Development and validation of a generic 3D model of the distal femur

The development and validation of a virtual generic 3D model of the distal femur using computer graphical methods is presented. The synthesis of the generic model requires the following steps: acquisition of bony 3D morphology using standard computed tomography (CT) imaging; alignment of 3D models reconstructed from CT images with a common coordinate system; computer graphical sectioning of the models; extraction of bone contours from the image sections; combining and averaging of extracted contours; and 3D reconstruction of the averaged contours. The generic models reconstructed from the averaged contours of six cadaver femora were validated by comparing their surface geometry on a point to point basis with that of the CT reconstructed reference models. The mean errors ranged from 0.99 to 2.5 mm and were in agreement with the qualitative assessment of the models.     

Quantitative comparison of freeware software for bone mesh from DICOM files

Musculo-skeletal modelling, 3D printing of bone models and also custom design of relevant prostheses starts from accurate STL files. These are obtained from medical imaging after careful segmentation and 3D reconstruction using specialized software, but most of these are very expensive. The aim of the present study is to assess and compare alternative software available for free. Three freeware software were selected from the most popular, and one standard platform was made available at the institute of the authors. Using each of these four software and starting from available DICOM files obtained previously by a CT scanner, three different bone models were reconstructed from each of five different human anatomical areas for a total of 60 bone model reconstructions. A young radiographer performed the bone reconstruction without specific technical training. 3D spatial matching of corresponding anatomical models was also performed to determine distance-maps for the assessment of final surface quality. In all four software many valuable features were available, with minimum differences, and bone models of good quality were obtained. Large differences in file sizes (mean range over the five anatomical models 66-338) and in the number of triangles (870-1350 thousands) were found, with triangles for MByte ratio ranging from about 4 to 20 thousands. The distance-map analysis revealed that root mean square deviation averaged over the five anatomical models ranged from 0.13 to 2.21 mm for the six spatial matches between the four software. These software are suitable for 3D bone model reconstruction, and do not require special training, and as such these can open up opportunities for biomechanical modelling and medical education.     

A biplanar reconstruction method based on 2D and 3D contours: application to the distal femur

A three-dimensional (3D) reconstruction algorithm based on contours identification from biplanar radiographs is presented. It requires, as technical prerequisites, a method to calibrate the biplanar radiographic environment and a surface generic object (anatomic atlas model) representing the structure to be reconstructed. The reconstruction steps consist of: the definition of anatomical regions, the identification of 2D contours associated to these regions, the calculation of 3D contours and projection onto the radiographs, the associations between points of the X-rays contours and points of the projected 3D contours, the optimization of the initial solution and the optimized object deformation to minimize the distance between X-rays contours and projected 3D contours. The evaluation was performed on 8 distal femurs comparing the 3D models obtained to CT-scan reconstructions. Mean error for each distal femur was 1 mm.     

Fit optimisation of a distal medial tibia plate

An iterative method for the fit optimisation of a pre-contoured fracture fixation plate for a given bone data set is presented. Both plate shape optimisation and plate fit quantification are conducted in a virtual environment utilising computer graphical methods and 3D bone and plate models. Two optimised shapes of the undersurface of an existing distal medial tibia plate were generated based on a dataset of 45 3D bone models reconstructed from computed tomography image data of Japanese tibiae. The existing plate shape achieved an anatomical fit on 13% of tibiae from the dataset. Modified plate 1 achieved an anatomical fit for 42% and modified plate 2 a fit for 67% of the bones. If either modified plate 1 or plate 2 is used, then the anatomical fit can be increased to 82% for the same dataset. Issues pertaining to any further improvement in plate fit/shape are discussed.     

