scholarly journals Towards an open-source pipeline for patient-specific neurosurgery simulation

2011 ◽  
Author(s):  
Andinet Enquobahrie ◽  
Michel Audette ◽  
Huai-ping Lee
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Significant Proportion ◽  
Patient Specific ◽  
Surgery Simulation ◽  
Software Pipeline ◽  
Simulation Based ◽  
Two Parameters ◽  
Surgery Simulator ◽  
Novice Surgeons

Surgery simulation is a technology based on interactive biomechanics as well as haptic and visual rendering for training novice surgeons. Another important component of a surgery simulator is the representation of a patient’s anatomy in terms of simple shapes, typically triangles and tetrahedra, coinciding with relevant tissues, whose manipulation, cutting and resection is simulated. While this technology has so far emphasized generic simulators, increasingly researchers are emphasizing models that derive from the images of patients whose pathology collectively are predictive of a significant proportion of the future caseload of surgeons. In addition, our philosophy of producing patient-specific neurosurgery simulators is to organize the architecture in terms of two parameters: the choice of approach- pterional, trans-nasal, frontal and so on, and the nature of the pathology, which in turn determines the specific nature of the treatment and choice of tools. This paper describes on-going work on the refinement of an open-source software pipeline for producing patient-specific neurosurgery simulation, based on segmentation tools such as those available in Slicer and BrainVisa, surface and volume meshing, such as public VTK-based tools and Tetgen respectively, and the SOFA simulation platform. Practical requirements of the various components of the pipeline, such as resolution control and fidelity of surface and volume meshing, and interactive nonlinear mechanics in the biomechanics engine, are discussed.

scholarly journals Integrated multi-modality image-guided navigation for neurosurgery: open-source software platform using state-of-the-art clinical hardware

2021 ◽  
Author(s):  
Jonathan Shapey ◽  
Thomas Dowrick ◽  
Rémi Delaunay ◽  
Eleanor C. Mackle ◽  
Stephen Thompson ◽  
...  
Keyword(s):  
Skull Base ◽  
Open Source ◽  
Open Source Software ◽  
Skull Base Surgery ◽  
Patient Specific ◽  
Software Platform ◽  
Image Guided ◽  
Phantom Model ◽  
Technical Requirements ◽  
Navigated Ultrasound

Abstract Purpose Image-guided surgery (IGS) is an integral part of modern neuro-oncology surgery. Navigated ultrasound provides the surgeon with reconstructed views of ultrasound data, but no commercial system presently permits its integration with other essential non-imaging-based intraoperative monitoring modalities such as intraoperative neuromonitoring. Such a system would be particularly useful in skull base neurosurgery. Methods We established functional and technical requirements of an integrated multi-modality IGS system tailored for skull base surgery with the ability to incorporate: (1) preoperative MRI data and associated 3D volume reconstructions, (2) real-time intraoperative neurophysiological data and (3) live reconstructed 3D ultrasound. We created an open-source software platform to integrate with readily available commercial hardware. We tested the accuracy of the system’s ultrasound navigation and reconstruction using a polyvinyl alcohol phantom model and simulated the use of the complete navigation system in a clinical operating room using a patient-specific phantom model. Results Experimental validation of the system’s navigated ultrasound component demonstrated accuracy of $$<4.5\,\hbox {mm}$$ < 4.5 mm and a frame rate of 25 frames per second. Clinical simulation confirmed that system assembly was straightforward, could be achieved in a clinically acceptable time of $$<15\,\hbox {min}$$ < 15 min and performed with a clinically acceptable level of accuracy. Conclusion We present an integrated open-source research platform for multi-modality IGS. The present prototype system was tailored for neurosurgery and met all minimum design requirements focused on skull base surgery. Future work aims to optimise the system further by addressing the remaining target requirements.

scholarly journals PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Mohammadreza Yaghoobi ◽  
Krzysztof S. Stopka ◽  
Aaditya Lakshmanan ◽  
Veera Sundararaghavan ◽  
John E. Allison ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Metals And Alloys ◽  
Analysis Tool ◽  
Computational Framework ◽  
Crystal Plasticity Finite Element ◽  
Polycrystalline Metals ◽  
Simulation Based ◽  
Open Source Framework

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

scholarly journals The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

2019 ◽  
Author(s):  
H. Soon Gweon ◽  
Liam P. Shaw ◽  
Jeremy Swann ◽  
Nicola De Maio ◽  
Manal AbuOun ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
Open Source Software ◽  
River Sediment ◽  
Taxonomic Composition ◽  
Sequencing Depth ◽  
Gene Content ◽  
Metagenomic Data ◽  
Software Pipeline ◽  
Shotgun Metagenomics

ABSTRACTBackgroundShotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (∼200 million reads per sample). Alongside this, we cultured single-colony isolates ofEnterobacteriaceaefrom the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, ‘ResPipe’.ResultsTaxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve <1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike ofThermus thermophilusDNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment.ConclusionsSequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available (https://gitlab.com/hsgweon/ResPipe).

scholarly journals The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
H. Soon Gweon ◽  
◽  
Liam P. Shaw ◽  
Jeremy Swann ◽  
Nicola De Maio ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
Open Source Software ◽  
River Sediment ◽  
Taxonomic Composition ◽  
Sequencing Depth ◽  
Gene Content ◽  
Metagenomic Data ◽  
Software Pipeline ◽  
Shotgun Metagenomics

Abstract Background Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, ‘ResPipe’. Results Taxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve < 1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike of Thermus thermophilus DNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment. Conclusions Sequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available (https://gitlab.com/hsgweon/ResPipe).

scholarly journals Vascular flow simulations using SimVascular and OpenFOAM

2021 ◽  
Author(s):  
Swetha Yogeswaran ◽  
Fei Liu
Keyword(s):  
Fluid Dynamics ◽  
Blood Flow ◽  
Open Source ◽  
Open Source Software ◽  
Flow Analysis ◽  
Coarctation Of The Aorta ◽  
Patient Specific ◽  
Specific Information ◽  
Imaging Data ◽  
Set Up

AbstractApplications of computational fluid dynamics (CFD) techniques to aid in the diagnosis and treatment of cardiovascular disease have entered the research domain in recent years, due to their ability to provide valuable patient-specific information without risks associated with highly invasive procedures. SimVascular [1] [2] is an open-source software which allows streamlined processing and CFD blood flow analysis of medical imaging data. OpenFOAM [3] is a proven open-source software which allows for versatile modeling of various fluid dynamics phenomena. In this study, both SimVascular and OpenFOAM simulations are set up with identical computational mesh, similar numerical schemes, boundary conditions, and material properties, to model blood flow in the coronary artery of a 10 year old patient with Coarctation of the Aorta (CoA) who underwent end-to-side anastomosis. Difference in the flow fields such as flow rate, pressure, vorticity, and wall shear stress between SimVascular and OpenFOAM are analyzed. Similar results are obtained in both simulations up to a certain model time, before the results become drastically different. Both the similarities and differences are documented and discussed.

BIOMODELLING OF CRANIO-MAXILLOFACIAL IMPLANT APPLYING OPEN SOURCE SOFTWARE

2015 ◽  
Vol 76 (7) ◽  
Author(s):  
Johari Yap Abdullah ◽  
Zainul Ahmad Rajion ◽  
Marzuki Omar
Keyword(s):  
Additive Manufacturing ◽  
Open Source ◽  
Open Source Software ◽  
Computer Modelling ◽  
3D Models ◽  
Physical Models ◽  
Implant Design ◽  
Patient Specific ◽  
Anatomical Structures ◽  
Computer Aided

Advances in craniofacial medical imaging has allowed the 3D reconstruction of anatomical structures for medical applications, including the design of patient specific implants based on computer-aided design and computer-aided manufacturing (CAD/CAM) platforms. This technology has provided new possibilities to visualize complex medical data through generation of 3–dimensional (3D) physical models via additive manufacturing that can be eventually utilised to assist in diagnosis, surgical planning, implant design, and patient management. Although the study on the construction of cranio-maxillofacial implant based on computer modelling and advanced biomaterial are growing rapidly from other parts of the world, however, in Malaysia is scanty, especially with open source application. For this reason, it leads us to embark in a study to produce a potential locally cranio-maxillofacial implant with equivalent standard as compared to the commercially available product applying open source software. As part of four sub-projects of USM Research University Team (RUT) project, the authors had investigated and applied open source software to perform image processing of CT data, to segment the region of interest of anatomical structures, to create virtual 3D models, and finally to convert the virtual 3D models to a format that compatible for additive manufacturing platform. Further research is ongoing to investigate on designing the cranio-maxillofacial implant using open source CAD software using suitable biomaterial.  

