Three-dimensional modeling and animation of two carpal bones: a technique

The objectives of this study were to (a). create 3D reconstructions of two carpal bones from single CT data sets and animate these bones with experimental in vitro motion data collected during dynamic loading of the wrist joint, (b). develop a technique to calculate the minimum interbone distance between the two carpal bones, and (c). validate the interbone distance calculation process. This method utilized commercial software to create the animations and an in-house program to interface with three-dimensional CAD software to calculate the minimum distance between the irregular geometries of the bones. This interbone minimum distance provides quantitative information regarding the motion of the bones studied and may help to understand and quantify the effects of ligamentous injury.     

Design of a custom angled abutment for dental implants using computer-aided design and nonlinear finite element analysis

Computer-aided design/computer-aided manufacturing (CAD/CAM) custom abutments have been attracting more and more attention due to their advantages of accuracy fit and esthetic emergence profile. However, the CAD key technology for custom abutments has been seldom studied as well as their biomechanical behavior. This paper explored a novel method to design a CAD/CAM custom angled abutment, evaluated the biomechanical performance of the whole system and compared the difference between the custom and the conventional abutment through 3D nonlinear finite element analysis (FEA). Firstly, the digital data of the dental casts at the healing abutment level was acquired by optical scanner. Thus the position of the healing abutment and the implant can be determined by CAD technology. The custom angled abutment was then designed according to the need of restoration and esthetics with CAD software. The described system can eliminate wax and cast, create an esthetic anatomical emergence profile and provide a satisfactory angle correction. Simulation results indicate that there was no distinct difference in the stress distribution and magnitude of implant-bone interface and screw using the custom or the conventional angled abutment.     

Accuracy and reproducibility of CFD predicted wall shear stress using 3D ultrasound images

Computational fluid dynamics (CFD) flow simulation techniques have the potential to enhance our understanding of how haemodynamic factors are involved in atherosclerosis. Recently, 3D ultrasound has emerged as an alternative to other 3D imaging techniques, such as magnetic resonance angiography (MRA). The method can be used to generate realistic vascular geometry suitable for CFD simulations. In order to assess accuracy and reproducibility of the procedure from image acquisition to reconstruction to CFD simulation, a human carotid artery bifurcation phantom was scanned three times using 3D ultrasound. The geometry was reconstructed and flow simulations were carried out on the three sets as well as on a model generated using computer aided design (CAD) from the geometric information given by the manufacturer. It was found that the three reconstructed sets showed good reproducibility as well as satisfactory quantitative agreement with the CAD model. Analyzing two selected locations probably representing the 'worst cases,' accuracy comparing ultrasound and CAD reconstructed models was estimated to be between 7.2% and 7.7% of the maximum instantaneous WSS and reproducibility comparing the three scans to be between 8.2% and 10.7% of their average maximum.     

An evaluation of the analysis system of video transects used to sample subtidal epibiota

Two popular methods of benthic cover estimation (the point intercept technique with two sets of position points, and digital interactive color segmentation) were compared with an alternative method of digital cover estimation using Bezier curves as a tool for outlining the objects on an images and AutoCAD® software for the final evaluation of abundance. The comparison was done using still video images obtained from two 10-m transects on subtidal rocks off the Rimsky-Korsakov islands in the Sea of Japan (Russia). Ten rectangular sectors (1×0.4 m each) selected randomly within both video transects were analyzed. One-way ANOVA for repeated measurements was used to test the differences between methods. The point intercept technique differed significantly from both methods of digital estimation and had an essential positive bias. The Tukey multiple comparison test revealed the differences among digital estimation methods in the species, which have the complicated color with many contrast spots. The proposed approach using Bezier curves has an advantage over the interactive color segmentation if the objects under selection are lit at different levels or have a contrast coloration or are hidden by canopy organisms. Besides, estimation of cover in the field of AutoCAD® software is more precise and takes less time than that obtained using a scaled grid, available for automatically segmented species. The results showed that digital cover estimation using Bezier curves and AutoCAD® software is a convenient method for analyzing benthic samples at large spatial scales.     