Additive Manufacturing of Anatomical Models from Computed Tomography Scan Data

The purpose of the study presented here was to investigate the manufacturability of human anatomical models from Computed Tomography (CT) scan data via a 3D desktop printer which uses fused deposition modelling (FDM) technology. First, Digital Imaging and Communications in Medicine (DICOM) CT scan data were converted to 3D Standard Triangle Language (STL) format by using InVaselius digital imaging program. Once this STL file is obtained, a 3D physical version of the anatomical model can be fabricated by a desktop 3D FDM printer. As a case study, a patient’s skull CT scan data was considered, and a tangible version of the skull was manufactured by a 3D FDM desktop printer. During the 3D printing process, the skull was built using acrylonitrile-butadiene-styrene (ABS) co-polymer plastic. The printed model showed that the 3D FDM printing technology is able to fabricate anatomical models with high accuracy. As a result, the skull model can be used for preoperative surgical planning, medical training activities, implant design and simulation to show the potential of the FDM technology in medical field. It will also improve communication between medical stuff and patients. Current result indicates that a 3D desktop printer which uses FDM technology can be used to obtain accurate anatomical models.     

Development of a 3D optical scanner for evaluating patient-specific dose distributions

PurposeThis paper describes the hardware and software characteristics of a 3D optical scanner (P3DS) developed in-house. The P3DS consists of an LED light source, diffuse screen, step motor, CCD camera, and scanner management software with 3D reconstructed software.Materials and methodWe performed optical simulation, 2D and 3D reconstruction image testing, and pre-clinical testing for the P3DS. We developed the optical scanner with three key characteristics in mind. First, we developed a continuous scanning method to expand possible clinical applications. Second, we manufactured a collimator to improve image quality by reducing scattering from the light source. Third, we developed an optical scanner with changeable camera positioning to enable acquisition of optimal images according to the size of the gel dosimeter.ResultsWe confirmed ray-tracing in P3DS with optic simulation and found that 2D projection and 3D reconstructed images were qualitatively similar to the phantom images. For pre-clinical tests, the dose distribution and profile showed good agreement among RTP, optical CT, and external beam radiotherapy film data for the axial and coronal views. The P3DS has shown that it can scan and reconstruct for evaluation of the gel dosimeter within 1 min. We confirmed that the P3DS system is a useful tool for the measurement of 3D dose distributions for 3D radiation therapy QA. Further experiments are needed to investigate quantitative analysis for 3D dose distribution.     

3D虚拟复原精度的差异对头骨测量数值的影响——以Mimics软牛为例

近年来,根据三维软件虚拟复原的头骨来获取测量数据的方法被越来越多地应用在古生物,特别是古人类学的研究中,然而对于三维软件不同精度虚拟复原的头骨,其测量数值是否有差异,研究者并不是很清楚。本文以Mimics软件为例,根据其复原模型简化规则,选择未精简的最佳精度模型作为标准进行配对t检验或非参数检验,通过对43例云南人头骨的顶骨矢状弦长、颅周长、头盖部面积、乳突小房表面积、颅容量、乳突小房体积等六个测量项目的对比和分析,对Mimics软件低、中、高、最佳四种精度3D虚拟复原头骨间的测量差异进行了研究。结果显示：颅周长、头盖部面积、颅容量、乳突小房体积四项的所有简化精度模型的测量数据均与最佳精度模型测量数据的差异具有显著性;而除高精度组外,顶骨矢状弦长及乳突小房表面积的其余精度组测量数据均与最佳精度组差异具有显著性;此外,顶骨矢状弦长、颅周长、头盖部面积、颅容量的简化精度与最佳精度的测量差异占比均小于3%.而乳突小房表面积的低精度与最佳精度测量差异占比可超过50%,乳突小房体积的低精度与最佳精度测量差异占比可超过120%。这一结果提示我们,在测量Mimics复原的三维模型时,体量大差异小的测量项可以在较低精度的复原模型上进行测量;而对头骨内部腔窦这样体量小表面粗糙的结构,复原模型的精度选择及测量数据比较需要格外谨慎。     

4D‐analysis of early pelvic girdle development in the mouse (Mus musculus)