scholarly journals Real-Time Smoke and Bleeding Simulation in Virtual Surgery

2006 ◽  
Author(s):  
Stefan Daenzer ◽  
Kevin Montgomery ◽  
Ruediger Dillmann ◽  
Roland Unterhinninghofen
Keyword(s):  
Minimally Invasive Surgery ◽  
Soft Tissue ◽  
Minimally Invasive ◽  
Open Source ◽  
Real Time ◽  
Invasive Surgery ◽  
Collision Detection ◽  
Virtual Surgery ◽  
Surgery Simulation ◽  
Surgery Simulator

We describe the implementation of smoke and bleeding simulation in the open source surgery simulator SPRING , which is particularly targeted for minimally invasive surgery simulation. Many smoke and bleeding simulations offer high physical and visual accuracy, but the underlaying models are to complex to run in real-time while performing soft-tissue simulation, collision detection and haptic device support at the same time. Our algorithms are based on simple models, that allow the surgery simulation to run in real-time.

A patient-specific numerical model of the ankle joint for the analysis of contact pressure distribution

2020 ◽  
Vol 234 (9) ◽  
pp. 909-920
Author(s):  
Laxmi Muralidharan ◽  
Philip Cardiff ◽  
Karen Fitzgerald ◽  
Robert Flavin ◽  
Alojz Ivanković
Keyword(s):  
Numerical Model ◽  
Open Source ◽  
Ankle Joint ◽  
Open Source Software ◽  
Contact Area ◽  
Material Properties ◽  
Stance Phase ◽  
Gait Cycle ◽  
Material Model ◽  
Patient Specific

A patient-specific numerical model of the ankle joint has been developed using open-source software with realistic material properties that mimics the physiological movement of the foot during the stance phase of the gait cycle. The patient-specific ankle geometry has been segmented as a castellated surface using 3DSlicer from the computed tomography image scans of a subject with no congenital or acquired pathology; subsequently, the bones are smoothed, and cartilage is included as a uniform thickness extruded layer. A high-resolution Cartesian mesh has been generated using cfMesh. The material properties are assigned in the model based on the CT image Hounsfield intensities and compared to a sandwich-based material model. Gait data of the same subject was obtained and used to relatively position the tibia, talus, and calcaneus bones in the model. The stance phase of the gait cycle is simulated using a cell-centred finite-volume method implemented in open-source software OpenFOAM. The predicted peak contact pressures occur in the range of 4.85–5.53 MPa with average pressures in the range of 1.56–1.95 MPa, and the contact area ranges between 429 and 707.8 mm2 for the entire stance phase with the mid-stance phase predicting the maximum contact area. These predictions are in agreement with results from the literature. The effect of arthritis on the contact characteristics of the ankle joint has also been examined. A concentrated increase in pressure was predicted that could be manifested as pain, thereby leading to reduced motion in the ankle. The model, with continued development, has the capability to understand the effect of joint degradation and furthermore, could help provide a tool to predict the efficiency of therapeutic surgical procedures as well as guide the development of next generation ankle prostheses. The work would be made available in the University College Dublin depository ( https://github.com/laxmimurali/anklejoint ) as well as research gate once the article has been published.

Vascular flow simulations using SimVascular and OpenFOAM (Preprint)

2021 ◽  
Author(s):  
Swetha Yogeswaran ◽  
Fei Liu
Keyword(s):  
Fluid Dynamics ◽  
Blood Flow ◽  
Open Source ◽  
Open Source Software ◽  
Flow Analysis ◽  
Coarctation Of The Aorta ◽  
Patient Specific ◽  
Specific Information ◽  
Imaging Data ◽  
Set Up

UNSTRUCTURED Applications of computational fluid dynamics (CFD) techniques to aid in the diagnosis and treatment of cardiovascular disease have entered the research domain in recent years, due to their ability to provide valuable patient-specific information without risks associated with highly invasive procedures. SimVascular is an open-source software which allows streamlined processing and CFD blood flow analysis of medical imaging data. OpenFOAM is a proven open-source software which allows for versatile modeling of various fluid dynamics phenomena. In this study, both SimVascular and OpenFOAM simulations are set up with identical computational mesh, similar numerical schemes, boundary conditions, and material properties, to model blood flow in the coronary artery of a 10 year old patient with Coarctation of the Aorta (CoA) who underwent end-to-side anastomosis. Difference in the flow fields such as flow rate, pressure, vorticity, and wall shear stress between SimVascular and OpenFOAM are analyzed. Similar results are obtained in both simulations up to a certain model time, before the results become drastically different. Both the similarities and differences are documented and discussed.

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