Three-dimensional Biomimetic Technology: Novel Biorubber Creates Defined Micro- and Macro-scale Architectures in Collagen Hydrogels

Tissue scaffolds play a crucial role in the tissue regeneration process. The ideal scaffold must fulfill several requirements such as having proper composition, targeted modulus, and well-defined architectural features. Biomaterials that recapitulate the intrinsic architecture of in vivo tissue are vital for studying diseases as well as to facilitate the regeneration of lost and malformed soft tissue. A novel biofabrication technique was developed which combines state of the art imaging, three-dimensional (3D) printing, and selective enzymatic activity to create a new generation of biomaterials for research and clinical application. The developed material, Bovine Serum Albumin rubber, is reaction injected into a mold that upholds specific geometrical features. This sacrificial material allows the adequate transfer of architectural features to a natural scaffold material. The prototype consists of a 3D collagen scaffold with 4 and 3 mm channels that represent a branched architecture. This paper emphasizes the use of this biofabrication technique for the generation of natural constructs. This protocol utilizes a computer-aided software (CAD) to manufacture a solid mold which will be reaction injected with BSA rubber followed by the enzymatic digestion of the rubber, leaving its architectural features within the scaffold material.     

Quantitative method for in vitro matrigel invasiveness measurement through image analysis software

The determination of cell invasion by matrigel assay is usually evaluated by counting cells able to pass through a porous membrane and attach themselves to the other side, or by an indirect quantification of eluted specific cell staining dye by means of optical density measurement. This paper describes a quantitative analytical imaging approach for determining the invasiveness of tumor cells using a simple method, based on images processing with the public domain software, ImageJ. Images obtained by direct capture are split into the red channel, and the generated image is used to measure the area that cells cover in the picture. To overcome the several disadvantages that classical cell invasion determinations present, we propose this method because it generates more accurate and sensitive determinations, and it could be a reasonable option for improving the quality of the results. The cost-effective alternative method proposed is based on this simple and robust software that is worldwide affordable.     

Development, parallelization, and automation of a gas-inducing milliliter-scale bioreactor for high-throughput bioprocess design (HTBD)

A novel milliliter-scale bioreactor equipped with a gas-inducing impeller was developed with oxygen transfer coefficients as high as in laboratory and industrial stirred-tank bioreactors. The bioreactor reaches oxygen transfer coefficients of >0.4 s(-1). Oxygen transfer coefficients of >0.2 s(-1) can be maintained over a range of 8- to 12-mL reaction volume. A reaction block with integrated heat exchangers was developed for 48-mL-scale bioreactors. The block can be closed with a single gas cover spreading sterile process gas from a central inlet into the headspace of all bioreactors. The gas cover simultaneously acts as a sterile barrier, making the reaction block a stand-alone device that represents an alternative to 48 parallel-operated shake flasks on a much smaller footprint. Process control software was developed to control a liquid-handling system for automated sampling, titration of pH, substrate feeding, and a microtiter plate reader for automated atline pH and atline optical density analytics. The liquid-handling parameters for titration agent, feeding solution, and cell samples were optimized to increase data quality. A simple proportional pH-control algorithm and intermittent titration of pH enabled Escherichia coli growth to a dry cell weight of 20.5 g L(-1) in fed-batch cultivation with air aeration. Growth of E. coli at the milliliter scale (10 mL) was shown to be equivalent to laboratory scale (3 L) with regard to growth rate, mu, and biomass yield, Y(XS).     