The formation of limb girdles is a key‐novelty in vertebrate evolution. Although the knowledge of pattern formation, genetic, and molecular analysis of limb development has prodigiously grown over the past four decades, the morphogenesis of the pelvic element, joining the appendicular with the axial skeleton has poorly been investigated. Because of their heterochrony in development and evolution, axial and appendicular skeletal elements have seldom been seen as a cojoined morphological complex. The present study examines the pelvis morphogenesis in the mouse (Mus musculus), with special focuses on the axio‐appendicular linkage, the formation and number of elements, and the joint formation. Serial histological sections of specimens from Theiler stages (TH) 18–25 (Theiler, 1972) were examined using bright field microscopy. 3D‐models of the growing pelvis were reconstructed from these serial sections. The generated 3D‐models were subsequently integrated into a computer‐animated 4D‐visualization illustrating the complex developmental dynamics of the mammalian pelvis morphogenesis. The findings demonstrate that the pelvic element forms from a single mesenchymal condensation in close vicinity to the appendicular skeleton. From the early start of development the pelvic element is limb‐associated, and quite lately connects to the axial skeleton. Additionally, the 4D‐visualization of the entire developmental process reveals a yet unnoticed reorientation of the mouse pelvic element from an initial posteriorly oblique developmental position to a ventrally oblique definitive position. J. Morphol., 2010. © 2009 Wiley‐Liss, Inc.     

3D Modelling of Biological Systems for Biomimetics

1　IntroductionBasedonthereviewofthepreviousworkof 3Dgeometricalmodellingtechniquesandsystemsdevelopedforindustrial,medicalandanimationapplications,thispaperdiscussestheproblemsassociatedwiththeexist ingtechniquesandsystems ,especiallywhenappliedto3Dmodellingof plants ,insectsandanimalsforbiomimeticsresearchanddevelopment .Then ,paperproposessomeareasofresearchinterestsin 3Dmod ellingofplants ,insectsandanimalsforBiomimetics .Toavoidtherepeating ,inthispaper ,biologicalobjectswillbeusedtorep…     

3-D finite element modelling of facial soft tissue and preliminary application in orthodontics

Prediction of soft tissue aesthetics is important for achieving an optimal outcome in orthodontic treatment planning. Previously, applicable procedures were mainly restricted to 2-D profile prediction. In this study, a generic 3-D finite element (FE) model of the craniofacial soft and hard tissue was constructed, and individualisation of the generic model based on cone beam CT data and mathematical transformation was investigated. The result indicated that patient-specific 3-D facial FE model including different layers of soft tissue could be obtained through mathematical model transformation. Average deviation between the transformed model and the real reconstructed one was 0.47 ± 0.77 mm and 0.75 ± 0.84 mm in soft and hard tissue, respectively. With boundary condition defined according to treatment plan, such FE model could be used to predict the result of orthodontic treatment on facial soft tissue.     

High Resolution 3D Imaging of Ex-Vivo Biological Samples by Micro CT

Non-destructive volume visualization can be achieved only by tomographic techniques, of which the most efficient is the x-ray micro computerized tomography (μCT).High resolution μCT is a very versatile yet accurate (1-2 microns of resolution) technique for 3D examination of ex-vivo biological samples^{1, 2}. As opposed to electron tomography, the μCT allows the examination of up to 4 cm thick samples. This technique requires only few hours of measurement as compared to weeks in histology. In addition, μCT does not rely on 2D stereologic models, thus it may complement and in some cases can even replace histological methods^{3, 4}, which are both time consuming and destructive. Sample conditioning and positioning in μCT is straightforward and does not require high vacuum or low temperatures, which may adversely affect the structure. The sample is positioned and rotated 180° or 360°between a microfocused x-ray source and a detector, which includes a scintillator and an accurate CCD camera, For each angle a 2D image is taken, and then the entire volume is reconstructed using one of the different available algorithms^5-7. The 3D resolution increases with the decrease of the rotation step. The present video protocol shows the main steps in preparation, immobilization and positioning of the sample followed by imaging at high resolution.     

