Acceleration of image filtering algorithms for 3D visualization of murine lungs using dataflow engines

Image filtering is one of the most common and important tasks in image processing applications. In this paper, image processing using a mean filtering algorithm combined with thresholding and binarization algorithms for the 3D visualization and analysis of murine lungs is explained. These algorithms are then mapped on the Maxler's MAX2336B Dataflow Engine (DFE) to significantly increase calculation speed. Several different DFE configurations were tested and each yielded different performance characteristics. Optimal algorithm calculation speed was up to 30 fold baseline calculation speed.

Computational flow dynamics in a geometric model of intussusceptive angiogenesis.

Intussusceptive angiogenesis is a process that forms new blood vessels by the intraluminal division of a single blood vessel into two lumens. Referred to as nonsprouting or intussusceptive angiogenesis, this angiogenic process has been described in morphogenesis and chronic inflammation. Mechanical forces are relevant to the structural changes associated with intussusceptive angiogenesis because of the growing evidence that physiologic forces influence gene transcription. To provide a detailed analysis of the spatial distribution of physiologic shear stresses, we developed a 3D finite element model of the intraluminal intussusceptive pillar. Based on geometries observed in adult intussuscep…

Mapping cyclic stretch in the postpneumonectomy murine lung

In many mammalian species, the removal of one lung [pneumonectomy (PNX)] is associated with the compensatory growth of the remaining lung. To investigate the hypothesis that parenchymal deformation may trigger lung regeneration, we used respiratory-gated micro-computed tomography scanning to create three-dimensional finite-element geometric models of the murine cardiac lobe with cyclic breathing. Models were constructed of respiratory-gated micro-computed tomography scans pre-PNX and 24 h post-PNX. The computational models demonstrated that the maximum stretch ratio map was patchy and heterogeneous, particularly in subpleural, juxta-diaphragmatic, and cephalad regions of the lobe. In these…

Correlation of Vertebral Absolute Axial Rotations in CAD 3D Models of Adolescent Idiopathic Scoliosis Non-Invasively Diagnosed

This paper presents preliminary results on non-invasive optical diagnosis of patient with adolescent idiopathic scoliosis (AIS) with recently developed tool ScolioSIM. This tool generates intrinsic and extrinsic indicators of the spinal deformity and 3D CAD (Computer-aided Design) deformity model based only on a digitalized dorsal surface of the examined patient. Our primary focus in this paper are absolute axial rotations (AAR) of each vertebra in AIS patients and their correlations. Clinical relevance of this research is high, as we intend to avoid traditional methods which rely on highly complicated reading and measuring of AARs on planar x-ray films, as these methods involve ionizing ra…

Selective Laser Photocoagulation Manipulates Blood Flow Dynamics in Microcirculation

Stretch-induced Intussuceptive and Sprouting Angiogenesis in the Chick Chorioallantoic Membrane

Vascular systems grow and remodel in response to not only metabolic needs, but also mechanical influences as well. Here, we investigated the influence of tissue-level mechanical forces on the patterning and structure of the chick chorioallantoic membrane (CAM) microcirculation. A dipole stretch field was applied to the CAM using custom computer-controlled servomotors. The topography of the stretch field was mapped using finite element models. After 3 days of stretch, Sholl analysis of the CAM demonstrated a 7-fold increase in conducting vessel intersections within the stretch field (p 0.05). In contrast, corrosion casting and SEM of the stretch field capillary meshwork demonstrated intense …

An Early Stage Researcher's Primer on Systems Medicine Terminology

Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. Thes…

Blood flow shapes intravascular pillar geometry in the chick chorioallantoic membrane.

The relative contribution of blood flow to vessel structure remains a fundamental question in biology. To define the influence of intravascular flow fields, we studied tissue islands--here defined as intravascular pillars--in the chick chorioallantoic membrane. Pillars comprised 0.02 to 0.5% of the vascular system in 2-dimensional projection and were predominantly observed at vessel bifurcations. The bifurcation angle was generally inversely related to the length of the pillar (R = -0.47, P .05). 3-dimensional computational flow simulations indicated that the intravascular pillars were located in regions of low shear stress. Both wide-angle and acute-angle models mapped the pillars to regio…

Intravascular pillars and pruning in the extraembryonic vessels of chick embryos.

To investigate the local mechanical forces associated with intravascular pillars and vessel pruning, we studied the conducting vessels in the extraembryonic circulation of the chick embryo. During the development days 13-17, intravascular pillars and blood flow parameters were identified using fluorescent vascular tracers and digital time-series video reconstructions. The geometry of selected vessels was confirmed by corrosion casting and scanning electron microscopy. Computational simulations of pruning vessels suggested that serial pillars form along pre-existing velocity streamlines; blood pressure demonstrated no obvious spatial relationship with the intravascular pillars. Modeling a Re…

Computational analysis of lung deformation after murine pneumonectomy. [corrected].

In many mammalian species, the removal of one lung (pneumonectomy) is associated with the compensatory growth of the remaining lung. To investigate the hypothesis that parenchymal deformation may trigger lung regeneration, we used microCT scanning to create 3-dimensional finite element geometric models of the murine lung pre- and post-pneumonectomy (24 hours). The structural correspondence between models was established using anatomic landmarks and an iterative computational algorithm. When compared with the pre-pneumonectomy lung, the post-pneumonectomy models demonstrated significant translation and rotation of the cardiac lobe into the post-pneumonectomy pleural space. 2-dimensional maps…