Point-cloud registration using adaptive radial basis functions

Non-rigid registration is a common part of bioengineering model-generation workflows. Compared to common mesh-based methods, radial basis functions can provide more flexible deformation fields due to their meshless nature. We introduce an implementation of RBF non-rigid registration with iterative knot-placement to adaptively reduce registration error. The implementation is validated on surface meshes of the femur, hemi-pelvis, mandible, and lumbar spine. Mean registration surface errors ranged from 0.37 to 0.99?mm, Hausdorff distance from 1.84 to 2.47?mm, and DICE coefficients from 0.97 to 0.99. The implementation is available for use in the free and open-source GIAS2 library.     

Non-rigid registration of breast surfaces using the laplace and diffusion equations

A semi-automated, non-rigid breast surface registration method is presented that involves solving the Laplace or diffusion equations over undeformed and deformed breast surfaces. The resulting potential energy fields and isocontours are used to establish surface correspondence. This novel surface-based method, which does not require intensity images, anatomical landmarks, or fiducials, is compared to a gold standard of thin-plate spline (TPS) interpolation. Realistic finite element simulations of breast compression and further testing against a tissue-mimicking phantom demonstrate that this method is capable of registering surfaces experiencing 6 - 36 mm compression to within a mean error of 0.5 - 5.7 mm.     

Structural analysis of interphase X-chromatin based on statistical shape theory

The 3D folding structure formed by different genomic regions of a chromosome is still poorly understood. So far, only relatively simple geometric features, like distances and angles between different genomic regions, have been evaluated. This work is concerned with more complex geometric properties, i.e., the complete shape formed by genomic regions. Our work is based on statistical shape theory and we use different approaches to analyze the considered structures, e.g., shape uniformity test, 3D point-based registration, Fisher distribution, and 3D non-rigid image registration for shape normalization. We have applied these approaches to analyze 3D microscopy images of the X-chromosome where four consecutive genomic regions (BACs) have been simultaneously labeled by multicolor FISH. We have acquired two sets of four consecutive genomic regions with an overlap of three regions. From the experimental results, it turned out that for all data sets the complete structure is non-random. In addition, we found that the shapes of active and inactive X-chromosomal genomic regions are statistically independent. Moreover, we reconstructed the average 3D structure of chromatin in a small genomic region (below 4 Mb) based on five BACs resulting from two overlapping four BAC regions. We found that geometric normalization with respect to the nucleus shape based on non-rigid image registration has a significant influence on the location of the genomic regions.     

A Robust and Accurate Two-Step Auto-Labeling Conditional Iterative Closest Points (TACICP) Algorithm for Three-Dimensional Multi-Modal Carotid Image Registration

Atherosclerosis is among the leading causes of death and disability. Combining information from multi-modal vascular images is an effective and efficient way to diagnose and monitor atherosclerosis, in which image registration is a key technique. In this paper a feature-based registration algorithm, Two-step Auto-labeling Conditional Iterative Closed Points (TACICP) algorithm, is proposed to align three-dimensional carotid image datasets from ultrasound (US) and magnetic resonance (MR). Based on 2D segmented contours, a coarse-to-fine strategy is employed with two steps: rigid initialization step and non-rigid refinement step. Conditional Iterative Closest Points (CICP) algorithm is given in rigid initialization step to obtain the robust rigid transformation and label configurations. Then the labels and CICP algorithm with non-rigid thin-plate-spline (TPS) transformation model is introduced to solve non-rigid carotid deformation between different body positions. The results demonstrate that proposed TACICP algorithm has achieved an average registration error of less than 0.2mm with no failure case, which is superior to the state-of-the-art feature-based methods.     

Deformation analysis of microcapsules compressed by two rigid parallel plates

Alginate-poly(l)lysine-alginate microcapsules with a diameter of 200–300 μm were produced and subjected to compression experiments using two rigid parallel plates. The deformed shape was observed, and the relationship between the applied force and the displacement of the plate was measured. A practical analysis method is proposed for the prediction of mechanical properties of microcapsules, namely, the changes in force, transmural pressure, and deformed shape due to the change in the displacement of the plate. The analysis is based on a microcapsule model comprising an axi-symmetric elastic membrane with a constant capsule volume during deformation. Young’s modulus of the membrane, which is used in the analysis, was determined by applying the Hertz contact theory to the experimental results obtained by using an atomic force microscope. The bending stiffness and permeability of the membrane as well as the frictional force between the membrane and the plate were neglected in the analysis. A non-dimensional relationship between the applied force and the displacement of the plate was shown. The theoretically predicted compression force was smaller than the experimentally measured force in the small displacement region, whereas both forces were in good agreement in the large displacement region. The effects of change in Poisson’s ratio, which varied from 0 to 0.5, on the force, transmural pressure, and deformed shape were shown. Under the same displacement conditions, it was observed that the calculated deformed shape was almost coincident with the shape observed in the experiment.     