Printing Thermoresponsive Reverse Molds for the Creation of Patterned Two-component Hydrogels for 3D Cell Culture

Bioprinting is an emerging technology that has its origins in the rapid prototyping industry. The different printing processes can be divided into contact bioprinting^1-4 (extrusion, dip pen and soft lithography), contactless bioprinting^5-7 (laser forward transfer, ink-jet deposition) and laser based techniques such as two photon photopolymerization⁸. It can be used for many applications such as tissue engineering^9-13, biosensor microfabrication^14-16 and as a tool to answer basic biological questions such as influences of co-culturing of different cell types¹⁷. Unlike common photolithographic or soft-lithographic methods, extrusion bioprinting has the advantage that it does not require a separate mask or stamp. Using CAD software, the design of the structure can quickly be changed and adjusted according to the requirements of the operator. This makes bioprinting more flexible than lithography-based approaches.Here we demonstrate the printing of a sacrificial mold to create a multi-material 3D structure using an array of pillars within a hydrogel as an example. These pillars could represent hollow structures for a vascular network or the tubes within a nerve guide conduit. The material chosen for the sacrificial mold was poloxamer 407, a thermoresponsive polymer with excellent printing properties which is liquid at 4 °C and a solid above its gelation temperature ~20 °C for 24.5% w/v solutions¹⁸. This property allows the poloxamer-based sacrificial mold to be eluted on demand and has advantages over the slow dissolution of a solid material especially for narrow geometries. Poloxamer was printed on microscope glass slides to create the sacrificial mold. Agarose was pipetted into the mold and cooled until gelation. After elution of the poloxamer in ice cold water, the voids in the agarose mold were filled with alginate methacrylate spiked with FITC labeled fibrinogen. The filled voids were then cross-linked with UV and the construct was imaged with an epi-fluorescence microscope.     

Three-dimensional printing: technologies,applications, and limitations in neurosurgery

Three-dimensional (3D) printers are a developing technology penetrating a variety of markets, including the medical sector. Since its introduction to the medical field in the late 1980s, 3D printers have constructed a range of devices, such as dentures, hearing aids, and prosthetics. With the ultimate goals of decreasing healthcare costs and improving patient care and outcomes, neurosurgeons are utilizing this dynamic technology, as well. Digital Imaging and Communication in Medicine (DICOM) can be translated into Stereolithography (STL) files, which are then read and methodically built by 3D Printers. Vessels, tumors, and skulls are just a few of the anatomical structures created in a variety of materials, which enable surgeons to conduct research, educate surgeons in training, and improve pre-operative planning without risk to patients. Due to the infancy of the field and a wide range of technologies with varying advantages and disadvantages, there is currently no standard 3D printing process for patient care and medical research. In an effort to enable clinicians to optimize the use of additive manufacturing (AM) technologies, we outline the most suitable 3D printing models and computer-aided design (CAD) software for 3D printing in neurosurgery, their applications, and the limitations that need to be overcome if 3D printers are to become common practice in the neurosurgical field.     

An Analytical Tool that Quantifies Cellular Morphology Changes from Three-dimensional Fluorescence Images

