Purpose: In surgical navigation, pre-operative organ models are presented to surgeons during the intervention to help them in efficiently finding their target. In the case of soft tissue, these models need to be deformed and adapted to the current situation by using intra-operative sensor data. A promising method to realize this are real-time capable biomechanical models. Methods: We train a fully convolutional neural network to estimate a displacement field of all points inside an organ when given only the displacement of a part of the organ's surface. The network trains on entirely synthetic data of random organ-like meshes, which allows us to generate much more data than is otherwise available. The input and output data is discretized into a regular grid, allowing us to fully utilize the capabilities of convolutional operators and to train and infer in a highly parallelized manner. Results: The system is evaluated on in-silico liver models, phantom liver data and human in-vivo breathing data. We test the performance with varying material parameters, organ shapes and amount of visible surface. Even though the network is only trained on synthetic data, it adapts well to the various cases and gives a good estimation of the internal organ displacement. The inference runs at over 50 frames per second. Conclusions: We present a novel method for training a data-driven, real-time capable deformation model. The accuracy is comparable to other registration methods, it adapts very well to previously unseen organs and does not need to be re-trained for every patient. The high inferring speed makes this method useful for many applications such as surgical navigation and real-time simulation.
@cite_7 show that neural networks can estimate the deformation of a liver from the known displacement of a partial surface. They report very small errors while using only 3 Approaches which generalize to new patients were made by @cite_9 , who estimate the liver's deformation from breathing motion using various machine learning methods and Martínez- @cite_4 who estimate breast compression. However, both methods focus on single scenarios where the main direction of the forces stay similar throughout all experiments.
@cite_9 @cite_4 @cite_7
2558562220 2758941972 2769483004
Deformation estimation of elastic object assuming an internal organ is important for the computer navigation of surgery. The aim of this study is to estimate the deformation of an entire three-dimensional elastic object using displacement information of very few observation points. A learning approach with a neural network was introduced to estimate the entire deformation of an object. We applied our method to two elastic objects; a rectangular parallelepiped model, and a human liver model reconstructed from computed tomography data. The average estimation error for the human liver model was 0.041 mm when the object was deformed up to 66.4 mm, from only around 3 observations. These results indicate that the deformation of an entire elastic object can be estimated with an acceptable level of error from limited observations by applying a trained neural network to a new deformation. Machine learning (ML) to model the liver biomechanical behaviour during breathing.ML is much faster than the popular FEM, allowing real-time soft tissue modelling.Modelling scheme able to predict deformation for a new load and a new liver.ML regression models were used: three tree-based methods and two simpler ones.Good prediction performance was obtained: all samples with an error under 1źmm. Progress in biomechanical modelling of human soft tissue is the basis for the development of new clinical applications capable of improving the diagnosis and treatment of some diseases (e.g. cancer), as well as the surgical planning and guidance of some interventions. The finite element method (FEM) is one of the most popular techniques used to predict the deformation of the human soft tissue due to its high accuracy. However, FEM has an associated high computational cost, which makes it difficult its integration in real-time computer-aided surgery systems. An alternative for simulating the mechanical behaviour of human organs in real time comes from the use of machine learning (ML) techniques, which are much faster than FEM. This paper assesses the feasibility of ML methods for modelling the biomechanical behaviour of the human liver during the breathing process, which is crucial for guiding surgeons during interventions where it is critical to track this deformation (e.g. some specific kind of biopsies) or for the accurate application of radiotherapy dose to liver tumours. For this purpose, different ML regression models were investigated, including three tree-based methods (decision trees, random forests and extremely randomised trees) and other two simpler regression techniques (dummy model and linear regression). In order to build and validate the ML models, a labelled data set was constructed from modelling the deformation of eight ex-vivo human livers using FEM. The best prediction performance was obtained using extremely randomised trees, with a mean error of 0.07źmm and all the samples with an error under 1źmm. The achieved results lay the foundation for the future development of some real-time software capable of simulating the human liver deformation during the breathing process during clinical interventions. Presents a novel method for validation of nonrigid medical image registration. This method is based on the simulation of physically plausible, biomechanical tissue