Computer modelling of vascular systems

A model of the vascular system perfusing an internal organ is presented in the paper. The system's development is driven by the increasing needs of growing tissue. The modelled network consists of 2 or 3 (in the case of the liver) vascular trees connected on the macro-cell level. Each appearance of a new macro-cell activates an angiogenic process. The geometry of newly formed vessels is determined as a result of local optimization of the bifurcation volume. The model can simulate modifications of the vascular network caused by pathological processes

Physiological modeling of tumor-affected renal circulation.

International audienceOne way of gaining insight into what can be observed in medical images is through physiological modeling. For instance, anatomical and functional modifications occur in the organ during the appearance and the growth of a tumor. Some of these changes concern the vascularization. We propose a computational model of tumor-affected renal circulation that represents the local heterogeneity of different parts of the kidney (cortex, medulla). We present a simulation of vascular modifications related to vessel structure, geometry, density, and blood flow in case of renal cell carcinoma. We also use our model to simulate computed tomography scans of a kidney affected by the renal cell carcinoma, at two acquisition times after injection of a contrast product. This framework, based on a physiological model of the organ and physical model of medical image acquisition, offers an opportunity to help radiologists in their diagnostic tasks. This includes the possibility of linking image descriptors with physiological perturbations and markers of pathological processes

Mechanizm zrównoważenia obciążenia w równoległej implementacji rozwoju sieci naczyń krwionośnych

In this paper, load balancing mechanisms in a parallel algorithm of vascular network development are investigated. The main attention is focused on the perfusion process (connection of new cells to vascular trees) as it is the most time demanding part of the vascular algorithm. We propose several techniques that aim at balancing load among processors, decreasing their idle time and reducing the communication overhead. The core solution is based on the centralized dynamic load balancing approach. The model behaviors are analyzed and a tradeoff between the different mechanisms is found. The proposed mechanisms are implemented on a computing cluster with the use of the message passing interface (MPI) standard. The experimental results show that the introduced improvements provide a more efficient solution and consequently further accelerate the simulation process.W artykule rozważane są mechanizmy zrównoważające obciążenie w równoległym algorytmie rozwoju sieci naczyń krwionośnych. Główną uwagę zwrócono na proces perfuzji (podłączanie nowych komórek do drzew krwionośnych) jako, że proces ten jest najbardziej czasochłonnym fragmentem rozpatrywanego algorytmu. Zaproponowane przez autorów rozwiązania mają na celu zrównoważenie obciążenia pomiędzy procesorami, skrócenie ich czasu bezczynności oraz zredukowanie narzutu komunikacyjnego. Jądro rozwiązania jest oparte na scentralizowanym dynamicznym podejściu równoważenia obciążenia. Zachowania modelu zostały przeanalizowane i kompromis pomiędzy różnymi technikami został zaproponowany. Przedstawione mechanizmy zostały zaimplementowane na klastrze obliczeniowym przy wykorzystaniu standardu MPI. Otrzymane rezultaty jednoznacznie pokazuja˛ iż wprowadzone usprawnienia zapewniają bardziej efektywne rozwiązanie co w konsekwencji pozwala na jeszcze większe przyśpieszenie procesu symulacji

Texture feature extraction in liver CT image analysis

W pracy przedstawiono nową metodę opisu tekstur, przystosowaną do analizy grupy obrazów, przedstawiających na różne sposoby ten sam fragment organu. Charakteryzując obszary zainteresowania, uwzględniono nie tylko cechy teksturalne wyliczone na ich podstawie, ale również ich zależność od warunków pozyskiwania obrazów. Zaproponowano kilka sposobów konstrukcji przestrzeni parametrów odzwierciedlających zmianę tekstury, która zachodzi pod wpływem zmian warunków akwizycji. Proponowaną metodę zweryfikowano doświadczalnie w klasyfikacji obrazów tomograficznych wątroby. Rozpoznawano cztery typy tkanki, dla każdego przypadku rozważono trzy momenty akwizycji, związane z obecnością i propagacją środka kontrastującego. Wyniki uzyskane przy użyciu różnych zestawów cech teksturalnych i klasyfikatora w postaci dipolowych drzew decyzyjnych pokazują, że uwzględnienie zmian tekstury pod wpływem propagacji środka kontrastującego znacznie poprawia diagnozę.In the work, a new method of texture characterization from multiple scan series is presented. Images with the same slice position, acquired at different conditions, are analyzed simultaneously. Thereby not only texture characteristics of the considered region of interest are taken into account, but also their variations over the different acquisition moments. A few approaches to description of these variations were proposed. They were applied in recognition of four types of hepatic tissue. Liver CT images were acquired during the three typical phases related to presence and propagation of contrast material. Experiments with various sets of texture parameters and dipolar decision tree as a classifier showed that simultaneous analysis of texture features derived from three subsequent acquisition moments could considerably improve the classification accuracy

