scholarly journals A Re-Engineered Software Interface and Workflow for the Open-Source SimVascular Cardiovascular Modeling Package

2018 ◽  
Vol 140 (2) ◽  
Author(s):  
Hongzhi Lan ◽  
Adam Updegrove ◽  
Nathan M. Wilson ◽  
Gabriel D. Maher ◽  
Shawn C. Shadden ◽  
...  
Keyword(s):  
Open Source ◽  
Computer Aided Design ◽  
Three Dimensional ◽  
User Interaction ◽  
Solid Modeling ◽  
Patient Specific ◽  
Cardiovascular Modeling ◽  
Software Interface ◽  
Open Source Software Package ◽  
3D Solid

Patient-specific simulation plays an important role in cardiovascular disease research, diagnosis, surgical planning and medical device design, as well as education in cardiovascular biomechanics. simvascular is an open-source software package encompassing an entire cardiovascular modeling and simulation pipeline from image segmentation, three-dimensional (3D) solid modeling, and mesh generation, to patient-specific simulation and analysis. SimVascular is widely used for cardiovascular basic science and clinical research as well as education, following increased adoption by users and development of a GATEWAY web portal to facilitate educational access. Initial efforts of the project focused on replacing commercial packages with open-source alternatives and adding increased functionality for multiscale modeling, fluid–structure interaction (FSI), and solid modeling operations. In this paper, we introduce a major SimVascular (SV) release that includes a new graphical user interface (GUI) designed to improve user experience. Additional improvements include enhanced data/project management, interactive tools to facilitate user interaction, new boundary condition (BC) functionality, plug-in mechanism to increase modularity, a new 3D segmentation tool, and new computer-aided design (CAD)-based solid modeling capabilities. Here, we focus on major changes to the software platform and outline features added in this new release. We also briefly describe our recent experiences using SimVascular in the classroom for bioengineering education.

scholarly journals Improved technique of personalised surgical guides generation for mandibular free flap reconstruction using an open-source tool

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Luka Šimić ◽  
Vjekoslav Kopačin ◽  
Ivan Mumlek ◽  
Josip Butković ◽  
Vedran Zubčić
Keyword(s):  
Open Source ◽  
Computer Aided Design ◽  
Three Dimensional ◽  
Alternative Methods ◽  
Patient Treatment ◽  
3D Cad ◽  
Surgical Guides ◽  
Open Source Software Package ◽  
Radiology Technicians ◽  
Improved Technique

AbstractWith advancements in computer systems, computer graphics and medical imaging technologies, clinicians strive for a personalised approach to patient treatment. Therefore, the production of personalised surgical guides is becoming standard. While proprietary software solutions for mandibular reconstruction planning exist, they are often not available due to their high costs. There are multiple alternative methods available, which utilise open-source technologies and free software, but they use advanced three-dimensional (3D) computer-aided design (CAD) concepts. The goal of this article is to provide end-users (surgeons, radiologists, or radiology technicians) with a tool that offers an intuitive interface and a simple workflow. The tool provides only the necessary methods offering a high degree of automation and abstracting the underlying 3D CAD concepts. This is accomplished by providing an add-on (written in Python) for a free and open-source software package Blender.

scholarly journals Accuracy Assessment of Molded, Patient-Specific Polymethylmethacrylate Craniofacial Implants Compared to Their 3D Printed Originals

2020 ◽  
Vol 9 (3) ◽  
pp. 832 ◽  
Author(s):  
Dave Chamo ◽  
Bilal Msallem ◽  
Neha Sharma ◽  
Soheila Aghlmandi ◽  
Christoph Kunz ◽  
...  
Keyword(s):  
Computer Aided Design ◽  
Accuracy Assessment ◽  
Three Dimensional ◽  
Production Costs ◽  
Patient Specific ◽  
Patient Specific Implants ◽  
3D Printed ◽  
Cost Efficient ◽  
Craniofacial Implants ◽  
Aided Design

