Model-Based Identification of Anatomical Boundary Conditions in Living Tissues

International audienceIn this paper, we present a novel method dealing with the identification of boundary conditions of a deformable organ, a particularly important step for the creation of patient-specific biomechani-cal models of the anatomy. As an input, the method requires a set of scans acquired in different body positions. Using constraint-based finite element simulation, the method registers the two data sets by solving an optimization problem minimizing the energy of the deformable body while satisfying the constraints located on the surface of the registered organ. Once the equilibrium of the simulation is attained (i.e. the organ registration is computed), the surface forces needed to satisfy the constraints provide a reliable estimation of location, direction and magnitude of boundary conditions applied to the object in the deformed position. The method is evaluated on two abdominal CT scans of a pig acquired in flank and supine positions. We demonstrate that while computing a physically admissible registration of the liver, the resulting constraint forces applied to the surface of the liver strongly correlate with the location of the anatomical boundary conditions (such as contacts with bones and other organs) that are visually identified in the CT images

Visual Quality Enhancement in Optoacoustic Tomography using Active Contour Segmentation Priors

Segmentation of biomedical images is essential for studying and characterizing anatomical structures, detection and evaluation of pathological tissues. Segmentation has been further shown to enhance the reconstruction performance in many tomographic imaging modalities by accounting for heterogeneities of the excitation field and tissue properties in the imaged region. This is particularly relevant in optoacoustic tomography, where discontinuities in the optical and acoustic tissue properties, if not properly accounted for, may result in deterioration of the imaging performance. Efficient segmentation of optoacoustic images is often hampered by the relatively low intrinsic contrast of large anatomical structures, which is further impaired by the limited angular coverage of some commonly employed tomographic imaging configurations. Herein, we analyze the performance of active contour models for boundary segmentation in cross-sectional optoacoustic tomography. The segmented mask is employed to construct a two compartment model for the acoustic and optical parameters of the imaged tissues, which is subsequently used to improve accuracy of the image reconstruction routines. The performance of the suggested segmentation and modeling approach are showcased in tissue-mimicking phantoms and small animal imaging experiments.Comment: Accepted for publication in IEEE Transactions on Medical Imagin

Atlas-based Transfer of Boundary Conditions for Biomechanical Simulation

International audienceAn environment composed of different types of living tissues (such as the abdominal cavity) reveals a high complexity of boundary conditions, which are the attachments (e.g. connective tissues, ligaments) connecting different anatomical structures. Together with the material properties, the boundary conditions have a significant influence on the mechanical response of the organs, however corresponding correct me- chanical modeling remains a challenging task, as the connective struc- tures are difficult to identify in certain standard imaging modalities. In this paper, we present a method for automatic modeling of boundary con- ditions in deformable anatomical structures, which is an important step in patient-specific biomechanical simulations. The method is based on a statistical atlas which gathers data defining the connective structures at- tached to the organ of interest. In order to transfer the information stored in the atlas to a specific patient, the atlas is registered to the patient data using a physics-based technique and the resulting boundary conditions are defined according to the mean position and variance available in the atlas. The method is evaluated using abdominal scans of ten patients. The results show that the atlas provides a sufficient information about the boundary conditions which can be reliably transferred to a specific patient. The boundary conditions obtained by the atlas-based transfer show a good match both with actual segmented boundary conditions and in terms of mechanical response of deformable organs

In silico evaluation of the thermal stress induced by MRI switched gradient fields in patients with metallic hip implant

This work focuses on the in silico evaluation of the energy deposed by MRI switched gradient fields in bulk metallic implants and the consequent temperature increase in the surrounding tissues. An original computational strategy, based on the subdivision of the gradient coil switching sequences into sub-signals and on the time-harmonic electromagnetic field solution, allows to realistically simulate the evolution of the phenomena produced by the gradient coils fed according to any MRI sequence. Then, Pennes' bioheat equation is solved through a Douglas-Gunn time split scheme to compute the time-dependent temperature increase. The procedure is validated by comparison with laboratory results, using a component of a realistic hip implant embedded within a phantom, obtaining an agreement on the temperature increase better than 5%, lower than the overall measurement uncertainty. The heating generated inside the body of a patient with a unilateral hip implant when undergoing an Echo-Planar Imaging (EPI) MRI sequence is evaluated and the role of the parameters affecting the thermal results (body position, coil performing the frequency encoding, effects of thermoregulation) is discussed. The results show that the gradient coils can generate local increases of temperature up to some kelvin when acting without radiofrequency excitation. Hence, their contribution in general should not be disregarded when evaluating patients' safety

Data-driven Intra-operative Estimation of Anatomical Attachments for Autonomous Tissue Dissection

