Publications of Andrea Mendizabal

2019

Journal articles

titre: Physics-based Deep Neural Network for Augmented Reality during Liver Surgery
auteur: Jean-Nicolas Brunet, Andrea Mendizabal, Antoine Petit, Nicolas Golse, Eric Vibert, Stéphane Cotin
article: Medical image computing and computer-assisted intervention : MICCAI .. International Conference on Medical Image Computing and Computer-Assisted Intervention, Springer, In press
resume: In this paper we present an approach combining a finite element method and a deep neural network to learn complex elastic deformations with the objective of providing augmented reality during hep-atic surgery. Derived from the U-Net architecture, our network is built entirely from physically-based simulations of a preoperative segmenta-tion of the organ. These simulations are performed using an immersed-boundary method, which offers several numerical and practical benefits, such as not requiring boundary-conforming volume elements. We perform a quantitative assessment of the method using synthetic and ex vivo patient data. Results show that the network is capable of solving the deformed state of the organ using only a sparse partial surface displacement data and achieve similar accuracy as a FEM solution, while being about 100x faster. When applied to an ex vivo liver example, we achieve the registration in only 3 ms with a mean target registration error (TRE) of 2.9 mm.
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Preprints, Working Papers, …

titre: Simulation of hyperelastic materials in real-time using deep learning
auteur: Andrea Mendizabal, Pablo Márquez-Neila, Stéphane Cotin
article: 2019
resume: The finite element method (FEM) is among the most commonly used numerical methods for solving engineering problems. Due to its computational cost, various ideas have been introduced to reduce computation times, such as domain decomposition, parallel computing, adaptive meshing, and model order reduction. In this paper we present U-Mesh: a data-driven method based on a U-Net architecture that approximates the non-linear relation between a contact force and the displacement field computed by a FEM algorithm. We show that deep learning, one of the latest machine learning methods based on artificial neural networks, can enhance computational mechanics through its ability to encode highly non-linear models in a compact form. Our method is applied to two benchmark examples: a cantilever beam and an L-shape subject to moving punctual loads. A comparison between our method and proper orthogonal decomposition (POD) is done through the paper. The results show that U-Mesh can perform very fast simulations on various geometries, mesh resolutions and number of input forces with very small errors.
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2018

Journal articles

titre: A Combined Simulation & Machine Learning Approach for Image-based Force Classification during Robotized Intravitreal Injections
auteur: Andrea Mendizabal, Tatiana Fountoukidou, Jan Hermann, Raphael Sznitman, Stéphane Cotin
article: Medical image computing and computer-assisted intervention : MICCAI .. International Conference on Medical Image Computing and Computer-Assisted Intervention, Springer, 2018
resume: Intravitreal injection is one of the most common treatment strategies for chronic ophthalmic diseases. The last decade has seen the number of intravitreal injections dramatically increase, and with it, adverse effects and limitations. To overcome these issues, medical assistive devices for robotized injections have been proposed and are projected to improve delivery mechanisms for new generation of pharmacological solutions. In our work, we propose a method aimed at improving the safety features of such envisioned robotic systems. Our vision-based method uses a combination of 2D OCT data, numerical simulation and machine learning to estimate the range of the force applied by an injection needle on the sclera. We build a Neural Network (NN) to predict force ranges from Optical Coherence Tomography (OCT) images of the sclera directly. To avoid the need of large training data sets, the NN is trained on images of simulated deformed sclera. We validate our approach on real OCT images collected on five ex vivo porcine eyes using a robotically-controlled needle. Results show that the applied force range can be predicted with 94% accuracy. Being real-time, this solution can be integrated in the control loop of the system, allowing for in-time withdrawal of the needle.
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2017

Conference papers

titre: Face-based Smoothed Finite Element Method for Real-time Simulation of soft tissue
auteur: Andrea Mendizabal, Rémi Duparc, Huu Phuoc Bui, Christoph Paulus, Igor Peterlik, Stéphane Cotin
article: SPIE Medical Imaging, Feb 2017, Orlando, United States
resume: In soft tissue surgery, a tumor and other anatomical structures are usually located using the preoperative CT or MR images. However, due to the deformation of the concerned tissues, this information suffers from inaccuracy when employed directly during the surgery. In order to account for these deformations in the planning process, the use of a bio-mechanical model of the tissues is needed. Such models are often designed using the finite element method (FEM), which is, however, computationally expensive, in particular when a high accuracy of the simulation is required. In our work, we propose to use a smoothed finite element method (S-FEM) in the context of modeling of the soft tissue deformation. This numerical technique has been introduced recently to overcome the overly stiff behavior of the standard FEM and to improve the solution accuracy and the convergence rate in solid mechanics problems. In this paper, a face-based smoothed finite element method (FS-FEM) using 4-node tetrahedral elements is presented. We show that in some cases, the method allows for reducing the number of degrees of freedom, while preserving the accuracy of the discretization. The method is evaluated on a simulation of a cantilever beam loaded at the free end and on a simulation of a 3D cube under traction and compression forces. Further, it is applied to the simulation of the brain shift and of the kidney’s deformation. The results demonstrate that the method outperforms the standard FEM in a bending scenario and that has similar accuracy as the standard FEM in the simulations of brain shift and kidney deformation.
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