Prediction of femoral strength using 3D finite element models reconstructed from DXA images: validation against experiments

Computed tomography (CT)-based finite element (FE) models may improve the current osteoporosis diagnostics and prediction of fracture risk by providing an estimate for femoral strength. However, the need for a CT scan, as opposed to the conventional use of dual-energy X-ray absorptiometry (DXA) for osteoporosis diagnostics, is considered a major obstacle. The 3D shape and bone mineral density (BMD) distribution of a femur can be reconstructed using a statistical shape and appearance model (SSAM) and the DXA image of the femur. Then, the reconstructed shape and BMD could be used to build FE models to predict bone strength. Since high accuracy is needed in all steps of the analysis, this study aimed at evaluating the ability of a 3D FE model built from one 2D DXA image to predict the strains and fracture load of human femora. Three cadaver femora were retrieved, for which experimental measurements from ex vivo mechanical tests were available. FE models were built using the SSAM-based reconstructions: using only the SSAM-reconstructed shape, only the SSAM-reconstructed BMD distribution, and the full SSAM-based reconstruction (including both shape and BMD distribution). When compared with experimental data, the SSAM-based models predicted accurately principal strains (coefficient of determination >0.83, normalized root-mean-square error <16%) and femoral strength (standard error of the estimate 1215 N). These results were only slightly inferior to those obtained with CT-based FE models, but with the considerable advantage of the models being built from DXA images. In summary, the results support the feasibility of SSAM-based models as a practical tool to introduce FE-based bone strength estimation in the current fracture risk diagnostics.     

Automatic 4D Reconstruction of Patient-Specific Cardiac Mesh with 1-to-1 Vertex Correspondence from Segmented Contours Lines

We propose an automatic algorithm for the reconstruction of patient-specific cardiac mesh models with 1-to-1 vertex correspondence. In this framework, a series of 3D meshes depicting the endocardial surface of the heart at each time step is constructed, based on a set of border delineated magnetic resonance imaging (MRI) data of the whole cardiac cycle. The key contribution in this work involves a novel reconstruction technique to generate a 4D (i.e., spatial–temporal) model of the heart with 1-to-1 vertex mapping throughout the time frames. The reconstructed 3D model from the first time step is used as a base template model and then deformed to fit the segmented contours from the subsequent time steps. A method to determine a tree-based connectivity relationship is proposed to ensure robust mapping during mesh deformation. The novel feature is the ability to handle intra- and inter-frame 2D topology changes of the contours, which manifests as a series of merging and splitting of contours when the images are viewed either in a spatial or temporal sequence. Our algorithm has been tested on five acquisitions of cardiac MRI and can successfully reconstruct the full 4D heart model in around 30 minutes per subject. The generated 4D heart model conforms very well with the input segmented contours and the mesh element shape is of reasonably good quality. The work is important in the support of downstream computational simulation activities.     

CT based conformal brachytherapy treatment planning

PURPOSE: To introduce the CT based three dimensional (3D) conformal brachytherapy treatment planning for interstitial implants, to compare the conventional X-ray film based planning with the 3D planning from the point of view of reconstruction and dosimetry, to discuss the differences and highlight the advantages. MATERIAL AND METHODS: On 10 patients with breast and 5 with head and neck tumor treated with HDR interstitial implants, following the catheter implantations, CT scans were taken at 5 mm spacing. The images were loaded into the PLATO BPS v14.0 3D planning system for brachytherapy. The contours of the target volume and critical structures were outlined on each slice, the catheter describing points were identified and the anatomical structures and catheter positions were reconstructed in 3D. Having taken into account the target volume, the active lengths were determined in each catheter, and dose optimization on dose points on target was performed. RESULTS: The 3D treatment planning was applied at interstitial breast treatments and head and neck implants. We investigated the dose distribution on axial, reconstructed coronal / sagittal planes and in 3D view with respect to anatomical structures. Dose volume histograms related to the target volume and critical structures were used for quantitative assessment of the plans. We found that the conformal dose distribution might result in increase of dose inhomogeneity within the target volume. CONCLUSIONS: The three dimensional brachytherapy treatment planning can be introduced into the clinical practice under proper technical conditions. A tradeoff between conformality and dose homogeneity results in an acceptable dose plan. The dose inhomogeneity can be decreased with the use of CT scans taken before the implantation. The guidelines and quantitative parameters describing the dose distribution, which can be used for determining the optimal dose distribution in clinical point of view, are still waiting to be established.     

