Multimodal image fusion of anatomical structures for diagnosis, therapy planning and assistance

This paper provides an overview of work done in recent years by our research group to fuse multimodal images of the trunk of patients with Adolescent Idiopathic Scoliosis (AIS) treated at Sainte-Justine University Hospital Center (CHU). We first describe our surface acquisition system and introduce a set of clinical measurements (indices) based on the trunk's external shape, to quantify its degree of asymmetry. We then describe our 3D reconstruction system of the spine and rib cage from biplanar radiographs and present our methodology for multimodal fusion of MRI, X-ray and external surface images of the trunk We finally present a physical model of the human trunk including bone and soft tissue for the simulation of the surgical outcome on the external trunk shape in AIS.

Twofold adaptive partition of unity implicits

Partition of Unity Implicits (PUI) has been recently introduced for surface reconstruction from point clouds. In this work, we propose a PUI method that employs a set of well-observed solutions in order to produce geometrically pleasant results without requiring time consuming or mathematically overloaded computations. One feature of our technique is the use of multivariate orthogonal polynomials in the least-squares approximation, which allows the recursive refinement of the local fittings in terms of the degree of the polynomial. However, since the use of high-order approximations based only on the number of available points is not reliable, we introduce the concept of coverage domain. In addition, the method relies on the use of an algebraically defined triangulation to handle two important tasks in PUI: the spatial decomposition and an adaptive polygonization. As the spatial subdivision is based on tetrahedra, the generated mesh may present poorly-shaped triangles that are improved in this work by means a specific vertex displacement technique. Furthermore, we also address sharp features and raw data treatment. A further contribution is based on the PUI locality property that leads to an intuitive scheme for improving or repairing the surface by means of editing local functions.

Uma Aplicação de Redes Neurais Auto-Organizaveis à Reconstrução Tridimensional de Superfícies

We propose a multi-resolution approach for surface reconstruction from clouds of unorganized points representing an object surface in 3D space. The proposed method uses a set of mesh operators and simple rules for selective mesh refinement, with a strategy based on Kohonen s self-organizing map. Basically, a self-adaptive scheme is used for iteratively moving vertices of an initial simple mesh in the direction of the set of points, ideally the object boundary. Successive refinement and motion of vertices are applied leading to a more detailed surface, in a multi-resolution, iterative scheme. Reconstruction was experimented with several point sets, induding different shapes and sizes. Results show generated meshes very dose to object final shapes. We include measures of performance and discuss robustness.

Effect of amniotic membrane transplantation on corneal healing and proteoglycan expression in an experimental model of limbal deficiency in rabbits

PURPOSE. Amniotic membrane transplantation (AMT) has been used as a graft or as a dressing in ocular surface reconstruction, facilitating epithelization, maintaining normal epithelial phenotype, and reducing inflammation, vascularization, and scarring. The corneal transparency is due, at least in part, to the arrangement in orthogonal lamellae of collagen fibrils, surrounded by proteoglycans (PGs). These PGs regulate fibrilogenesis, the matrix assembly, and ultimately the corneal transparency. The purpose of the present study was to investigate the effects of AMT upon the corneal PGs after severe limbal injury.METHODS. Experiments were performed on the right corneas of 22 New Zealand female albino rabbits, and their left corneas were used as matched controls. These animals were divided into 3 groups: G1 (n = 10): total peritomy and keratolimbectomy, followed by application of 0.5 M NaOH; G2 (n = 10): submitted to the same trauma as G1, and treated by AMT; G3: no trauma, only AMT (n = 2). The right corneas of G2 and G3 were covered by DMSO 4 cryopreserved human amniotic membrane, fixed by interrupted 9-0 mononylon sutures, with its stromal face toward the ocular surface. After 7 or 30 days, the corneas were removed and PGs were extracted.RESULTS. Normal corneas contained approximately 9 mg of PGs per gram of dry tissue. AMT on intact cornea (G3) did not cause any changes in the concentration of PGs. In contrast, injured corneas contained much less PGs, both on the seventh and on the 30th day posttrauma. The PG concentration was even lower in injured corneas treated by AMT. This decrease was due almost exclusively to dermatan sulfate PGs, and the structure of dermatan sulfate was also modified, indicating changes in the biosynthesis patterns.CONCLUSIONS. Although beneficial effects have been observed on clinical observation and concentration of soluble proteins after AMT, the normal PG composition of cornea was not attained, even 30 days postinjury, indicating that the normal ocular surface reconstruction, if possible, is a long-term process. (Eur J Ophthalmol 2010; 20: 290-9)