Effect of prolonged gastric distension on motor function of LES and of proximal stomach

Gastric distension is a potent stimulus of transient lower esophageal sphincter (LES) relaxation. To investigate the time effect of prolonged gastric distension on the rate of transient LES relaxations, LES pressure, and the motor and sensory functions of the proximal stomach, we performed a continuous isobaric distension of the proximal stomach at the 75% threshold pressure for discomfort for 2 h in seven healthy subjects. A multilumen assembly incorporating a sleeve and an electronic barostat was used. The rate of transient LES relaxations (n/30 min) was constant during the first hour [4.1 +/- 1.2 (0-30 min) and 5.4 +/- 1.1 (30-60 min)] but markedly decreased (P < 0.05) in the second hour [2.1 +/- 0.5 (60-90 min) and 2.3 +/- 0.9 (90-120 min)], whereas LES pressure, baseline volume and volume waves within the gastric bag, hunger, and fullness did not change throughout the experiment. It is concluded that the rate of transient LES relaxations decreases with time during prolonged gastric distension, thus suggesting that this type of stimulus should not be used in sequential experimental conditions.     

Estimation of the deformations induced by articulated bodies: Registration of the spinal column

We present a new non-rigid registration algorithm estimating the displacement field generated by articulated bodies. Indeed the bony structures between different patient images may rigidly move while other tissues may deform in a more complex way. Our algorithm tracks the displacement induced in the column by a movement of the patient between two acquisitions. The volumetric deformation field in the whole body is then inferred from those displacements using a linear elastic biomechanical finite element model. We demonstrate in this paper that this method provides accurate results on 3D sets of computed tomography (CT), MR and positron emission tomography (PET) images and that the results of the registration algorithm show significant decreases in the mean, min and max errors.     

Patient-specific model of brain deformation: application to medical image registration

This contribution presents finite element computation of the deformation field within the brain during craniotomy-induced brain shift. The results were used to illustrate the capabilities of non-linear (i.e. accounting for both geometric and material non-linearities) finite element analysis in non-rigid registration of pre- and intra-operative magnetic resonance images of the brain. We used patient-specific hexahedron-dominant finite element mesh, together with realistic material properties for the brain tissue and appropriate contact conditions at boundaries. The model was loaded by the enforced motion of nodes (i.e. through prescribed motion of a boundary) at the brain surface in the craniotomy area. We suggest using explicit time-integration scheme for discretised equations of motion, as the computational times are much shorter and accuracy, for practical purposes, the same as in the case of implicit integration schemes. Application of the computed deformation field to register (i.e. align) the pre-operative images with the intra-operative ones indicated that the model very accurately predicts the displacements of the tumour and the lateral ventricles even for limited information about the brain surface deformation. The prediction accuracy improves when information about deformation of not only exposed (during craniotomy) but also unexposed parts of the brain surface is used when prescribing loading. However, it appears that the accuracy achieved using information only about the deformation of the exposed surface, that can be determined without intra-operative imaging, is acceptable. The presented results show that non-linear biomechanical models can complement medical image processing techniques when conducting non-rigid registration. Important advantage of such models over the previously used linear ones is that they do not require unrealistic assumptions that brain deformations are infinitesimally small and brain stress-strain relationship is linear.     

Intraluminal modulation of gastric sensitivity to distension: effects of hydrochloric acid and meal

Conscious sensations in response to gut distensions may be modulated by temporospatial interactions among different stimuli. This study investigated whether symptoms induced by gastric distension may be modified by hydrochloric acid (HCl) gastric infusion and meal ingestion. In nine healthy subjects, fixed pressure (isobaric) and fixed volume (isovolumetric) distensions were performed during continuous (4 ml/min) intragastric saline or HCl infusion, during fasting and after meal ingestion, until the maximal distension step defined as discomfort or a predefined maximal volume. During fasting isobaric distensions, the maximal distension step was significantly decreased during HCl compared with saline. The intragastric volumes were not significantly different, but the wall tension was significantly lower during HCl than saline. HCl increased gastric compliance. Meal ingestion relaxed the stomach and decreased the pressure at the maximal distension step during saline, but HCl did not further decrease it compared with fasting. During isovolumetric distensions, HCl also increased gastric compliance, but in both fasted and fed states it did not modify the maximal distension steps. In conclusion, sensations in response to gastric isobaric distensions, but not to isovolumetric distensions, are influenced by gastric acid infusion and meal ingestion. The effects of HCl might be related to a sensitization of mucosal mechanoreceptors.     