deformations using finite-element methods. Applying a range of displacements to finite-element models of different patient anatomies generates model solutions which simulate gold standard deformations. From these solutions, deformed images are generated with a range of deformations typical of those likely to occur in vivo. The registration accuracy with respect to the finite-element simulations is quantified by co-registering the deformed images with the original images and comparing the recovered voxel displacements with the biomechanically simulated ones. The functionality of the validation method is demonstrated for a previously described nonrigid image registration technique based on free-form deformations using B-splines and normalized mutual information as a voxel similarity measure, with an application to contrast-enhanced magnetic resonance mammography image pairs. The exemplar nonrigid registration technique is shown to be of subvoxel accuracy on average for this particular application. The validation method presented here is an important step toward more generic simulations of biomechanically plausible tissue deformations and quantification of tissue motion recovery using nonrigid image registration. It will provide a basis for improving and comparing different nonrigid registration techniques for a diversity of medical applications, such as intrasubject tissue deformation or motion correction in the brain, liver or heart. Purpose: To investigate the potential of the normalized probabilistic atlases and computer-aided medical image analysis to automatically segment and quantify livers and spleens for extracting imaging biomarkers (volume and height). Methods: A clinical tool was developed to segment livers and spleen from 257 abdominal contrast-enhanced CT studies. There were 51 normal livers, 44 normal spleens, 128 splenomegaly, 59 hepatomegaly, and 23 partial hepatectomy cases. 20 more contrast-enhanced CT scans from a public site with manual segmentations of mainly pathological livers were used to test the method. Data were acquired on a variety of scanners from different manufacturers and at varying resolution. Probabilistic atlases of livers and spleens were created using manually segmented data from ten noncontrast CT scans (five male and five female). The organ locations were modeled in the physical space and normalized to the position of an anatomical landmark, the xiphoid. The construction and exploitation of liver and spleen atlases enabled the automated quantifications of liver spleen volumes and heights (midhepatic liver height and cephalocaudal spleen height) from abdominal CT data. The quantification was improved incrementally by a geodesic active contour, patient specific contrast-enhancement characteristics passed to an adaptive convolution, and correction for shape and location errors. Results: The livers and spleens were robustly segmented from normal and pathological cases. For the liver, the Dice Tanimoto volume overlaps were 96.2 92.7 , the volume height errors were 2.2 2.8 , the root-mean-squared error (RMSE) was 2.3 mm, and the average surface distance (ASD) was 1.2 mm. The spleen quantification led to 95.2 91 Dice Tanimoto overlaps, 3.3 1.7 volume height errors, 1.1 mm RMSE, and 0.7 ASD. The correlations ( R 2 ) with clinical manual height measurements were 0.97 and 0.93 for the spleen and liver, respectively ( p 0.0001 ) . No significant difference ( p > 0.2 ) was found comparing interobserver and automatic-manual volume height errors for liver and spleen. Conclusions: The algorithm is robust to segmenting normal and enlarged spleens and livers, and in the presence of tumors and large morphological changes due to partial hepatectomy. Imaging biomarkers of the liver and spleen from automated computer-assisted tools have the potential to assist the diagnosis of abdominal disorders from routine analysis of clinical data and guide clinical management. Accurate knowledge of the liver structure, including liver surface and lesion localization, is usually required in treatments such as liver tumor ablations and or radiotherapy. This paper presents a new method and corresponding algorithm for fast segmentation of the liver and its internal lesions from CT scans. No interaction between the user and analysis system is required for initialization since the algorithm is fully automatic. A statistical model-based approach was created to distinguish hepatic tissue from other abdominal organs. It was combined to an active contour technique using gradient vector flow in order to obtain a smoother and more natural liver surface segmentation. Thereafter, automatic classification was performed to isolate hepatic lesions from liver parenchyma. Twenty-one datasets, presenting different anatomical and pathological situations, have been processed and analyzed. Special focus has been driven to the resulting processing time together with quality assessment. Our method allowed robust and efficient liver and lesion segmentations very close to the ground truth, in a relatively short processing time (average of 11.4 s for a 512 × 512-pixel slice). A volume overlap of 94.2 and an accuracy of 3.7 mm were achieved for liver surface segmentation. Sensitivity and specificity for tumor lesion detection were 82.6 and 87.5 , respectively. Abstract This work presents a data-driven method to simulate, in real-time, the biomechanical behavior of the breast tissues in some image-guided interventions such as biopsies or radiotherapy dose delivery as well as to speed up multimodal registration