registration of three-dimensional (3D) human facial images
holds great potential for studies of human trait diversity, disease genetics,
and forensics. Non-rigid registration is particularly useful for establishing
dense anatomical correspondences between faces. Here we describe a novel
non-rigid registration method for fully automatic 3D facial image mapping. This
method comprises two steps: first, seventeen facial landmarks are automatically
annotated, mainly via PCA-based feature recognition following 3D-to-2D data
transformation. Second, an efficient thin-plate spline (TPS) protocol is used
to establish the dense anatomical correspondence between facial images, under
the guidance of the predefined landmarks. We demonstrate that this method is
robust and highly accurate, even for different ethnicities. The average face is
calculated for individuals of Han Chinese and Uyghur origins. While fully
automatic and computationally efficient, this method enables high-throughput
analysis of human facial feature variation.Comment: 33 pages, 6 figures, 1 tabl
Anatomical landmark based registration of contrast enhanced T1-weighted MR images
In many problems involving multiple image analysis, an im- age registration step is required. One such problem appears in brain tumor imaging, where baseline and follow-up image volumes from a tu- mor patient are often to-be compared. Nature of the registration for a change detection problem in brain tumor growth analysis is usually rigid or affine. Contrast enhanced T1-weighted MR images are widely used in clinical practice for monitoring brain tumors. Over this modality, con- tours of the active tumor cells and whole tumor borders and margins are visually enhanced. In this study, a new technique to register serial contrast enhanced T1 weighted MR images is presented. The proposed fully-automated method is based on five anatomical landmarks: eye balls, nose, confluence of sagittal sinus, and apex of superior sagittal sinus. Af- ter extraction of anatomical landmarks from fixed and moving volumes, an affine transformation is estimated by minimizing the sum of squared distances between the landmark coordinates. Final result is refined with a surface registration, which is based on head masks confined to the sur- face of the scalp, as well as to a plane constructed from three of the extracted features. The overall registration is not intensity based, and it depends only on the invariant structures. Validation studies using both synthetically transformed MRI data, and real MRI scans, which included several markers over the head of the patient were performed. In addition, comparison studies against manual landmarks marked by a radiologist, as well as against the results obtained from a typical mutual information based method were carried out to demonstrate the effectiveness of the proposed method
Computationally efficient cardiac views projection using 3D Convolutional Neural Networks
4D Flow is an MRI sequence which allows acquisition of 3D images of the
heart. The data is typically acquired volumetrically, so it must be reformatted
to generate cardiac long axis and short axis views for diagnostic
interpretation. These views may be generated by placing 6 landmarks: the left
and right ventricle apex, and the aortic, mitral, pulmonary, and tricuspid
valves. In this paper, we propose an automatic method to localize landmarks in
order to compute the cardiac views. Our approach consists of first calculating
a bounding box that tightly crops the heart, followed by a landmark
localization step within this bounded region. Both steps are based on a 3D
extension of the recently introduced ENet. We demonstrate that the long and
short axis projections computed with our automated method are of equivalent
quality to projections created with landmarks placed by an experienced cardiac
radiologist, based on a blinded test administered to a different cardiac
radiologist
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Automated multimodal volume registration based on supervised 3D anatomical landmark detection
We propose a new method for automatic 3D multimodal registration based on anatomical landmark detection. Landmark detectors are learned independantly in the two imaging modalities using Extremely Randomized Trees and multi-resolution voxel windows. A least-squares fitting algorithm is then used for rigid registration based on the landmark positions as predicted by these detectors in the two imaging modalities. Experiments are carried out with this method on a dataset of pelvis CT and CBCT scans related to 45 patients. On this dataset, our fully automatic approach yields results very competitive with respect to a manually assisted state-of-the-art rigid registration algorithm
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
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Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach
The detection of anatomical landmarks in bioimages is a necessary but tedious step for geometric morphometrics studies in many research domains. We propose variants of a multi-resolution tree-based approach to speed-up the detection of landmarks in bioimages. We extensively evaluate our method variants on three different datasets (cephalometric, zebrafish, and drosophila images). We identify the key method parameters (notably the multi-resolution) and report results with respect to human ground truths and existing methods. Our method achieves recognition performances competitive with current existing approaches while being generic and fast. The algorithms are integrated in the open-source Cytomine software and we provide parameter configuration guidelines so that they can be easily exploited by end-users. Finally, datasets are readily available through a Cytomine server to foster future research
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