The use of patient-specific implants (PSIs) in craniofacial surgery is often limited due to a lack of expertise and/or production costs. Therefore, a simple and cost-efficient template-based fabrication workflow has been developed to overcome these disadvantages. The aim of this study is to assess the accuracy of PSIs made from their original templates. For a representative cranial defect (CRD) and a temporo-orbital defect (TOD), ten PSIs were made from polymethylmethacrylate (PMMA) using computer-aided design (CAD) and three-dimensional (3D) printing technology. These customized implants were measured and compared with their original 3D printed templates. The implants for the CRD revealed a root mean square (RMS) value ranging from 1.128 to 0.469 mm with a median RMS (Q1 to Q3) of 0.574 (0.528 to 0.701) mm. Those for the TOD revealed an RMS value ranging from 1.079 to 0.630 mm with a median RMS (Q1 to Q3) of 0.843 (0.635 to 0.943) mm. This study demonstrates that a highly precise duplication of PSIs can be achieved using this template-molding workflow. Thus, virtually planned implants can be accurately transferred into haptic PSIs. This workflow appears to offer a sophisticated solution for craniofacial reconstruction and continues to prove itself in daily clinical practice.

scholarly journals Main Clinical Use of Additive Manufacturing (Three-Dimensional Printing) in Finland Restricted to the Head and Neck Area in 2016–2017

2019 ◽  
Vol 109 (2) ◽  
pp. 166-173 ◽  
Author(s):  
A.B.V. Pettersson ◽  
M. Salmi ◽  
P. Vallittu ◽  
W. Serlo ◽  
J. Tuomi ◽  
...  
Keyword(s):  
Additive Manufacturing ◽  
Computer Aided Design ◽  
Three Dimensional ◽  
Patient Specific ◽  
Future Research ◽  
Imaging Data ◽  
University Hospitals ◽  
Three Dimensional Printing ◽  
Dimensional Printing ◽  
Head Area

Background and Aims: Additive manufacturing or three-dimensional printing is a novel production methodology for producing patient-specific models, medical aids, tools, and implants. However, the clinical impact of this technology is unknown. In this study, we sought to characterize the clinical adoption of medical additive manufacturing in Finland in 2016–2017. We focused on non-dental usage at university hospitals. Materials and Methods: A questionnaire containing five questions was sent by email to all operative, radiologic, and oncologic departments of all university hospitals in Finland. Respondents who reported extensive use of medical additive manufacturing were contacted with additional, personalized questions. Results: Of the 115 questionnaires sent, 58 received answers. Of the responders, 41% identified as non-users, including all general/gastrointestinal (GI) and vascular surgeons, urologists, and gynecologists; 23% identified as experimenters or previous users; and 36% identified as heavy users. Usage was concentrated around the head area by various specialties (neurosurgical, craniomaxillofacial, ear, nose and throat diseases (ENT), plastic surgery). Applications included repair of cranial vault defects and malformations, surgical oncology, trauma, and cleft palate reconstruction. Some routine usage was also reported in orthopedics. In addition to these patient-specific uses, we identified several off-the-shelf medical components that were produced by additive manufacturing, while some important patient-specific components were produced by traditional methodologies such as milling. Conclusion: During 2016–2017, medical additive manufacturing in Finland was routinely used at university hospitals for several applications in the head area. Outside of this area, usage was much less common. Future research should include all patient-specific products created by a computer-aided design/manufacture workflow from imaging data, instead of concentrating on the production methodology.

scholarly journals Three-Dimensional Printed Molds for Image-Guided Surgical Biopsies: An Open Source Computational Platform

2020 ◽  
pp. 736-748
Author(s):  
Mireia Crispin-Ortuzar ◽  
Marcel Gehrung ◽  
Stephan Ursprung ◽  
Andrew B. Gill ◽  
Anne Y. Warren ◽  
...  
Keyword(s):  
Open Source ◽  
Tumor Heterogeneity ◽  
Spatial Scales ◽  
Three Dimensional ◽  
Patient Specific ◽  
Sampling Location ◽  
Precision Oncology ◽  
Similarity Coefficients ◽  
Tissue Samples ◽  
Manual Intervention