Satiety: the roles of peptides from the stomach and the intestine

Rats were surgically prepared to allow perfusions of anatomically limited portions of the gastrointestinal (GI) surface during test meals. The results demonstrated that at least one potent satiety signal was generated when ingested food accumulated in the stomach and did not enter the small intestine. This gastric satiety signal did not require the vagus nerve for its operation. In addition, at least one other potent satiety signal was generated when food perfused the small intestine. This intestinal satiety signal did not require gastric distension for its operation. We tested a variety of GI peptides to determine whether any met the criteria imposed by this evidence for regionally specific satiety signals. Bombesin (BBS), a peptide present in high concentration in the stomach, was a potent and behaviorally specific inhibitor of food intake. Its satiating effect was not altered by subdiaphragmatic vagotomy. Cholecystokinin (CCK), a peptide hormone that is released from the small intestine by food, was also a potent and behaviorally specific inhibitor of food intake; its satiating effect did not require gastric distension for its expression, but its satiating effect was markedly reduced or abolished by subdiaphragmatic vagotomy. Thus, BBS and CCK may mediate at least part of the satiating effect of food acting in the stomach and in the small intestine, respectively.     

基于配准的插值

断层间图像插值是三维重建的一个关键步骤,因为图像上像素之间的间隔常常小于断层图像之间的距离,而在三维重建需要它们有一致的分辨率.由于是同模态断层图像层间插值,对于解决同模态弹性配准问题,Thirion的demons算法比较适合.所以配准采用Demons方法.Demons算法先判断出待配准图像上各个象素点的运动方法,通过对各个象素点的移动来实现非刚性配准.在这个算法中,每张图像都被视为同灰度值轮廓的集合.该算法可以应用于精度要求比较高的体数据插值重建过程.     

Amplitude-dependent modulation of brush border enzymes and proliferation by cyclic strain in human intestinal Caco-2 monolayers

Little is known about the effects of repetitive deformation during peristaltic distension and contraction or repetitive villus shortening on the proliferation and differentiation of the intestinal epithelium. We sought to characterize the effects of repetitive deformation of a physiologically relevant magnitude and frequency on the proliferation and differentiation of human intestinal epithelial Caco-2 cells, a common cell culture model for intestinal epithelial biology. Human intestinal epithelial Caco-2 cells were cultured on collagen-coated membranes deformed by −20 kPa vacuum at 10 cycles/minute, producing an average 10% strain on the adherent cells. Proliferation was assessed by cell counting and ³H-thymidine incorporation. Alkaline phosphatase and dipeptidyl dipeptidase specific activity were measured in cell lysates. Since cells at the membrane periphery experience higher strain than cells in the center, the topography of brush border enzyme histochemical and immunohistochemical staining was analyzed for strain-dependence. Cyclic strain stimulated proliferation compared to static cells. Proliferation was highest in the membrane periphery where strain was maximal. Strain also modulated differentiation independently of its mitogenic effects, selectively stimulating dipeptidyl dipeptidase while inhibiting alkaline phosphatase. Strain-associated enzyme changes were also maximal in areas of greatest strain. The PKC inhibitors staurosporine and calphostin C ablated strain mitogenic effects while intracellular PKC activity was increased by strain. The strain-associated brush border enzyme changes were attenuated but not blocked by PKC inhibition. Thus, strain of a physiologically relevant frequency and magnitude promotes proliferation and modulates the differentiation of a well-differentiated human intestinal epithelial cell line in an amplitude-dependent fashion. PKC may be involved in coupling strain to increased proliferation. © 1996 Wiley-Liss, Inc.     