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for inclusion and exclusion of data points, and computer-aided pattern recognition to support the interpretation and findings of the analysis. It has become increasingly important to be able to measure fluorescence images constructed from three-dimensional (3D) datasets in order to be able to capture the complexity of cellular dynamics and understand the basis of cellular plasticity within biological systems. Sophisticated microscopy instruments have permitted the visualization of 3D fluorescence images through the acquisition of multispectral fluorescence images and powerful analytical software that reconstructs the images from confocal stacks that then provide a 3D representation of the collected 2D images. Advanced design-based stereology methods have progressed from the approximation and assumptions of the original model-based stereology¹ even in complex tissue sections². Despite these scientific advances in microscopy, a need remains for an automated analytic method that fully exploits the intrinsic 3D data to allow for the analysis and quantification of the complex changes in cell morphology, protein localization and receptor trafficking. Current techniques available to quantify fluorescence images include Meta-Morph (Molecular Devices, Sunnyvale, CA) and Image J (NIH) which provide manual analysis. Imaris (Andor Technology, Belfast, Northern Ireland) software provides the feature MeasurementPro, which allows the manual creation of measurement points that can be placed in a volume image or drawn on a series of 2D slices to create a 3D object. This method is useful for single-click point measurements to measure a line distance between two objects or to create a polygon that encloses a region of interest, but it is difficult to apply to complex cellular network structures. Filament Tracer (Andor) allows automatic detection of the 3D neuronal filament-like however, this module has been developed to measure defined structures such as neurons, which are comprised of dendrites, axons and spines (tree-like structure). This module has been ingeniously utilized to make morphological measurements to non-neuronal cells³, however, the output data provide information of an extended cellular network by using a software that depends on a defined cell shape rather than being an amorphous-shaped cellular model. To overcome the issue of analyzing amorphous-shaped cells and making the software more suitable to a biological application, Imaris developed Imaris Cell. This was a scientific project with the Eidgenössische Technische Hochschule, which has been developed to calculate the relationship between cells and organelles. While the software enables the detection of biological constraints, by forcing one nucleus per cell and using cell membranes to segment cells, it cannot be utilized to analyze fluorescence data that are not continuous because ideally it builds cell surface without void spaces. To our knowledge, at present no user-modifiable automated approach that provides morphometric information from 3D fluorescence images has been developed that achieves cellular spatial information of an undefined shape (Figure 1). We have developed an analytical platform using the Imaris core software module and Imaris XT interfaced to MATLAB (Mat Works, Inc.). These tools allow the 3D measurement of cells without a pre-defined shape and with inconsistent fluorescence network components. Furthermore, this method will allow researchers who have extended expertise in biological systems, but not familiarity to computer applications, to perform quantification of morphological changes in cell dynamics.     

Importance of closed landfills as green space in urbanized areas: ecological assessment using carabid beetles

In a closed landfill, we investigated the diversity and ecological characters of carabid beetles to understand the ecological importance of closed landfills that have the potential as a multi-functional habitat for improving biodiversity in urbanized areas. In addition, we studied the influence of environmental factors (vegetation structure, soil) on distribution and diversity of carabid beetles. A total of 92,495 individuals representing 15 carabid species were collected from the closed landfill. Although the species richness of carabid beetles recorded in the closed landfill was not higher than the other green spaces in the city, the closed landfill could sufficiently provides a stable habitat as a semi-natural area for carabid beetles. Soil pH, Na, and tall grass plant cover influenced carabid assemblage in the closed landfill. However, other environmental variables (e.g., K⁺, Na⁺, Mg²⁺, bare land cover, weedy cover, and tree cover) were not correlated with carabid species composition. It is implied that in the closed landfill, which is a highly modified engineered environment, other abiotic environmental (e.g., drainage, soil texture, leachate, and landscape context, etc.) and biotic factors (e.g., intra- and interspecific competition) may have affected carabid assemblage. Although artificial drainages are essential facilities for landfill management, they are a critical factor that affects the species inhabiting the landfill. However, carabid beetles seemed to randomly fall into the artificial drainage. For successful management of closed landfills, it is very important that minimize the intervention and that develop the ecological sensitively management method.     

A new registration method for three-dimensional knee nearthrosis model using two X-ray images

The purpose of this study is to develop a method to analyse the pose of the knee nearthrosis mounted and to automate the registration procedure for easy use in clinical applications. The proposed registration method is essentially a model-based method, in which the CAD model is acquired by reverse engineering. The CAD model is converted into a two-dimensional (2D) image by a rendering technique, and the compatibility of the X-ray image and the image of the CAD model is investigated. To avoid the optimisation of six unknown parameters with respect to the relative pose between the condyle and tibial models, a 2D coordinate system is set on each component of the X-ray images. A 3D coordinate system is also set on each of the two nearthrosis components. With such a setup, there is only one unknown rotational angle on each component, which is determined by an optimum algorithm in accordance with the contour error between the X-ray image and the image of the CAD model. Extensive computer simulation and in vitro experiments using real X-ray images have been implemented to investigate the feasibility of the proposed registration method.     