PURPOSE Spatial heterogeneity of tumors is a major challenge in precision oncology. The relationship between molecular and imaging heterogeneity is still poorly understood because it relies on the accurate coregistration of medical images and tissue biopsies. Tumor molds can guide the localization of biopsies, but their creation is time consuming, technologically challenging, and difficult to interface with routine clinical practice. These hurdles have so far hindered the progress in the area of multiscale integration of tumor heterogeneity data. METHODS We have developed an open-source computational framework to automatically produce patient-specific 3-dimensional–printed molds that can be used in the clinical setting. Our approach achieves accurate coregistration of sampling location between tissue and imaging, and integrates seamlessly with clinical, imaging, and pathology workflows. RESULTS We applied our framework to patients with renal cancer undergoing radical nephrectomy. We created personalized molds for 6 patients, obtaining Dice similarity coefficients between imaging and tissue sections ranging from 0.86 to 0.96 for tumor regions and between 0.70 and 0.76 for healthy kidneys. The framework required minimal manual intervention, producing the final mold design in just minutes, while automatically taking into account clinical considerations such as a preference for specific cutting planes. CONCLUSION Our work provides a robust and automated interface between imaging and tissue samples, enabling the development of clinical studies to probe tumor heterogeneity on multiple spatial scales.

scholarly journals Study of Morpho-Geometric Variables to Improve the Diagnosis in Keratoconus with Mild Visual Limitation

Symmetry ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 306 ◽  
Author(s):  
Francisco Cavas-Martínez ◽  
Daniel Fernández-Pacheco ◽  
Francisco Cañavate ◽  
Jose Velázquez-Blázquez ◽  
Jose Bolarín ◽  
...  
Keyword(s):  
Computer Aided Design ◽  
Operating Characteristic ◽  
Three Dimensional ◽  
Patient Specific ◽  
Control Group ◽  
Spatial Profile ◽  
New Methods ◽  
Geometric Variables ◽  
Aided Design

The validation of new methods for the diagnosis of incipient cases of Keratoconus (KC) with mild visual limitation is of great interest in the field of ophthalmology. During the asymmetric progression of the disease, the current diagnostic indexes do not record the geometric decompensation of the corneal curvature nor the variation of the spatial profile that occurs in singular points of the cornea. The purpose of this work is to determine the structural characterization of the asymmetry of the disease by using morpho-geometric parameters in KC eyes with mild visual limitation including using an analysis of a patient-specific virtual model with the aid of computer-aided design (CAD) tools. This comparative study included 80 eyes of patients classified as mild KC according to the degree of visual limitation and a control group of 122 eyes of normal patients. The metric with the highest area under the receiver operating characteristic (ROC) curve was the posterior apex deviation. The most prominent correlation was found between the anterior and posterior deviations of the thinnest point for the mild keratoconic cases. This new custom computational approach provides the clinician with a three-dimensional view of the corneal architecture when the visual loss starts to impair.

scholarly journals Solid Modeling of Geometric Objects in Point Calculus

2021 ◽  
Author(s):  
Evgeniy Konopatskiy ◽  
Andrey Bezditnyi
Keyword(s):  
Solid State ◽  
Computer Aided Design ◽  
Mechanical Engineering ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Analytical Description ◽  
Solid Modeling ◽  
Geometric Objects ◽  
State Models ◽  
Three Dimensional Space

The paper describes an approach to solid modeling of geometric objects in the form of an organized three-parameter set of points in three-dimensional space. The relevance of the research topic is due to the widespread use of solid-state models in various branches of science and technology, mechanical engineering, construction and medicine. Solid-state computer models are currently one of the basic computer graphics tools and an integral part of computer- aided design and calculation systems. It is widely used as one of the control elements of CNC machines and 3D printing, the development of information systems in the design and construction of buildings and structures, finite element calculations of deformed states in aircraft and mechanical engineering, their manufacture in medicine, etc. The choice of point calculus as a mathematical apparatus for the analytical description of solid models of geometric objects is substantiated. Examples of modeling sets of elliptical bodies and toroidal bodies in a simplex of three-dimensional space are given.