A low cost structured light system

The aim of this paper is to present the current development status of a low cost system for surface reconstruction with structured light. The acquisition system is composed of a single off-the-shelf digital camera and a pattern projector. A pattern codification strategy was developed to allow the pattern recognition automatically and a calibration methodology ensures the determination of the direction vector of each pattern. The experiments indicated that an accuracy of 0.5mm in depth could be achieved for typical applications.

Simplificação de malhas visando representações em multirresolução

The representation of real objects in virtual environments has applications in many areas, such as cartography, mixed reality and reverse engineering. The generation of these objects can be performed through two ways: manually, with CAD (Computer Aided Design) tools, or automatically, by means of surface reconstruction techniques. The simpler the 3D model, the easier it is to process and store it. However, this methods can generate very detailed virtual elements, that can result in some problems when processing the resulting mesh, because it has a lot of edges and polygons that have to be checked at visualization. Considering this context, it can be applied simplification algorithms to eliminate polygons from resulting mesh, without change its topology, generating a lighter mesh with less irrelevant details. The project aimed the study, implementation and comparative tests of simplification algorithms applied to meshes generated through a reconstruction pipeline based on point clouds. This work proposes the realization of the simplification step, like a complement to the pipeline developed by (ONO et al., 2012), that developed reconstruction through cloud points obtained by Microsoft Kinect, and then using Poisson algorithm

Um método para reconstrução de superfícies baseado em nuvem de pontos visando representações em multirresolução

The representation of real objects in virtual environments has applications in many areas, such as cartography, mixed reality and reverse engineering. The generation of these objects can be performed in two ways: manually, with CAD (Computer Aided Design) tools, or automatically, by means of surface reconstruction techniques. The simpler the 3D model, the easier it is to process and store it. Multiresolution reconstruction methods can generate polygonal meshes in different levels of detail and, to improve the response time of a computer program, distant objects can be represented with few details, while more detailed models are used in closer objects. This work presents a new approach to multiresolution surface reconstruction, particularly interesting to noisy and low definition data, for example, point clouds captured with Kinect sensor

Human immature dental pulp stem cells share key characteristic features with limbal stem cells

Objectives: Limbal stem cells (LSC) are self-renewing, highly proliferative cells in vitro, which express a set of specific markers and in vivo have the capacity to reconstruct the entire corneal epithelium in cases of ocular surface injury. Currently, LSC transplantation is a commonly used procedure in patients with either uni- or bilateral total limbal stem cells deficiency (TLSCD). Although LSC transplantation holds great promise for patients, several problems need to be overcome. In order to find an alternative source of cells that can partially substitute LSC in cornea epithelium reconstruction, we aimed at investigating whether human immature dental pulp stem cells (hIDPSC) would present similar key characteristics as LSC and whether they could be used for corneal surface reconstruction in a rabbit TLSCD model. Materials: We used hIDPSC, which co-express mesenchymal and embryonic stem cell markers and present the capacity to differentiate into derivative cells of the three germinal layers. TLSCD was induced by chemical burn in one eye of rabbits. After 30 days, the opaque tissue formed was removed by superficial keratectomy. Experimental group received undifferentiated hIDPSC, while control group only received amniotic membrane (AM). Both groups were sacrificed after 3 months. Results and conclusions: We have demonstrated, using immunohistochemistry and reverse transcription-polymerase chain reaction, that hIDPSCs express markers in common with LSC, such as ABCG2, integrin beta 1, vimentin, p63, connexin 43 and cytokeratins 3/12. They were also capable of reconstructing the eye surface after induction of unilateral TLSCD in rabbits, as shown by morphological and immunohistochemical analysis using human-specific antibodies against limbal and corneal epithelium. Our data suggest that hIDPSCs share similar characteristics with LSC and might be used as a potential alternative source of cells for corneal reconstruction.