Immunohistochemical analysis of connexin26 and 43 expression in the mouse alimentary tract

The spatial pattern of connexins26 (Cx26) and 43 (Cx43) expressions were investigated in the mouse digestive tract by immunocytochemistry. High levels of connexin43 in the epithelium of the oesophagus, non-glandular part of the stomach, and the circular layer of duodenal and ilea muscularis externa were detected. Cx26 was expressed in stratum granulosum of oesophagal folds and in the non-glandular part of the stomach. A low level of immunoreactivity of Cx43 was observed in the circular, and very low in the longitudinal layer of the muscularis externa in the stomach and colon. No immunoreactivity for Cx26 and Cx43 was found in the entire muscularis externa of the oesophagus or in the longitudinal muscle layers of the duodenum and ileum.     

The stomach, cholecystokinin, and satiety

The stomach of the rhesus monkey empties liquids in a fashion that varies with the character of the solutions. Physiological saline empties exponentially. Glucose solutions empty biphasically--rapidly for the first minutes, then slowly and proportionately to glucose concentration to deliver glucose calories through the pylorus at a regulated rate (0.4 kcal/min). This prolonged and regulated second phase of gastric emptying depends on intestinal inhibition of the stomach. Cholecystokinin (CCK), a hormone released by food in the intestine, is an inhibitor of gastric emptying. In vitro receptor autoradiography demonstrates CCK receptors to be clustered on the circular muscle of the pylorus. Exogenous CCK, in doses that inhibit gastric emptying, will reduce food intake only if combined with an infusion of saline in the stomach. These observations indicate how gastric distension can be a means for provoking satiety. The variably sustained distension produced by the stomach's slow, calorically regulated emptying could prolong intermeal intervals and thus permit high-calorie meals to inhibit further caloric intake over time. CCK, by directly inhibiting gastric emptying during a meal, could promote gastric distension and so restrict the duration and size of individual meals.     

Capsaicin-sensitive vagal fibres and 5-HT3-, gastrin releasing peptide- and cholecystokinin A-receptors are involved in distension-induced inhibition of gastric emptying in the rat.

The present study was undertaken to investigate how the activation of gastric mechanoreceptors by distension of the stomach in conscious gastric fistula rats influences gastric emptying; and the roles of capsaicin sensitive vagal afferent fibres and the 5-HT3, GRP and CCK-A receptors involved in mediating these responses. To activate mechanoreceptors by non-nutrient dependent pathways, methylcellulose in saline was used to distend the stomach (5 cm H2O) and the subsequent emptying of saline was examined immediately, and at 3, 5 and 10 min following distension. Prior distension delayed the subsequent emptying of saline instilled into the stomach compared with non-distended controls (2.28+/-0.09 ml/5 min; P < 0.001). Topical application of capsaicin, completely abolished the distension-induced inhibition of gastric emptying when compared with vehicle treated rats (2.82+/-0.09 vs. 2.38+/-0.04 ml/5 min; P < 0.001). Peripheral administration of a GRP antagonist (2258 U89UJ, 1 mg/kg), and a 5-HT3 antagonist (BRL4369UA, 50 microg/kg) significantly reversed (2.56+/-0.14 ml/5 min; P < 0.05 and 2.61+/-0.07 ml/5 min; P < 0.01; respectively) the delay in gastric emptying induced by distension. When the rats were treated with the CCK-A antagonist, gastric emptying of saline following distension was also significantly facilitated (2.56+/-0.07 ml/5 min; P < 0.001). In contrast, the CCK-B/gastrin receptor antagonist had no significant effect on the distension induced delay in gastric emptying (1.95+/-0.12 ml/5 min). The present results suggest that gastric distension in conscious gastric fistula rats delays gastric emptying by activating capsaicin-sensitive extrinsic afferent nerve fibres. Moreover, the results also indicate that distension-induced mechanisms involve GRP, 5-HT3 and CCK-A receptors, but not CCK-B receptors.     

