Stéphane Cotin

Stéphane Cotin
National Institute for Research in Computer Science and Control | INRIA · MIMESIS Team (Strasbourg) - Physics-based Simulation for Virtual and Augmented Reality

PhD in Computer Science and Applied Mathematics

About

249
Publications
51,377
Reads
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7,299
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Introduction
I am a Research Director at INRIA and the head of the SHACRA team, which research activities relate to the simulation of medical procedures, for training, planning and per-operative guidance. Our current projects are in the following areas: cataract surgery, deep brain stimulation, hepatic tumor ablation, middle ear surgery, cardiac electrophysiology, and interventional neuroradiology.
Additional affiliations
January 2015 - present
IHU de Strasbourg
Position
  • Project Manager
May 2007 - June 2014
National Institute for Research in Computer Science and Control
Position
  • Research Director
January 2007 - present
National Institute for Research in Computer Science and Control
Position
  • INRIA - Institut National de Recherche en Informatique et en Automatique

Publications

Publications (249)
Preprint
Full-text available
The nonrigid alignment between a pre-operative biomechanical model and an intra-operative observation is a critical step to track the motion of a soft organ in augmented surgery. While many elastic registration procedures introduce artificial forces into the direct physical model to drive the registration, we propose in this paper a method to recon...
Article
Real‐time simulation of elastic structures is essential in many applications, from computer‐guided surgical interventions to interactive design in mechanical engineering. The Finite Element Method is often used as the numerical method of reference for solving the partial differential equations associated with these problems. Deep learning methods h...
Chapter
Patient-specific Biomechanical Models (PBMs) can enhance computer assisted surgical procedures with critical information. Although pre-operative data allow to parametrize such PBMs based on each patient’s properties, they are not able to fully characterize them. In particular, simulation boundary conditions cannot be determined from pre-operative m...
Preprint
Real-time simulation of elastic structures is essential in many applications, from computer-guided surgical interventions to interactive design in mechanical engineering. The Finite Element Method is often used as the numerical method of reference for solving the partial differential equations associated with these problems. Yet, deep learning meth...
Book
The eight-volume set LNCS 12901, 12902, 12903, 12904, 12905, 12906, 12907, and 12908 constitutes the refereed proceedings of the 24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021, held in Strasbourg, France, in September/October 2021.* The 542 revised full papers presented were carefully review...
Book
The eight-volume set LNCS 12901, 12902, 12903, 12904, 12905, 12906, 12907, and 12908 constitutes the refereed proceedings of the 24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021, held in Strasbourg, France, in September/October 2021.* The 542 revised full papers presented were carefully review...
Book
The eight-volume set LNCS 12901, 12902, 12903, 12904, 12905, 12906, 12907, and 12908 constitutes the refereed proceedings of the 24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021, held in Strasbourg, France, in September/October 2021.* The 542 revised full papers presented were carefully review...
Book
The eight-volume set LNCS 12901, 12902, 12903, 12904, 12905, 12906, 12907, and 12908 constitutes the refereed proceedings of the 24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021, held in Strasbourg, France, in September/October 2021.* The 542 revised full papers presented were carefully review...
Book
The eight-volume set LNCS 12901, 12902, 12903, 12904, 12905, 12906, 12907, and 12908 constitutes the refereed proceedings of the 24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021, held in Strasbourg, France, in September/October 2021.* The 542 revised full papers presented were carefully review...
Book
The eight-volume set LNCS 12901, 12902, 12903, 12904, 12905, 12906, 12907, and 12908 constitutes the refereed proceedings of the 24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021, held in Strasbourg, France, in September/October 2021.* The 542 revised full papers presented were carefully review...
Book
The eight-volume set LNCS 12901, 12902, 12903, 12904, 12905, 12906, 12907, and 12908 constitutes the refereed proceedings of the 24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021, held in Strasbourg, France, in September/October 2021.* The 542 revised full papers presented were carefully review...
Book
The eight-volume set LNCS 12901, 12902, 12903, 12904, 12905, 12906, 12907, and 12908 constitutes the refereed proceedings of the 24th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2021, held in Strasbourg, France, in September/October 2021.* The 542 revised full papers presented were carefully review...
Article
Full-text available
Objective: To develop consensus definitions of image-guided surgery, computer-assisted surgery, hybrid operating room, and surgical navigation systems. Summary background data: The use of minimally invasive procedures has increased tremendously over the past 2 decades, but terminology related to image-guided minimally invasive procedures has not...
Chapter
Intra-operative brain shift is a well-known phenomenon that describes non-rigid deformation of brain tissues due to gravity and loss of cerebrospinal fluid among other phenomena. This has a negative influence on surgical outcome that is often based on pre-operative planning where the brain shift is not considered. We present a novel brain-shift awa...
Chapter
In the context of ultrasound (US) guided breast biopsy, image fusion techniques can be employed to track the position of US-invisible lesions previously identified on a pre-operative image. Such methods have to account for the large anatomical deformations resulting from probe pressure during US scanning within the real-time constraint. Although bi...
Chapter
Full-text available