scholarly journals Three-dimensional printing of a patient-specific engineered nasal cartilage for augmentative rhinoplasty

2019 ◽  
Vol 10 ◽  
pp. 204173141882479 ◽  
Author(s):  
Hee-Gyeong Yi ◽  
Yeong-Jin Choi ◽  
Jin Woo Jung ◽  
Jinah Jang ◽  
Tae-Ha Song ◽  
...  
Keyword(s):  
Stem Cells ◽  
Computer Aided Design ◽  
Three Dimensional ◽  
Patient Specific ◽  
Adipose Derived Stem Cells ◽  
Three Dimensional Printing ◽  
Nasal Cartilage ◽  
Computer Aided ◽  
Aided Design ◽  
Dimensional Printing

Autologous cartilages or synthetic nasal implants have been utilized in augmentative rhinoplasty to reconstruct the nasal shape for therapeutic and cosmetic purposes. Autologous cartilage is considered to be an ideal graft, but has drawbacks, such as limited cartilage source, requirements of additional surgery for obtaining autologous cartilage, and donor site morbidity. In contrast, synthetic nasal implants are abundantly available but have low biocompatibility than the autologous cartilages. Moreover, the currently used nasal cartilage grafts involve additional reshaping processes, by meticulous manual carving during surgery to fit the diverse nose shape of each patient. The final shapes of the manually tailored implants are highly dependent on the surgeons’ proficiency and often result in patient dissatisfaction and even undesired separation of the implant. This study describes a new process of rhinoplasty, which integrates three-dimensional printing and tissue engineering approaches. We established a serial procedure based on computer-aided design to generate a three-dimensional model of customized nasal implant, and the model was fabricated through three-dimensional printing. An engineered nasal cartilage implant was generated by injecting cartilage-derived hydrogel containing human adipose-derived stem cells into the implant containing the octahedral interior architecture. We observed remarkable expression levels of chondrogenic markers from the human adipose-derived stem cells grown in the engineered nasal cartilage with the cartilage-derived hydrogel. In addition, the engineered nasal cartilage, which was implanted into mouse subcutaneous region, exhibited maintenance of the exquisite shape and structure, and striking formation of the cartilaginous tissues for 12 weeks. We expect that the developed process, which combines computer-aided design, three-dimensional printing, and tissue-derived hydrogel, would be beneficial in generating implants of other types of tissue.

A multi-modal data model for morphological segmentation in 3D dosimetry

2019 ◽  
Author(s):  
Werner Backfrieder
Keyword(s):  
Three Dimensional ◽  
Dose Calculation ◽  
User Interaction ◽  
Image Features ◽  
Whole Body ◽  
Patient Specific ◽  
Clinical Workflow ◽  
Real Patient ◽  
Radio Therapy ◽  
Principal Axes

"Patient specific dosimetry established during the last decade in modern radio-therapy. Usually, tracer kinetics in main compartments of observed metabolism is assessed from anterior and posterior whole body scans. The effective doses for each organ, derived by the MIRD scheme, provide evidence for following radiotherapeutic treatment and helps to meet vital dose limits for critical organs, e.g. kidneys. The calculation of individual dose in a three-dimensional context leads to more accurate dose estimates, as was proven by intensive research, but is still on the cusp to clinical application. In this work, a statistical approach, based on multi-modal image and feature data, is presented, to overcome manual segmentation, the most time consuming step, in 3D based dose calculation. 3D data volumes from a hybrid SPECT study, comprising SPECT and CT data, covering main compartments of metabolism, build the image features of a Gaussian classifier. From prior segmentations organspecific membership maps are derived, and substituted as additional feature into the segmentation procedure. Centroids, eccentricity and principal axes of organ models are registered to a rough thresholded image of the SPECT component, and define membership coefficients of the voxels. The new approach yields accurate results, even with real patient data. The new method needs minimal user interaction during selection of some sample regions, thus showing high potential for implementation in a clinical workflow."

