Imaging Informatics and the Human Brain Project: the Role of Structure, Review

(no abstract

TrauMAP - Integrating Anatomical and Physiological Simulation (Dissertation Proposal)

In trauma, many injuries impact anatomical structures, which may in turn affect physiological processes - not only those processes within the structure, but also ones occurring in physical proximity to them. Our goal with this research is to model mechanical interactions of different body systems and their impingement on underlying physiological processes. We are particularly concerned with pathological situations in which body system functions that normally do not interact become dependent as a result of mechanical behavior. Towards that end, the proposed TRAUMAP system (Trauma Modeling of Anatomy and Physiology) consists of three modules: (1) a hypothesis generator for suggesting possible structural changes that result from the direct injuries sustained; (2) an information source for responding to operator querying about anatomical structures, physiological processes, and pathophysiological processes; and (3) a continuous system simulator for simulating and illustrating anatomical and physiological changes in three dimensions. Models that can capture such changes may serve as an infrastructure for more detailed modeling and benefit surgical planning, surgical training, and general medical education, enabling students to visualize better, in an interactive environment, certain basic anatomical and physiological dependencies

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

On some interactive mesh deformations

Techniques devoted to deform 3D models are an important research field in Computer Graphics. They can be used in differentstages: the modelling phase, the animation process and also during some special simulations. Additionally, some applications may require the manipulation of 3D models under certain restrictions to preserve the volume of the modified object. Hence, thepresent PhD Dissertation explores new algorithms to perform flexible, robust and efficient 3D deformations. Apart from this, it also researches on a new methodology to restrict these deformations so that the volume of the manipulated model remains constant. Some of the most used methods to achieve smooth deformations are those included in the Cage-Based Deformation paradigm. Cage-based deformations enclose the model to be deformed in a coarse polyhedron, the cage. Then, they usually rely on Generalized Barycentric Coordinates to relate the model with the vertices, and other geometric elements, of this cage, which are the control points or the deformation handles. Finally, every time that one of these handles is dragged, the model is deformed accordingly. Although this paradigm is simple, elegant and performs efficient deformations, some cage-free space deformation techniques have recently appeared. They increase the flexibility of the deformation handles, which do not need to be connected, and define powerful tools that make the deformation process more versatile and intuitive. In this context, the Dissertation introduces new Generalized Barycentric Coordinate systems specially designed to be used in a cage-free environment. Any user who wants to use the presented schemes only needs to locate a set of control points in the vicinity of the model that he or she wants to deform. These handles can be placed wherever he or she considers mode suitable and the only requirement is that the model has to be enclosed in their convex hull. Up to now, there are few techniques to produce volume-preserving space deformations. However, in recent years there has been a growing interest in performing constrained deformations due to their more realistic and physically plausible results. Our contribution to this research line consists in a deformation framework that preserves the volume of the 3D models by means of its gradient and a control surface to restrict the movement of the handles. Moreover, the proposed methodology is not restricted to the cage-based schemes, but it can also be used in a cage-free environment. Finally, our research can be specially useful for spatial deformations of biological and medical models. This kind of models represent real organs and tissues, which are often soft and lack an internal rigid structure. In addition, they are elastic and incompressible. Any application designed to deal with this group of models and to train or assist doctors must be flexible, robust, efficient and user-friendly. The combination of the proposed cage-free systems with the presented volume-preserving deformation framework satisfiesLes deformacions de models 3D s'utilitzen en diverses etapes de la generació de continguts digitals: durant la fase de modelatge, durant el procés d'animació i en alguns tipus de simulacions. A més a més, hi ha aplicacions que necessiten que la manipulació dels models 3D es faci tenint en compte certes restriccions que permeten la conservació del volum de l'objecte modificat. Tot plegat fa que les tècniques de deformació 3D siguin un camp d'estudi molt important dins del món dels Gràfics. Per aquesta raó, aquesta Tesi Doctoral estudia nous algorismes que permetin realitzar deformacions 3D de manera flexible, robusta i eficient i que, a més a més, permetin conservar el volum dels objectes modificats. Un dels paradigmes més utilitzats per tal de realitzar deformacions suaus és el conegut amb el nom de Deformacions Basades en un Poliedre Englobant. Aquesta família de mètodes embolcalla el model que es vol deformar, normalment representat com una malla de triangles, dins d'un poliedre simple, amb poques cares. Un cop fet això, estableix un sistema de Coordenades Baricèntriques Generalitzades per tal de definir els vèrtexs del model a partir dels vèrtexs del poliedre englobant, els quals s'anomenen punts de control o controls de la deformació. D'aquesta manera, cada cop que s'arrossega o es modifica un d'aquests punts de control, el model que es troba dins del poliedre englobant es deforma segons el sistema de coordenades que s'ha definit. Tot i que aquest paradigma és simple, elegant i eficient, des de fa ja uns anys han començat a aparèixer noves tècniques que no necessiten el poliedre englobant per tal de realitzar la deformació. El seu principal objectiu és augmentar la flexibilitat dels controls de la deformació i definir eines que facin que el procés de deformació sigui més versàtil i intuïtiu. Tenint en compte aquest factor, aquesta Tesi també estudia sistemes de Coordenades Baricèntriques Generalitzades dissenyats per realitzar deformacions sense la necessitat de definir el poliedre englobant. D'aquesta manera, qualsevol usuari que vulgui utilitzar els mètodes que es presenten en aquesta Dissertació només s'ha d'encarregar de definir un conjunt de punts de control al voltant del model que vol deformar, podent-los posar allí on consideri més oportú segons la deformació que vulgui obtenir. L'únic requeriment necessari és que el model ha de quedar dins de l'envolupant convexa d'aquests punts de control. Actualment existeixen pocs mètodes que realitzin deformacions 3D amb preservació del volum. No obstant això, d'un temps ençà ha augmentat l'interès per realitzar deformacions subjectes a certes restriccions que fan que el resultat sigui més realista i físicament versemblant. La contribució d'aquesta Tesi dins d'aquesta línia de recerca consisteix en un sistema de deformació que preserva el volum dels objectes 3D gràcies a còmput del seu gradient i a una superfície de control que restringeix el moviment dels punts de control. Aquest mètode es pot aplicar tant als sistemes de deformació que necessiten un poliedre englobant com als que no el necessiten. Finalment, i ja per acabar, la recerca realitzada pot ser especialment útil per tal de realitzar deformacions de models mèdics i biològics. Aquests tipus de models poden representar òrgans i teixits reals, els quals, normalment, són tous, mancats d'una estructura rígida interna, elàstics i incompressibles. Qualsevol aplicació dissenyada per treballar amb aquest tipus de models i per entrenar i donar assistència a usuaris mèdics hauria de ser flexible, robusta, eficient i fàcil d'utilitzar. La combinació dels mètodes de deformació proposats conjuntament amb el sistema de preservació de volum satisfà totes aquestes condicions. Per aquesta raó es creu que les contribucions realitzades poden esdevenir eines importants per produir deformacions mèdiques.Postprint (published version