Verifying Three-Dimensional Skull Model Reconstruction Using Cranial Index of Symmetry

Background

Difficulty exists in scalp adaptation for cranioplasty with customized computer-assisted design/manufacturing (CAD/CAM) implant in situations of excessive wound tension and sub-cranioplasty dead space. To solve this clinical problem, the CAD/CAM technique should include algorithms to reconstruct a depressed contour to cover the skull defect. Satisfactory CAM-derived alloplastic implants are based on highly accurate three-dimensional (3-D) CAD modeling. Thus, it is quite important to establish a symmetrically regular CAD/CAM reconstruction prior to depressing the contour. The purpose of this study is to verify the aesthetic outcomes of CAD models with regular contours using cranial index of symmetry (CIS).

Materials and methods

From January 2011 to June 2012, decompressive craniectomy (DC) was performed for 15 consecutive patients in our institute. 3-D CAD models of skull defects were reconstructed using commercial software. These models were checked in terms of symmetry by CIS scores.

Results

CIS scores of CAD reconstructions were 99.24±0.004% (range 98.47–99.84). CIS scores of these CAD models were statistically significantly greater than 95%, identical to 99.5%, but lower than 99.6% (p<0.001, p = 0.064, p = 0.021 respectively, Wilcoxon matched pairs signed rank test). These data evidenced the highly accurate symmetry of these CAD models with regular contours.

Conclusions

CIS calculation is beneficial to assess aesthetic outcomes of CAD-reconstructed skulls in terms of cranial symmetry. This enables further accurate CAD models and CAM cranial implants with depressed contours, which are essential in patients with difficult scalp adaptation.     

ConfocalVR: Immersive Visualization for Confocal Microscopy

ConfocalVR is a virtual reality (VR) application created to improve the ability of researchers to study the complexity of cell architecture. Confocal microscopes take pictures of fluorescently labeled proteins or molecules at different focal planes to create a stack of two-dimensional images throughout the specimen. Current software applications reconstruct the three-dimensional (3D) image and render it as a two-dimensional projection onto a computer screen where users need to rotate the image to expose the full 3D structure. This process is mentally taxing, breaks down if you stop the rotation, and does not take advantage of the eye's full field of view. ConfocalVR exploits consumer-grade VR systems to fully immerse the user in the 3D cellular image. In this virtual environment, the user can (1) adjust image viewing parameters without leaving the virtual space, (2) reach out and grab the image to quickly rotate and scale the image to focus on key features, and (3) interact with other users in a shared virtual space enabling real-time collaborative exploration and discussion. We found that immersive VR technology allows the user to rapidly understand cellular architecture and protein or molecule distribution. We note that it is impossible to understand the value of immersive visualization without experiencing it first hand, so we encourage readers to get access to a VR system, download this software, and evaluate it for yourself. The ConfocalVR software is available for download at http://www.confocalvr.com, and is free for nonprofits.     

Simplified Generation of Biomedical 3D Surface Model Data for Embedding into 3D Portable Document Format (PDF) Files for Publication and Education

The usefulness of the 3D Portable Document Format (PDF) for clinical, educational, and research purposes has recently been shown. However, the lack of a simple tool for converting biomedical data into the model data in the necessary Universal 3D (U3D) file format is a drawback for the broad acceptance of this new technology. A new module for the image processing and rapid prototyping framework MeVisLab does not only provide a platform-independent possibility to create surface meshes out of biomedical/DICOM and other data and to export them into U3D – it also lets the user add meta data to these meshes to predefine colors and names that can be processed by a PDF authoring software while generating 3D PDF files. Furthermore, the source code of the respective module is available and well documented so that it can easily be modified for own purposes.     