To build an augmented view of an organ during surgery, it is essential to have a biomechanical model with appropriate material parameters and boundary conditions, able to match patient specific properties. Adaptation to the patient’s anatomy is obtained by exploiting the image-rich context specific to our application domain. While information about...
Article
Full-text available
Purpose: Augmented reality can improve the outcome of hepatic surgeries, assuming an accurate liver model is available to estimate the position of internal structures. While researchers have proposed patient-specific liver simulations, very few have addressed the question of boundary conditions. Resulting mainly from ligaments attached to the live...
Article
Full-text available
This paper introduces a method for dynamic 3D registration of female pelvic organs using 2D dynamic magnetic‐resonance images (MRIs). The aim is to provide a better knowledge and understanding of pathologies such as prolapsus or abnormal mobility of tissues. 2D dynamic MRI sequences are commonly used in nowadays clinical routines in order to evalua...
Chapter
Identifying the elastic parameters of a finite element model from a dynamically acquired set of observations is a fundamental challenge in many data-driven medical applications going from soft surgical robotics to image-guided per-operative simulations. While various strategies exist to tackle the parameter-identification inverse problem (Aster et...
Conference Paper
Brain shift is a non-rigid deformation of brain tissue that is affected by loss of cerebrospinal fluid, tissue manipulation and gravity among other phenomena. This deformation can negatively influence the outcome of a surgical procedure since surgical planning based on pre-operative image becomes less valid. We present a novel method to compensate...
Article
IntroductionIntraoperative navigation during liver resection remains difficult and requires high radiologic skills because liver anatomy is complex and patient-specific. Augmented reality (AR) during open liver surgery could be helpful to guide hepatectomies and optimize resection margins but faces many challenges when large parenchymal deformation...
Article
Minimally invasive fluoroscopy-based procedures are the gold standard for diagnosis and treatment of various pathologies of the cardiovascular system. This kind of procedures imply for the clinicians to infer the 3D shape of the device from 2D images, which is known to be an ill-posed problem. In this paper we present a method to reconstruct the 3D...
Article
Full-text available
We present Calipso, an interactive method for editing images and videos in a physically-coherent manner. Our main idea is to realize physics-based manipulations by running a full physics simulation on proxy geometries given by non-rigidly aligned CAD models. Running these simulations allows us to apply new, unseen forces to move or deform selected...
Preprint
An automatic elastic registration method suited for vascularized organs is proposed. The vasculature in both the preoperative and intra-operative images is represented as a graph. A typical application of this method is the fusion of pre-operative information onto the organ during surgery, to compensate for the limited details provided by the intra...
Article
Full-text available
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-driv...
Article
Full-text available
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 hepatic surgery. Derived from the U-Net architecture, our network is built entirely from physically-based simulations of a preoperative segmentation of the or...
Article
An automatic elastic registration method suited for vascularized organs is proposed. The vasculature in both the preoperative and intra-operative images is represented as a graph. A typical application of this method is the fusion of pre-operative information onto the organ during surgery, to compensate for the limited details provided by the intra...
Article
Full-text available
Purpose Intravitreal injection is among the most frequent treatment strategies for chronic ophthalmic diseases. The last decade has seen a serious increase in the number of intravitreal injections, and with it, adverse effects and drawbacks. To tackle these problems, medical assistive devices for robotized injections have been suggested and are pro...
Article
Full-text available
Purpose Electromagnetic tracking is a core platform technology in the navigation and visualisation of image-guided procedures. The technology provides high tracking accuracy in non-line-of-sight environments, allowing instrument navigation in locations where optical tracking is not feasible. EMT can be beneficial in applications such as percutaneou...
Preprint
Full-text available
Purpose: Electromagnetic tracking is a core platform technology in the navigation and visualisation of image-guided procedures. The technology provides high tracking accuracy in non-line-of-sight environments, allowing instrument navigation in locations where optical tracking is not feasible. EMT can be beneficial in applications such as percutaneo...
Preprint
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-driv...
Conference Paper
Full-text available
Percutaneous needle-based procedures such as radiofrequency ablation (RFA) and electrochemotherapy are becoming more prevalent in the treatment of hep-atocellular carcinoma [6][3]. Ultrasound is a common imaging modality used in RFA, and numerous studies have demonstrated its effectiveness in treating shallow or superficial hepatic lesions (> 2cm)...
Chapter
Simulating the deformation of the human anatomy is a central element of Medical Image Computing and Computer-Assisted Interventions. Such simulations play a key role in nonrigid registration, augmented reality, and several other applications. Although the Finite Element Method is widely used as a numerical approach in this area, it is often hindere...
Conference Paper
Full-text available
Boundary conditions play an essential role in forming the predictive capacity of a biomechanical model of liver, which is used to facilitate the intra-operative navigation during surgery operation. However, these conditions are determined mainly by ligaments, and the properties of them cannot be measured reliably. Therefore, the idea is to propose...
Chapter
Full-text available
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 t...
Article
Full-text available
