Damien Rohmer

Reconstruction and visualization of fiber and laminar structure in the normal human heart from ex vivo diffusion tensor magnetic resonance imaging (DTMRI) data.

Objective:The human heart is composed of a helical network of muscle fibers organized to form sheets that are separated by cleavage planes responsible for the orthotropic mechanical properties of cardiac muscle. The purpose of this study is the reconstruction and visualization of these structures in 3 dimensions. Methods:Anisotropic least square filtering followed by fiber and sheet tracking techniques were applied to diffusion tensor magnetic resonance imaging data of the excised human heart. Fibers were reconstructed using the first eigenvectors of the diffusion tensors. The sheets were reconstructed using the second and third eigenvectors and visualized as surfaces. Results:The fibers are shown to lie in sheets that have transmural structure, which correspond to histologic studies published in the literature. Quantitative measurements show that the sheets as appose to the fibers are organized into laminar orientations without dominant populations. Conclusions:A visualization algorithm was developed to demonstrate the complex 3-dimensional orientation of the fibers and sheets in human myocardium.

Animation wrinkling: augmenting coarse cloth simulations with realistic-looking wrinkles

Moving garments and other cloth objects exhibit dynamic, complex wrinkles. Generating such wrinkles in a virtual environment currently requires either a time-consuming manual design process, or a computationally expensive simulation, often combined with accurate parameter-tuning requiring specialized animator skills. Our work presents an alternative approach for wrinkle generation which combines coarse cloth animation with a post-processing step for efficient generation of realistic-looking fine dynamic wrinkles. Our method uses the stretch tensor of the coarse animation output as a guide for wrinkle placement. To ensure temporal coherence, the placement mechanism uses a space-time approach allowing not only for smooth wrinkle appearance and disappearance, but also for wrinkle motion, splitting, and merging over time. Our method generates believable wrinkle geometry using specialized curve-based implicit deformers. The method is fully automatic and has a single user control parameter that enables the user to mimic different fabrics.

My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development

BackgroundEmbryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult.ResultsIn this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos.ConclusionsCombining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human developmental anatomy. Visualizing embryos with 3D geometric models and their animated deformations perhaps paves the way towards some kind of hypothesis-driven application. These can also be used to assist the learning process of this complex knowledge.Availabilityhttp://www.mycorporisfabrica.org/

A Bloch-Torrey Equation for Diffusion in a Deforming Media

Author(s): Rohmer, Damien; Gullberg, Grant T. | Abstract: Diffusion Tensor Magnetic Resonance Imaging (DTMRI) technique enables the measurement of diffusion parameters and therefore, informs on the structure of the biological tissue. This technique is applied with success to the static organs such as brain. However, the diffusion measurement on the dynamically deformable organs such as the in-vivo heart is a complex problem that has however a great potential in the measurement of cardiac health. In order to understand the behavior of the Magnetic Resonance (MR)signal in a deforming media, the Bloch-Torrey equation that leads the MR behavior is expressed in general curvilinear coordinates. These coordinates enable to follow the heart geometry and deformations through time. The equation is finally discretized and presented in a numerical formulation using implicit methods, in order to get a stable scheme that can be applied to any smooth deformations. Diffusion process enables the link between the macroscopic behavior of molecules and the microscopic structure in which they evolve. The measurement of diffusion in biological tissues is therefore of major importance in understanding the complex underlying structure that cannot be studied directly. The Diffusion Tensor Magnetic Resonance Imaging(DTMRI) technique enables the measurement of diffusion parameters and therefore provides information on the structure of the biological tissue. This technique has been applied with success to static organs such as the brain. However, diffusion measurement of dynamically deformable organs such as the in-vivo heart remains a complex problem, which holds great potential in determining cardiac health. In order to understand the behavior of the magnetic resonance (MR) signal in a deforming media, the Bloch-Torrey equation that defines the MR behavior is expressed in general curvilinear coordinates. These coordinates enable us to follow the heart geometry and deformations through time. The equation is finally discretized and presented in a numerical formulation using implicit methods in order to derive a stable scheme that can be applied to any smooth deformations.

Folded Paper Geometry from 2D Pattern and 3D Contour

Folded paper exhibits very characteristic shapes, due to the presence of sharp folds and to exact isometry with a given planar pattern. Therefore, none of the physically-based simulators developed so far can handle paper-like material. We propose a purely geometric solution to generate static folded paper geometry from a 2D pattern and a 3D placement of its contour curve. Fold lines are explicitly identified and used to control a recursive, local subdivision process, leading to an efficient procedural modeling of the surface through a fold-aligned mesh. Contrary to previous work, our method generates paper-like surfaces with sharp creases while maintaining approximate isometry with the input pattern.

Interactive Paper Tearing

We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical‐based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears.

A proposal of experimental protocol to assembly scanning

Acquisition of 3D objects using laser scans has become rather common. Most of the time in mechanical engineering, scanning processes are dedicated to standalone components, as part of a reverse eng...

Deformation Grammars: Hierarchical Constraint Preservation Under Deformation

Deformation grammars are a novel procedural framework enabling to sculpt hierarchical 3D models in an object‐dependent manner. They process object deformations as symbols thanks to user‐defined interpretation rules. We use them to define hierarchical deformation behaviours tailored for each model, and enabling any sculpting gesture to be interpreted as some adapted constraint‐preserving deformation. A variety of object‐specific constraints can be enforced using this framework, such as maintaining distributions of subparts, avoiding self‐penetrations or meeting semantic‐based user‐defined rules. The operations used to maintain constraints are kept transparent to the user, enabling them to focus on their design. We demonstrate the feasibility and the versatility of this approach on a variety of examples, implemented within an interactive sculpting system.

Simulation of the Beating Heart Based on Physically Modeling aDeformable Balloon

The motion of the beating heart is complex and createsartifacts in SPECT and x-ray CT images. Phantoms such as the JaszczakDynamic Cardiac Phantom are used to simulate cardiac motion forevaluationof acquisition and data processing protocols used for cardiacimaging. Two concentric elastic membranes filled with water are connectedto tubing and pump apparatus for creating fluid flow in and out of theinner volume to simulate motion of the heart. In the present report, themovement of two concentric balloons is solved numerically in order tocreate a computer simulation of the motion of the moving membranes in theJaszczak Dynamic Cardiac Phantom. A system of differential equations,based on the physical properties, determine the motion. Two methods aretested for solving the system of differential equations. The results ofboth methods are similar providing a final shape that does not convergeto a trivial circular profile. Finally,a tomographic imaging simulationis performed by acquiring static projections of the moving shape andreconstructing the result to observe motion artifacts. Two cases aretaken into account: in one case each projection angle is sampled for ashort time interval and the other case is sampled for a longer timeinterval. The longer sampling acquisition shows a clear improvement indecreasing the tomographic streaking artifacts.

Visualization of Fiber Structurein the Left and Right Ventricleof a Human Heart

The human heart is composed of a helical network of musclefibers. Anisotropic least squares filtering followed by fiber trackingtechniques were applied to Diffusion Tensor Magnetic Resonance Imaging(DTMRI) data of the excised human heart. The fiber configuration wasvisualized by using thin tubes to increase 3-dimensional visualperception of the complex structure. All visualizations were performedusing the high-quality ray-tracing software POV-Ray. The fibers are shownwithin the left and right ventricles. Both ventricles exhibit similarfiber architecture and some bundles of fibers are shown linking right andleft ventricles on the posterior region of the heart.