Atomic-scale characterization of diamond surfaces and fullerene self-assembly

In this thesis, elemental research towards the implantation of a diamond-based molecular quantum computer is presented. The approach followed requires linear alignment of endohedral fullerenes on the diamond C(100) surface in the vicinity of subsurface NV-centers. From this, four fundamental experimental challenges arise: 1) The well-controlled deposition of endohedral fullerenes on a diamond surface. 2) The creation of NV-centers in diamond close to the surface. 3) Preparation and characterization of atomically-flat diamondsurfaces. 4) Assembly of linear chains of endohedral fullerenes. First steps to overcome all these challenges were taken in the framework of this thesis. Therefore, a so-called “pulse injection” technique was implemented and tested in a UHV chamber that was custom-designed for this and further tasks. Pulse injection in principle allows for the deposition of molecules from solution onto a substrate and can therefore be used to deposit molecular species that are not stable to sublimation under UHV conditions, such as the endohedral fullerenes needed for a quantum register. Regarding the targeted creation of NV-centers, FIB experiments were carried out in cooperation with the group of Prof. Schmidt-Kaler (AG Quantum, Physics Department, Johannes Gutenberg-Universität Mainz). As an entry into this challenging task, argon cations were implanted into (111) surface-oriented CaF2 crystals. The resulting implantation spots on the surface were imaged and characterized using AFM. In this context, general relations between the impact of the ions on the surface and their valency or kinetic energy, respectively, could be established. The main part of this thesis, however, is constituted by NCAFM studies on both, bare and hydrogen-terminated diamond C(100) surfaces. In cooperation with the group of Prof. Dujardin (Molecular Nanoscience Group, ISMO, Université de Paris XI), clean and atomically-flat diamond surfaces were prepared by exposure of the substrate to a microwave hydrogen plasma. Subsequently, both surface modifications were imaged in high resolution with NC-AFM. In the process, both hydrogen atoms in the unit cell of the hydrogenated surface were resolved individually, which was not achieved in previous STM studies of this surface. The NC-AFM images also reveal, for the first time, atomic-resolution contrast on the clean, insulating diamond surface and provide real-space experimental evidence for a (2×1) surface reconstruction. With regard to the quantum computing concept, high-resolution NC-AFM imaging was also used to study the adsorption and self-assembly potential of two different kinds of fullerenes (C60 and C60F48) on aforementioned diamond surfaces. In case of the hydrogenated surface, particular attention was paid to the influence of charge transfer doping on the fullerene-substrate interaction and the morphology emerging from self-assembly. Finally, self-assembled C60 islands on the hydrogen-terminated diamond surface were subject to active manipulation by an NC-AFM tip. Two different kinds of tip-induced island growth modes have been induced and were presented. In conclusion, the results obtained provide fundamental informations mandatory for the realization of a molecular quantum computer. In the process it was shown that NC-AFM is, under proper circumstances, a very capable tool for imaging diamond surfaces with highest resolution, surpassing even what has been achieved with STM up to now. Particular attention was paid to the influence of transfer doping on the morphology of fullerenes on the hydrogenated diamond surface, revealing new possibilities for tailoring the self-assembly of molecules that have a high electron affinity.

Delay of cortical thinning in very preterm born children

BACKGROUND: Cortical gray matter thinning occurs during childhood due to pruning of inefficient synaptic connections and an increase in myelination. Preterms show alterations in brain structure, with prolonged maturation of the frontal lobes, smaller cortical volumes and reduced white matter volume. These findings give rise to the question if there is a differential influence of age on cortical thinning in preterms compared to controls. AIMS: To investigate the relationship between age and cortical thinning in school-aged preterms compared to controls. STUDY DESIGN AND OUTCOME MEASURES: The automated surface reconstruction software FreeSurfer was applied to obtain measurements of cortical thickness based on T1-weighted MRI images. SUBJECTS: Forty-one preterms (<32weeks gestational age and/or <1500g birth weight) and 30 controls were included in the study (7-12years). RESULTS: In preterms, age correlated negatively with cortical thickness in right frontal, parietal and inferior temporal regions. Furthermore, young preterms showed a thicker cortex compared to old preterms in bilateral frontal, parietal and temporal regions. In controls, age was not associated with cortical thickness. CONCLUSION: In preterms, cortical thinning still seems to occur between the age of 7 and 12years, mainly in frontal and parietal areas whereas in controls, a substantial part of cortical thinning appears to be completed before they reach the age of 7years. These data indicate slower cortical thinning in preterms than in controls.