Underwater photogrammetry for close‐range 3D imaging of dry‐sensitive objects: The case study of cephalopod beaks

• Technical advances in 3D imaging have contributed to quantifying and understanding biological variability and complexity. However, small, dry‐sensitive objects are not easy to reconstruct using common and easily available techniques such as photogrammetry, surface scanning, or micro‐CT scanning. Here, we use cephalopod beaks as an example as their size, thickness, transparency, and dry‐sensitive nature make them particularly challenging. We developed a new, underwater, photogrammetry protocol in order to add these types of biological structures to the panel of photogrammetric possibilities.
• We used a camera with a macrophotography mode in a waterproof housing fixed in a tank with clear water. The beak was painted and fixed on a colored rotating support. Three angles of view, two acquisitions, and around 300 pictures per specimen were taken in order to reconstruct a full 3D model. These models were compared with others obtained with micro‐CT scanning to verify their accuracy.
• The models can be obtained quickly and cheaply compared with micro‐CT scanning and have sufficient precision for quantitative interspecific morphological analyses. Our work shows that underwater photogrammetry is a fast, noninvasive, efficient, and accurate way to reconstruct 3D models of dry‐sensitive objects while conserving their shape. While the reconstruction of the shape is accurate, some internal parts cannot be reconstructed with photogrammetry as they are not visible. In contrast, these structures are visible using reconstructions based on micro‐CT scanning. The mean difference between both methods is very small (10⁻⁵ to 10⁻⁴ mm) and is significantly lower than differences between meshes of different individuals.
• This photogrammetry protocol is portable, easy‐to‐use, fast, and reproducible. Micro‐CT scanning, in contrast, is time‐consuming, expensive, and nonportable. This protocol can be applied to reconstruct the 3D shape of many other dry‐sensitive objects such as shells of shellfish, cartilage, plants, and other chitinous materials.

     

Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri nets

In order to improve our understanding of directly transmitted pathogens within host populations, epidemic models should take into account individual heterogeneities as well as stochastic fluctuations in individual parameters. The associated cost results in an increasing level of complexity of the mathematical models which generally lack consistent formalisms. In this paper, we demonstrate that complex epidemic models could be expressed as colored stochastic Petri nets (CSPN). CSPN is a mathematical tool developed in computer science. The concept is based on the Markov Chain theory and on a standard well codified graphical formalism. This approach presents an alternative to other computer simulation methods since it offers both a theoretical formalism and a graphical representation that facilitate the implementation, the understanding and thus the replication or modification of the model. We explain how common concepts of epidemic models--such as the incidence function--can be easily translated into an individual based point of view in the CSPN formalism. We then illustrate this approach by using the well documented susceptible-infected model with recruitment and death.     

Technical note: Virtual reconstruction of a fragmentary clavicle

We report a procedure for the virtual reconstruction of incomplete human bones applicable to skeletal remains from archaeological excavations or to reconstructive and prosthetic surgery. To test the procedure, we reconstructed a fragmented left clavicle on the basis of the contralateral clavicle. The procedure involved 3‐D laser scanner acquisition of the left clavicle (complete but broken into two parts), the same manually reconstructed bone, and the intact right clavicle, which was mirror‐imaged and used as a reference for the reconstruction of the whole left clavicle. Because it was not possible to recognize homologous anatomical landmarks, on the two reference models (a mirror‐image copy of the right clavicle and the main fragment of the left), we identified three grids with an increasing number of corresponding landmarks, which constituted the framework of the deformation process. The three reconstructed digital models of the clavicle closely approximated the model of the original clavicle. They also showed that an increasing number of landmarks did not significantly improve the reconstructed model. Am J Phys Anthropol 2009. © 2009 Wiley‐Liss, Inc.