We present a simple open-source semi-intrusive computational method to propagate uncertainties through hyperelastic models of soft tissues. The proposed method is up to two orders of magnitude faster than the standard Monte Carlo method. The material model of interest can be altered by adjusting few lines of (FEniCS) code. The method is able to (1)...
Article
Purpose: Augmenting intraoperative cone beam computed tomography (CBCT) images with preoperative computed tomography data in the context of image-guided liver therapy is proposed. The expected benefit is an improved visualization of tumor(s), vascular system and other internal structures of interest. Method: An automatic elastic registration bas...
Chapter
This chapter gives an overview of the new families of applications that have emerged or that have undergone massive development in the past over few years. It first analyzes the manufacturing industry, exploring the development of virtual reality (VR), the emergence of augmented reality (AR) and the question of return on investment. The chapter loo...
Article
Full-text available
We present a method for estimating visual and haptic force feedback on robotic surgical systems that currently do not include significant force feedback to the operator. Our approach permits to compute contact forces between instruments and tissues without additional sensors, relying only on endoscopic images acquired by a stereoscopic camera. Usin...
Conference Paper
This paper introduces an Augmented Reality (AR) system for open liver surgery. Although open surgery remains the gold-standard for the treatment of complex tumors and central lesions, technological issues actually prevent using AR with sufficient accuracy for clinical use. We propose a markers-based method allowing for the tracking and the deformat...
Article
A fast and accurate fusion of intra-operative images with a pre-operative data is a key component of computer-aided interventions which aim at improving the outcomes of the intervention while reducing the patient's discomfort. In this paper, we focus on the problematic of the intra-operative navigation during abdominal surgery, which requires an ac...
Article
Background: Preoperative images such as computed tomography scans or magnetic resonance imaging contain lots of valuable information that are not easily available for surgeons during an operation. To help the clinicians better target the structures of interest during an intervention, many registration methods that align preoperative images onto the...
Conference Paper
Advances in surgical simulation and surgical augmented reality have changed the way surgeons prepare for practice and conduct medical procedures. Despite considerable interest from surgeons, the use of simulation is still predominantly confined to pre-operative training of surgical tasks and the lack of robustness of surgical augmented reality mean...
Conference Paper
In computer-aided interventions, biomechanical models reconstructed from the pre-operative data are used via augmented reality to facilitate the intra-operative navigation. The predictive power of such models highly depends on the knowledge of boundary conditions. However, in the context of patient-specific modeling, neither the pre-operative nor t...
Conference Paper
Full-text available
Real-time simulations are becoming increasingly common for various applications, from geometric design to medical simulation. Two of the main factors concurrently involved in defining the accuracy of surgical simulations are: the modeling error and the discretization error. Most work in the area has been looking at the above sources of error as a c...
Article
Full-text available
Background: Augmented reality (AR) is the fusion of computer-generated and real-time images. AR can be used in surgery as a navigation tool, by creating a patient-specific virtual model through 3D software manipulation of DICOM imaging (e.g., CT scan). The virtual model can be superimposed to real-time images enabling transparency visualization of...
Article
Objective: To present the first a posteriori error-driven adaptive finite element approach for real-time simulation, and to demonstrate the method on a needle insertion problem. Methods: We use corotational elasticity and a frictional needle/tissue interaction model. The problem is solved using finite elements within SOFA.1For simulating soft ti...
Article
Full-text available
We present an error-controlled mesh refinement procedure for needle insertion simulation and apply it to the simulation of electrode implantation for deep brain stimulation, including brain shift. Our approach enables to control the error in the computation of the displacement and stress fields around the needle tip and needle shaft by suitably ref...
Conference Paper
Full-text available
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...
Article
Full-text available
Female pelvic disorders have a large social impact; the diagnosis of which relies on a key indication: pelvic mobility. The normal mobility is present in a healthy patient, meanwhile the hypermobility can be a sign of female pelvic prolapse and the hypomobility for endometriosis. The evaluation of pelvic mobility is based on medical image analysis....
Article
PurposeLocating the internal structures of an organ is a critical aspect of many surgical procedures. Minimally invasive surgery, associated with augmented reality techniques, offers the potential to visualize inner structures, allowing for improved analysis, depth perception or for supporting planning and decision systems. Methods Most of the curr...
Article
Full-text available
This paper presents the first real-time discretization-error-driven adaptive finite element approach for corotational elasticity problems involving strain localization. We propose a hexahedron-based finite element method, combined with a posteriori error estimation driven local h-refinement, for simulating soft tissue deformation. This enables to c...
Article
Endovascular interventions can benefit from interactive simulation in their training phase but also during pre-operative and intra-operative phases if simulation scenarios are based on patient data. A key feature in this context is the ability to extract, from patient images, models of blood vessels that impede neither the realism nor the performan...