棕色田鼠胃的形态与组织学观察

目的研究棕色田鼠胃的适应性特征。方法采用大体解剖、组织学和扫描电镜研究方法,观察棕色田鼠胃部形态学结构特征。结果根据形态特征棕色田鼠胃部可明显的分为2个胃室,根据有无腺体分布可分为有腺区和无腺区,第一胃室及第二胃室的大部分区为无腺区,胃的无腺区表面为角质化复层扁平上皮;有腺区上皮为单层柱状上皮;第一胃室与第二胃室交界处存在有19～21个特殊的瓣膜结构。结论棕色田鼠胃的形态发生了明显的适应性变化特征,出现了两个胃室,胃室之间首次发现有瓣膜结构存在。     

Cholecystokinin and stomach distension combine to reduce food intake in humans

The aim of this study was to test the hypothesis that gastric distension can enhance the effect of cholecystokinin (CCK) on reduction of food intake in men and women. Eight normal-weight subjects of each gender were tested four times each with either CCK or saline infusion crossed with gastric distension or no distension. Intravenous infusion of a low dose of CCK octapeptide (CCK-8; 112 ng/min for 23 min) combined with a subthreshold gastric distension induced by a water-filled balloon (300 ml) resulted in a significant (means +/- SED: 191 +/- 61 g in men, 209 +/- 61 g in women, and 200 +/- 43 g combined) reduction in intake of a liquid meal compared with saline infusion and unfilled gastric balloon. This combined effect was the result of a large and significant CCK effect when the stomach was distended (CCK vs. saline with distension: 169 +/- 43 g) and a small and insignificant distension effect (distension vs. no distension without CCK: 31 +/- 43 g). The CCK effect alone on intake (CCK vs. saline) without distension was not significant in men (72 +/- 61 g) but was significant in women (121 +/- 61 g). These results are consistent with the hypothesis that CCK's suppression of food intake is enhanced when the stomach is distended.     

Correlations between variations of electrical field at the body surface and contractions of the stomach in guinea pig.

1. The slow potentiel changes of the base line of the electrocardiogram recorded by cutaneous electrodes, here called EGEG (electrogastroenterogram) have been recorded simultaneously with the electromyogram and pressure variations of the stomach antrum. 2. Periodic fluctuations of EGEG, 400 microV amplitude, were correlated with activities of the antrum EMG consisting of 3 to 6 mV spikes superimposed on slow wave of depolarization, and with gastric intraluminal pressure of 5 to 7 cm of water. 3. An anticholinergic drug abolished all those activities. A gastric contracture flattened the EGEG. 4. Rhythmic distensions of the antrum induced a synchronous modulation of EGEG, the magnitude of which was correlated with the amplitude of distension. These result suggest that the origin of EGEG is essentially the movements of stomach.     

In vivo ankle joint kinematics from dynamic magnetic resonance imaging using a registration-based framework

In this paper, we propose a method for non-invasively measuring three-dimensional in vivo kinematics of the ankle joint from a dynamic MRI acquisition of a single range-of-motion cycle. The proposed approach relies on an intensity-based registration method to estimate motion from multi-plane dynamic MRI data. Our approach recovers not only the movement of the skeleton, but also the possibly non-rigid temporal deformation of the joint. First, the rigid motion of each ankle bone is estimated. Second, a four-dimensional (3D+time) high-resolution dynamic MRI sequence is estimated through the use of the log-euclidean framework for the computation of temporal dense deformation fields. This approach has been then applied and evaluated on in vivo dynamic MRI data acquired for a pilot study on six healthy pediatric cohort in order to establish in vivo normative joint biomechanics. Results demonstrate the robustness of the proposed pipeline and very promising high resolution visualization of the ankle joint.     

A new method to measure cortical growth in the developing brain

Folding of the cerebral cortex is a critical phase of brain development in higher mammals but the biomechanics of folding remain incompletely understood. During folding, the growth of the cortical surface is heterogeneous and anisotropic. We developed and applied a new technique to measure spatial and directional variations in surface growth from longitudinal magnetic resonance imaging (MRI) studies of a single animal or human subject. MRI provides high resolution 3D image volumes of the brain at different stages of development. Surface representations of the cerebral cortex are obtained by segmentation of these volumes. Estimation of local surface growth between two times requires establishment of a point-to-point correspondence ("registration") between surfaces measured at those times. Here we present a novel approach for the registration of two surfaces in which an energy function is minimized by solving a partial differential equation on a spherical surface. The energy function includes a strain-energy term due to distortion and an "error energy" term due to mismatch between surface features. This algorithm, implemented with the finite element method, brings surface features into approximate alignment while minimizing deformation in regions without explicit matching criteria. The method was validated by application to three simulated test cases and applied to characterize growth of the ferret cortex during folding. Cortical surfaces were created from MRI data acquired in vivo at 14 days, 21 days, and 28 days of life. Deformation gradient and Lagrangian strain tensors describe the kinematics of growth over this interval. These quantitative results illuminate the spatial, temporal, and directional patterns of growth during cortical folding.