A Systems Approach to the Physiology of Weightlessness

A systems approach to the unraveling of the complex response pattern of the human subjected to weightlessness is presented. The major goal of this research is to obtain an understanding of the role that each of the major components of the human system plays following the transition to and from space. The cornerstone of this approach is the utilization of a variety of mathematical models in order to pose and test alternative hypotheses concerned with the adaptation process. An integrated hypothesis for the human physiological response to weightlessness is developed

Neurosurgery and brain shift: review of the state of the art and main contributions of robotics

Este artículo presenta una revisión acerca de la neurocirugía, los asistentes robóticos en este tipo de procedimiento, y el tratamiento que se le da al problema del desplazamiento que sufre el tejido cerebral, incluyendo las técnicas para la obtención de imágenes médicas. Se abarca de manera especial el fenómeno del desplazamiento cerebral, comúnmente conocido como brain shift, el cual causa pérdida de referencia entre las imágenes preoperatorias y los volúmenes a tratar durante la cirugía guiada por imágenes médicas. Hipotéticamente, con la predicción y corrección del brain shift sobre el sistema de neuronavegación, se podrían planear y seguir trayectorias de mínima invasión, lo que conllevaría a minimizar el daño a los tejidos funcionales y posiblemente a reducir la morbilidad y mortalidad en estos delicados y exigentes procedimientos médicos, como por ejemplo, en la extirpación de un tumor cerebral. Se mencionan también otros inconvenientes asociados a la neurocirugía y se muestra cómo los sistemas robotizados han ayudado a solventar esta problemática. Finalmente se ponen en relieve las perspectivas futuras de esta rama de la medicina, la cual desde muchas disciplinas busca tratar las dolencias del principal órgano del ser humano.This paper presents a review about neurosurgery, robotic assistants in this type of procedure, and the approach to the problem of brain tissue displacement, including techniques for obtaining medical images. It is especially focused on the phenomenon of brain displacement, commonly known as brain shift, which causes a loss of reference between the preoperative images and the volumes to be treated during image-guided surgery. Hypothetically, with brain shift prediction and correction for the neuronavigation system, minimal invasion trajectories could be planned and shortened. This would reduce damage to functional tissues and possibly lower the morbidity and mortality in delicate and demanding medical procedures such as the removal of a brain tumor. This paper also mentions other issues associated with neurosurgery and shows the way robotized systems have helped solve these problems. Finally, it highlights the future perspectives of neurosurgery, a branch of medicine that seeks to treat the ailments of the main organ of the human body from the perspective of many disciplines