Delay of cortical thinning in very preterm born children

Objective: Cortical gray matter thinning takes place during childhood due to pruning of inefficient synaptic connections and an increase in myelination. Alterations in brain structure occur in very preterm born children with prolonged maturation of the frontal lobes and smaller cortical and white matter volume. These findings give rise to the question if age affects cortical thinning differently in very preterm born children compared to controls. The aim of the present study was to investigate the relationship between age and cortical thickness in very preterm born children when compared to controls. Participants and Methods: Forty-one very preterm born children (<32 weeks gestational age and/or < 1500 gram birth weight) and 30term born controls were included in the study (7-12 years). The automated surface reconstruction software FreeSurfer was applied to obtain measurements of cortical thickness based on T1-weighted MRI images. Results: Cortical thickness was lower in bilateral frontal and left parietal regions and higher in left temporal gyri in very preterm born children compared to controls. However, these differences depended on age. In very preterm born children, age correlated negatively with cortical thickness in right frontal, parietal and inferior temporal regions. Accordingly, cortical thickness was higher in young compared to old very preterm born children in bilateral frontal, parietal and temporal regions. In controls, age was not associated with cortical thickness. Conclusions: In very preterm born children, cortical thinning still occurs between the age of 7 and 12 years, mainly in frontal and parietal areas. In controls, however, a substantial part of cortical thinning appears to be completed in these regions before they reach the age of 7 years. These data indicate a delay in cortical thinning in very preterm born children.

Cortical thickness decreases with age in very preterm born school-children but not in term born controls

Background: Cortical gray matter thinning occurs during childhood due to pruning of inefficient synaptic connections and an increase in myelination. Preterms show alterations in brain structure, with prolonged maturation of the frontal lobes, smaller cortical volumes and reduced white matter volume. These findings give rise to the question if there is a differential influence of age on cortical thinning in preterms compared to controls. Aims: To investigate the relationship between age and cortical thickness in preterms when compared to controls. Study design and outcome measures: The automated surface reconstruction software FreeSurfer was applied to obtain measurements of cortical thickness based on T1-weighted MRI images. Subjects: Forty-one preterms (< 32 weeks gestational age and/or < 1500 gram birth weight) and 30 controls were included in the study (7-12 years). Results: Cortical thickness was lower in bilateral frontal and left parietal regions and higher in left temporal gyri in preterms compared to controls. However, these differences depended on age. In preterms, age correlated negatively with cortical thickness in right frontal, parietal and inferior temporal regions. Accordingly, cortical thickness was higher in young compared to old preterms in bilateral frontal, parietal and temporal regions. In controls, age was not associated with cortical thickness. Conclusion: In preterms, cortical thinning still seems to occur between the age of 7 and 12 years, mainly in frontal and parietal areas whereas in controls, a substantial part of cortical thinning appears to be completed before they reach the age of 7 years. These data indicate slower cortical thinning in preterms than in controls.

Uncalibrated Near-Light Photometric Stereo

In this work we solve the uncalibrated photometric stereo problem with lights placed near the scene. We investigate different image formation models and find the one that best fits our observations. Although the devised model is more complex than its far-light counterpart, we show that under a global linear ambiguity the reconstruction is possible up to a rotation and scaling, which can be easily fixed. We also propose a solution for reconstructing the normal map, the albedo, the light positions and the light intensities of a scene given only a sequence of near-light images. This is done in an alternating minimization framework which first estimates both the normals and the albedo, and then the light positions and intensities. We validate our method on real world experiments and show that a near-light model leads to a significant improvement in the surface reconstruction compared to the classic distant illumination case.

Low-density InAs QDs with subcritical coverage obtained by conversion of In nanocrystals

We report growth of InAs/GaAs quantum dots (QDs) by molecular beam epitaxy with low density of 2 μm−2 by conversion of In nanocrystals deposited at low temperatures. The total amount of InAs used is about one monolayer, which is less than the critical thickness for conventional Stranski–Krastanov QDs. We also demonstrate the importance of the starting surface reconstruction for obtaining uniform QDs. The QD emission wavelength is easily tunable upon post-growth annealing with no wetting layer signal visible for short anneals. Microphotoluminescence measurements reveal well separated and sharp emission lines of individual QDs.