algorithms. Ten real breasts were used for this work. Their deformation due to the displacement of two compression plates was simulated off-line using the finite element (FE) method. Three machine learning models were trained with the data from those simulations. Then, they were used to predict in real-time the deformation of the breast tissues during the compression. The models were a decision tree and two tree-based ensemble methods (extremely randomized trees and random forest). Two different experimental setups were designed to validate and study the performance of these models under different conditions. The mean 3D Euclidean distance between nodes predicted by the models and those extracted from the FE simulations was calculated to assess the performance of the models in the validation set. The experiments proved that extremely randomized trees performed better than the other two models. The mean error committed by the three models in the prediction of the nodal displacements was under 2 mm, a threshold usually set for clinical applications. The time needed for breast compression prediction is sufficiently short to allow its use in real-time ( 0.2 s). A citing sentence is one that appears in a scientific article and cites previous work. Citing sentences have been studied and used in many applications. For example, they have been used in scientific paper summarization, automatic survey generation, paraphrase identification, and citation function classification. Citing sentences that cite multiple papers are common in scientific writing. This observation should be taken into consideration when using citing sentences in applications. For instance, when a citing sentence is used in a summary of a scientific paper, only the fragments of the sentence that are relevant to the summarized paper should be included in the summary. In this paper, we present and compare three different approaches for identifying the fragments of a citing sentence that are related to a given target reference. Our methods are: word classification, sequence labeling, and segment classification. Our experiments show that segment classification achieves the best results. In this paper the authors present a new approach for the nonrigid registration of contrast-enhanced breast MRI. A hierarchical transformation model of the motion of the breast has been developed. The global motion of the breast is modeled by an affine transformation while the local breast motion is described by a free-form deformation (FFD) based on B-splines. Normalized mutual information is used as a voxel-based similarity measure which is insensitive to intensity changes as a result of the contrast enhancement. Registration is achieved by minimizing a cost function, which represents a combination of the cost associated with the smoothness of the transformation and the cost associated with the image similarity. The algorithm has been applied to the fully automated registration of three-dimensional (3-D) breast MRI in volunteers and patients. In particular, the authors have compared the results of the proposed nonrigid registration algorithm to those obtained using rigid and affine registration techniques. The results clearly indicate that the nonrigid registration algorithm is much better able to recover the motion and deformation of the breast than rigid or affine registration algorithms. This paper proposes a method to realize desired contact normal forces between humanoids and their compliant environment. By using contact models, desired contact forces are converted to desired deformations of compliant surfaces. To achieve desired forces, deformations are controlled by controlling the contact point positions. Parameters of contact models are assumed to be known or estimated using the approach described in this paper. The proposed methods for estimating the contact parameters and controlling the contact normal force are implemented on a LWR KUKA IV arm. To verify both methods, experiments are performed with the KUKA arm while its end-effector is in contact with two different soft objects. In this paper, we present a new method to estimate the mechanical parameters of soft bodies directly from videos of solids getting deformed under external user action. Our method requires one standard camera, a deformable solid made of homogeneous material, and a regular light source. We make estimations using an inverse method based on a quasi-static FEM simulation and a visual error metric. The result is a set of two parameters, the Young modulus and the Poisson ratio, that can be used for more complex simulations, or force feedback applications like virtual surgery, for example. We also present a new device for capturing the external forces applied on the deformable solids. Respiratory rate is an important vital sign that can indicate progression of illness but to also predict rapid decline in health. For the purpose, non-contact monitoring systems are becoming more popular due to the self-evident increase in patient comfort. As a cost effective solution for non-invasive breathing monitoring, utilizing the received signal strength measurements of inexpensive transceivers has been proposed. However, the applicability of the available solutions is limited since they rely on numerous sensors. In this work, considerable improvement is made, and a respiratory rate monitoring system based on a single commercial off-the-shelf transmitter-receiver pair is presented. Methods that enable estimation and enhance the accuracy are presented and their effects are evaluated. Moreover, it