Modeling of tumor conspicuity in hepatic CT images: combined compartment and vascular models

International audienceThe aim of this work is to simulate dynamic CT scan of the liver, in normal tissue and in a hypervascular tumor. Two models are developed: a physiological vascular model for the main vessels, until arterioles and venules, and a compartment model for parenchyma enhancement. Combining these two models allows us to compute locally the contrast product concentration, all along the propagation, after injection in the hepatic artery and the portal vein. In the second step, a density representation of the organ is created and CT scans are simulated by using the standard reconstruction algorithm - filtered backprojection. As a final step, enhancement curves are extracted from the obtained images, showing very good agreement with real hepatic enhancement in CT

A physiologically based pharmacokinetic model of vascular-extravascular exchanges during liver carcinogenesis: application to MRI contrast agents.

This is a preprint of an article published in Contrast Media & Molecular Imaging Copyright © 2007 Wiley Periodicals, Inc. http://www.insterscience.wiley.comInternational audienceThe extraction of physiological parameters by non-invasive imaging techniques such as dynamic magnetic resonance imaging (MRI) or positron emission tomography requires a knowledge of molecular distribution and exchange between microvascularization and extravascular tissues. These phenomena not only depend on the physicochemical characteristics of the injected molecules but also the pathophysiological state of the targeted organ. We developed a five-compartment physiologically based pharmacokinetic model focused on hepatic carcinogenesis and MRI contrast agents. This model includes physical characteristics of the contrast agent, dual specific liver supply, microvessel wall properties and transport parameters that are compatible with hepatocarcinoma development. The evolution of concentrations in the five compartments showed significant differences in the distribution of three molecules (differentiated by their diameters and diffusion coefficients ranging, respectively, from 0.9 to 62 nm and from 68.10(-9) to 47.10(-7) cm(2) s(-1)) in simulated regeneration nodules and dysplastic nodules, as well as in medium- and poorly differentiated hepatocarcinoma. These results are in agreement with known vascular modifications such as arterialization that occur during hepatocarcinogenesis. This model can be used to study the pharmacokinetics of contrast agents and consequently to extract parameters that are characteristic of the tumor development (like permeability), after fitting simulated to in vivo data

Multiscale modeling and imaging: the challenges of biocomplexity

International audienceComputational modeling and imaging in biology and medicine are gaining more and more interest with the discovery of in-depth structural and functional knowledge at all space and time scales (molecule to proteins, cells to organs and organisms). The recursion between description levels for highly dynamical, interacting and complex systems, i.e the integrative approach, is a very challenging topic where formal models, observational tools and experimental investigations have to be closely designed, coupled and confronted together. Imaging techniques play a major role in this interdisciplinary attempt to elucidate this biocomplexity: they convey relevant information about the underlying mechanisms, depict the conformations and anatomical topologies and draw the biophysical laws they may follow. Furthermore, the basic image analysis tools (from calibration to segmentation, motion estimation and registration up to pattern recognition) are generic enough to be of value whatever the objects under consideration. The same comments apply when Computer Graphics or Virtual Reality techniques are concerned. This paper will survey the recent contributions dealing with both models, imaging data and processing frames. Examples ranging over different scales, from macro to nano, will be given in order to enhance the mutual benefits and perspectives that can be expected from this coupling