A perspective of present approaches to EEG analyses performed with intention to find seizure predictors

In the late 90-s of the previous century the American Society of Epileptologists defined a priority for research as "possibilities to predict a seizure, early determinate and reduct". A method, which would allow the prediction of epileptical seizure's onset based on the EEG data registered with the patient with an epilepsy disease, would also allow implementing the new approach to treatment. If it became reliably possible to predict a moment of seizure, based on the EEG dynamics, one could create an automated closed loop system to prevent a seizure. In the article a number of works regarding this subject were reviewed. Also own results were discussed which were derived from analyses of brain electrical activity of rats with absence epilepsy and with the use of own developed software. Moreover specifics of absence initiation and course were discussed, as well as formation mechanism of thalamus-cortical loop, existing abilities of reduction not only absences, but also cognitive and emotional dissociations. Also described results of analyses of the EEG time series, that were derived by computation of correlation dimension with own developed software.     

Computer-aided dental prostheses construction using reverse engineering

The implementation of computer-aided design/computer-aided manufacturing (CAD/CAM) systems with virtual articulators, which take into account the kinematics, constitutes a breakthrough in the construction of customised dental prostheses. This paper presents a multidisciplinary protocol involving CAM techniques to produce dental prostheses. This protocol includes a step-by-step procedure using innovative reverse engineering technologies to transform completely virtual design processes into customised prostheses. A special emphasis is placed on a novel method that permits a virtual location of the models. The complete workflow includes the optical scanning of the patient, the use of reverse engineering software and, if necessary, the use of rapid prototyping to produce CAD temporary prostheses.     

Development of pipette tip gap closure migration assay (s-ARU method) for studying semi-adherent cell lines

This work presents a pipette tip gap closure migration assay prototype tool (semi-adherent relative upsurge—s-ARU—method) to study cell migration or wound healing in semi-adherent cell lines, such as lymph node carcinoma of the prostate (LNCaP). Basically, it consists of a 6-well cover plate modification, where pipette tips with the filter are shortened and fixed vertically to the inner surface of the cover plate, with their heights adjusted to touch the bottom of the well center. This provides a barrier for the inoculated cells to grow on, creating a cell-free gap. Such a uniform gap formed can be used to study migration assay for both adherent as well as semi-adherent cells. After performing time studies, effective measurement of gap area can be carried out conveniently through image analysis software. Here, the prototype was tested for LNCaP cells, treated with testosterone and flutamide as well as with bacteriophages T4 and M13. A scratch assay using PC3 adherent cells was also performed for comparison. It was observed that s-ARU method is suitable for studying LNCaP cells migration assay, as observed from our results with testosterone, flutamide, and bacteriophages (T4 and M13). Our method is a low-cost handmade prototype, which can be an alternative to the other migration assay protocol(s) for both adherent and semi-adherent cell cultures in oncological research along with other biological research applications.     

A new model-based RSA method validated using CAD models and models from reversed engineering

Roentgen stereophotogrammetric analysis (RSA) was developed to measure micromotion of an orthopaedic implant with respect to its surrounding bone. A disadvantage of conventional RSA is that it requires the implant to be marked with tantalum beads. This disadvantage can potentially be resolved with model-based RSA, whereby a 3D model of the implant is used for matching with the actual images and the assessment of position and rotation of the implant. In this study, a model-based RSA algorithm is presented and validated in phantom experiments. To investigate the influence of the accuracy of the implant models that were used for model-based RSA, we studied both computer aided design (CAD) models as well as models obtained by means of reversed engineering (RE) of the actual implant. The results demonstrate that the RE models provide more accurate results than the CAD models. If these RE models are derived from the very same implant, it is possible to achieve a maximum standard deviation of the error in the migration calculation of 0.06 mm for translations in x- and y-direction and 0.14 mm for the out of plane z-direction, respectively. For rotations about the y-axis, the standard deviation was about 0.1 degrees and for rotations about the x- and z-axis 0.05 degrees. Studies with clinical RSA-radiographs must prove that these results can also be reached in a clinical setting, making model-based RSA a possible alternative for marker-based RSA.