is empirically demonstrated that the performance of the system is comparable to the accuracy of a high-end device for 3-4 orders of magnitude less price; achieving mean absolute error of 0.12 breaths per minute in the most realistic scenario of the experiments. Abstract Objectives Accurate reconstruction and visualisation of soft tissue deformation in real time is crucial in image-guided surgery, particularly in augmented reality (AR) applications. Current deformation models are characterised by a trade-off between accuracy and computational speed. We propose an approach to derive a patient-specific deformation model for brain pathologies by combining the results of pre-computed finite element method (FEM) simulations with machine learning algorithms. The models can be computed instantaneously and offer an accuracy comparable to FEM models. Method A brain tumour is used as the subject of the deformation model. Load-driven FEM simulations are performed on a tetrahedral brain mesh afflicted by a tumour. Forces of varying magnitudes, positions, and inclination angles are applied onto the brain's surface. Two machine learning algorithms—artificial neural networks (ANNs) and support vector regression (SVR)—are employed to derive a model that can predict the resulting deformation for each node in the tumour's mesh. Results The tumour deformation can be predicted in real time given relevant information about the geometry of the anatomy and the load, all of which can be measured instantly during a surgical operation. The models can predict the position of the nodes with errors below 0.3 mm, beyond the general threshold of surgical accuracy and suitable for high fidelity AR systems. The SVR models perform better than the ANN's, with positional errors for SVR models reaching under 0.2 mm. Conclusions The results represent an improvement over existing deformation models for real time applications, providing smaller errors and high patient-specificity. The proposed approach addresses the current needs of image-guided surgical systems and has the potential to be employed to model the deformation of any type of soft tissue. Abstract It is now well-known that one can reconstruct sparse or compressible signals accurately from a very limited number of measurements, possibly contaminated with noise. This technique known as “compressed sensing” or “compressive sampling” relies on properties of the sensing matrix such as the restricted isometry property . In this Note, we establish new results about the accuracy of the reconstruction from undersampled measurements which improve on earlier estimates, and have the advantage of being more elegant. To cite this article: E.J. Candes, C. R. Acad. Sci. Paris, Ser. I 346 (2008). Display Omitted Survival prediction of HCC patients is modeled in a real and high complex scenario.Its complexity is due to a small dataset with heterogeneous and missing input data.We propose a new cluster-based oversampling method to overcome these drawbacks.Neural networks and logistic regression are applied in the classification stage.Experimental results show that our method outperforms previous existing approaches. Liver cancer is the sixth most frequently diagnosed cancer and, particularly, Hepatocellular Carcinoma (HCC) represents more than 90 of primary liver cancers. Clinicians assess each patients treatment on the basis of evidence-based medicine, which may not always apply to a specific patient, given the biological variability among individuals. Over the years, and for the particular case of Hepatocellular Carcinoma, some research studies have been developing strategies for assisting clinicians in decision making, using computational methods (e.g. machine learning techniques) to extract knowledge from the clinical data. However, these studies have some limitations that have not yet been addressed: some do not focus entirely on Hepatocellular Carcinoma patients, others have strict application boundaries, and none considers the heterogeneity between patients nor the presence of missing data, a common drawback in healthcare contexts. In this work, a real complex Hepatocellular Carcinoma database composed of heterogeneous clinical features is studied. We propose a new cluster-based oversampling approach robust to small and imbalanced datasets, which accounts for the heterogeneity of patients with Hepatocellular Carcinoma. The preprocessing procedures of this work are based on data imputation considering appropriate distance metrics for both heterogeneous and missing data (HEOM) and clustering studies to assess the underlying patient groups in the studied dataset (K-means). The final approach is applied in order to diminish the impact of underlying patient profiles with reduced sizes on survival prediction. It is based on K-means clustering and the SMOTE algorithm to build a representative dataset and use it as training example for different machine learning procedures (logistic regression and neural networks). The results are evaluated in terms of survival prediction and compared across baseline approaches that do not consider clustering and or oversampling using the Friedman rank test. Our proposed methodology coupled with neural networks outperformed all others, suggesting an improvement over the classical approaches currently used in Hepatocellular Carcinoma prediction models. A new form of document coupling called co-citation is defined as the frequency with which two documents are cited together. The co-citation frequency of two scientific papers can be determined by