On the Geometric Accuracy of RepRap Open-Source Three-Dimensional Printer

2015 ◽  
Vol 137 (10) ◽  
Author(s):  
Antonio Lanzotti ◽  
Domenico Maria Del Giudice ◽  
Antonio Lepore ◽  
Gabriele Staiano ◽  
Massimo Martorelli
Keyword(s):  
Open Source ◽  
Process Parameters ◽  
Computer Aided Design ◽  
Three Dimensional ◽  
Scientific Data ◽  
Correct Selection ◽  
Geometric Feature ◽  
Main Process ◽  
Geometric Features ◽  
The Impact

In the field of additive manufacturing (AM) processes, there is a significant lack of scientific data on the performance of open-source 3D printers in relation to process parameter values. The purpose of this paper is to assess the impact of the main process parameters on the accuracy of a set of typical geometric features, as obtained with an open-source 3D printer, the RepRap Prusa-Mendel I2. For this purpose, a benchmarking part was set up, composed of elementary shapes, representing a series of different geometric features. By means of a DoE approach, it was possible to assess the effects of two process parameters—layer thickness (Lt) and flow rate (Fr)—on five geometric features: cube, sphere, cylinder, cone, and angled surface. A high resolution Laser Scanner was used to evaluate the variation between the acquired geometric feature and the corresponding 3D computer-aided design (CAD) nominal model. On the basis of experimental results, it was possible to analyze and discuss the main effects of the above-mentioned process parameters on each geometric feature. These results can help RepRap users in the correct selection of process parameters with the aim of improving the quality of prototypes.

scholarly journals SlicerDMRI: Diffusion MRI and Tractography Research Software for Brain Cancer Surgery Planning and Visualization

2020 ◽  
pp. 299-309 ◽  
Author(s):  
Fan Zhang ◽  
Thomas Noh ◽  
Parikshit Juvekar ◽  
Sarah F. Frisken ◽  
Laura Rigolo ◽  
...  
Keyword(s):  
Open Source ◽  
Diffusion Tensor ◽  
Intraoperative Imaging ◽  
Time Integration ◽  
Three Dimensional ◽  
High Grade Glioma ◽  
Patient Specific ◽  
Imaging Data ◽  
3D Slicer ◽  
Research Software

PURPOSE We present SlicerDMRI, an open-source software suite that enables research using diffusion magnetic resonance imaging (dMRI), the only modality that can map the white matter connections of the living human brain. SlicerDMRI enables analysis and visualization of dMRI data and is aimed at the needs of clinical research users. SlicerDMRI is built upon and deeply integrated with 3D Slicer, a National Institutes of Health–supported open-source platform for medical image informatics, image processing, and three-dimensional visualization. Integration with 3D Slicer provides many features of interest to cancer researchers, such as real-time integration with neuronavigation equipment, intraoperative imaging modalities, and multimodal data fusion. One key application of SlicerDMRI is in neurosurgery research, where brain mapping using dMRI can provide patient-specific maps of critical brain connections as well as insight into the tissue microstructure that surrounds brain tumors. PATIENTS AND METHODS In this article, we focus on a demonstration of SlicerDMRI as an informatics tool to enable end-to-end dMRI analyses in two retrospective imaging data sets from patients with high-grade glioma. Analyses demonstrated here include conventional diffusion tensor analysis, advanced multifiber tractography, automated identification of critical fiber tracts, and integration of multimodal imagery with dMRI. RESULTS We illustrate the ability of SlicerDMRI to perform both conventional and advanced dMRI analyses as well as to enable multimodal image analysis and visualization. We provide an overview of the clinical rationale for each analysis along with pointers to the SlicerDMRI tools used in each. CONCLUSION SlicerDMRI provides open-source and clinician-accessible research software tools for dMRI analysis. SlicerDMRI is available for easy automated installation through the 3D Slicer Extension Manager.

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