The execution of surgical tasks by an Autonomous Robotic System (ARS) requires an up-to-date model of the current surgical environment, which has to be deduced from measurements collected during task execution. In this work, we propose to automate tissue dissection tasks by introducing a convolutional neural network, called BA-Net, to predict the location of attachment points between adjacent tissues. BA-Net identifies the attachment areas from a single partial view of the deformed surface, without any a-priori knowledge about their location. The proposed method guarantees a very fast prediction time, which makes it ideal for intra-operative applications. Experimental validation is carried out on both simulated and real world phantom data of soft tissue manipulation performed with the da Vinci Research Kit (dVRK). The obtained results demonstrate that BA-Net provides robust predictions at varying geometric configurations, material properties, distributions of attachment points and grasping point locations. The estimation of attachment points provided by BA-Net improves the simulation of the anatomical environment where the system is acting, leading to a median simulation error below 5mm in all the tested conditions. BA-Net can thus further support an ARS by providing a more robust test bench for the robotic actions intra-operatively, in particular when replanning is needed. The method and collected dataset are available at https://gitlab.com/altairLab/banet

Regional diversity in the murine cortical vascular network is revealed by synchrotron X-ray tomography and is amplified with age

Cortical bone is permeated by a system of pores, occupied by the blood supply and osteocytes. With ageing, bone mass reduction and disruption of the microstructure are associated with reduced vascular supply. Insight into the regulation of the blood supply to the bone could enhance the understanding of bone strength determinants and fracture healing. Using synchrotron radiation-based computed tomography, the distribution of vascular canals and osteocyte lacunae was assessed in murine cortical bone and the influence of age on these parameters was investigated. The tibiofibular junction from 15-week- and 10-month-old female C57BL/6J mice were imaged post-mortem. Vascular canals and three-dimensional spatial relationships between osteocyte lacunae and bone surfaces were computed for both age groups. At 15 weeks, the posterior region of the tibiofibular junction had a higher vascular canal volume density than the anterior, lateral and medial regions. Intracortical vascular networks in anterior and posterior regions were also different, with connectedness in the posterior higher than the anterior at 15 weeks. By 10 months, cortices were thinner, with cortical area fraction and vascular density reduced, but only in the posterior cortex. This provided the first evidence of age-related effects on murine bone porosity due to the location of the intracortical vasculature. Targeting the vasculature to modulate bone porosity could provide an effective way to treat degenerative bone diseases, such as osteoporosis

Colocation and role of polyphosphates and alkaline phosphatase in apatite biomineralization of elasmobranch tesserae

AbstractElasmobranchs (e.g. sharks and rays), like all fishes, grow continuously throughout life. Unlike other vertebrates, their skeletons are primarily cartilaginous, comprising a hyaline cartilage-like core, stiffened by a thin outer array of mineralized, abutting and interconnected tiles called tesserae. Tesserae bear active mineralization fronts at all margins and the tesseral layer is thin enough to section without decalcifying, making this a tractable but largely unexamined system for investigating controlled apatite mineralization, while also offering a potential analog for endochondral ossification. The chemical mechanism for tesserae mineralization has not been described, but has been previously attributed to spherical precursors, and alkaline phosphatase (ALP) activity. Here, we use a variety of techniques to elucidate the involvement of phosphorus-containing precursors in the formation of tesserae at their mineralization fronts. Using Raman spectroscopy, fluorescence microscopy and histological methods, we demonstrate that ALP activity is located with inorganic phosphate polymers (polyP) at the tessera–uncalcified cartilage interface, suggesting a potential mechanism for regulated mineralization: inorganic phosphate (Pi) can be cleaved from polyP by ALP, thus making Pi locally available for apatite biomineralization. The application of exogenous ALP to tissue cross-sections resulted in the disappearance of polyP and the appearance of Pi in uncalcified cartilage adjacent to mineralization fronts. We propose that elasmobranch skeletal cells control apatite biomineralization by biochemically controlling polyP and ALP production, placement and activity. Previous identification of polyP and ALP shown previously in mammalian calcifying cartilage supports the hypothesis that this mechanism may be a general regulating feature in the mineralization of vertebrate skeletons

Intra-operative Update of Boundary Conditions for Patient-specific Surgical Simulation

Patient-specific Biomechanical Models (PBMs) can enhance computer assisted surgical procedures with critical information. Although pre-operative data allow to parametrize such PBMs based on each patient's properties, they are not able to fully characterize them. In particular, simulation boundary conditions cannot be determined from pre-operative modalities, but their correct definition is essential to improve the PBM predictive capability. In this work, we introduce a pipeline that provides an up-to-date estimate of boundary conditions, starting from the pre-operative model of patient anatomy and the displacement undergone by points visible from an intra-operative vision sensor. The presented pipeline is experimentally validated in realistic conditions on an ex vivo pararenal fat tissue manipulation. We demonstrate its capability to update a PBM reaching clinically acceptable performances, both in terms of accuracy and intra-operative time constraints