comparing lists of citing documents in the Science Citation Index and counting identical entries. Networks of co-cited papers can be generated for specific scientific specialties, and an example is drawn from the literature of particle physics. Co-citation patterns are found to differ significantly from bibliographic coupling patterns, but to agree generally with patterns of direct citation. Clusters of co-cited papers provide a new way to study the specialty structure of science. They may provide a new approach to indexing and to the creation of SDI profiles. This paper presents a new method for simulating the deformation of organ models by using a neural network. The proposed method is based on the idea proposed by [2] that a deformed model can be estimated from the superposition of basic deformation modes. The neural network finds a relationship between external forces and the models deformed by the forces. The experimental results show that the trained network can achieve a real-time simulation while keeping the acceptable accuracy compared with the nonlinear FEM computation. We propose a novel approach to reconstruct complete 3D deformable models over time by a single depth camera, provided that most parts of the models are observed by the camera at least once. The core of this algorithm is based on the assumption that the deformation is continuous and predictable in a short temporal interval. While the camera can only capture part of a whole surface at any time instant, partial surfaces reconstructed from different times are assembled together to form a complete 3D surface for each time instant, even when the shape is under severe deformation. A mesh warping algorithm based on linear mesh deformation is used to align different partial surfaces. A volumetric method is then used to combine partial surfaces, fix missing holes, and smooth alignment errors. Our experiment shows that this approach is able to reconstruct visually plausible 3D surface deformation results with a single camera. The old Asian legend about the blind men and the elephant comes to mind when looking at how different authors of scientific papers describe a piece of related prior work. It turns out that different citations to the same paper often focus on different aspects of that paper and that neither provides a full description of its full set of contributions. In this article, we will describe our investigation of this phenomenon. We studied citation summaries in the context of research papers in the biomedical domain. A citation summary is the set of citing sentences for a given article and can be used as a surrogate for the actual article in a variety of scenarios. It contains information that was deemed by peers to be important. Our study shows that citation summaries overlap to some extent with the abstracts of the papers and that they also differ from them in that they focus on different aspects of these papers than do the abstracts. In addition to this, co-cited articles (which are pairs of articles cited by another article) tend to be similar. We show results based on a lexical similarity metric called cohesion to justify our claims. © 2008 Wiley Periodicals, Inc. In this paper, we introduce TR-BREATH, a time-reversal (TR)-based contact-free breathing monitoring system. It is capable of breathing detection and multiperson breathing rate estimation within a short period of time using off-the-shelf WiFi devices. The proposed system exploits the channel state information (CSI) to capture the miniature variations in the environment caused by breathing. To magnify the CSI variations, TR-BREATH projects CSIs into the TR resonating strength (TRRS) feature space and analyzes the TRRS by the Root-MUSIC and affinity propagation algorithms. Extensive experiment results indoor demonstrate a perfect detection rate of breathing. With only 10 s of measurement, a mean accuracy of @math can be obtained for single-person breathing rate estimation under the non-line-of-sight (NLOS) scenario. Furthermore, it achieves a mean accuracy of @math in breathing rate estimation for a dozen people under the line-of-sight scenario and a mean accuracy of @math in breathing rate estimation of nine people under the NLOS scenario, both with 63 s of measurement. Moreover, TR-BREATH can estimate the number of people with an error around 1. We also demonstrate that TR-BREATH is robust against packet loss and motions. With the prevailing of WiFi, TR-BREATH can be applied for in-home and real-time breathing monitoring. The article introduces digital image restoration to the reader who is just beginning in this field, and provides a review and analysis for the reader who may already be well-versed in image restoration. The perspective on the topic is one that comes primarily from work done in the field of signal processing. Thus, many of the techniques and works cited relate to classical signal processing approaches to estimation theory, filtering, and numerical analysis. In particular, the emphasis is placed primarily on digital image restoration algorithms that grow out of an area known as "regularized least squares" methods. It should be noted, however, that digital image restoration is a very broad field, as we discuss, and thus contains many other successful approaches that have been developed from different perspectives, such as optics, astronomy, and medical imaging, just to name a few. In the process of reviewing this topic, we address a number of very important issues in this field that are not typically discussed in the technical literature.