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All Topics > Biocomputational Focus > Visualization |
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13 projects in result set.
Practical Annotation and Exchange of Virtual Anatomy
- Representation of anatomy in a virtual form is at the heart of clinical decision making, biomedical research, and medical training. Virtual anatomy is not limited to description of geometry but also requires appropriate and efficient labeling of regions - to define spatial relationships and interactions between anatomical objects; effective strategies for pointwise operations - to define local properties, biological or otherwise; and support for diverse data formats and standards - to facilitate exchange between clinicians, scientists, engineers, and the general public. Development of aeva, a free and open source software package (library, user interfaces, extensions) capable of automated and interactive operations for virtual anatomy annotation and exchange, is in response to these currently unmet requirements. This site serves for aeva outreach, including dissemination the software and use cases. The use cases drive design and testing of aeva features and demonstrate various workflows that rely on virtual anatomy.
aeva downloads:
Downloads (https://simtk.org/frs/?group_id=1767)
Kitware data repository (https://data.kitware.com/#folder/5e7a4690af2e2eed356a17f2)
aeva documentation:
Guides and tutorials (https://aeva.readthedocs.io)
aeva videos:
Short instructions (https://www.youtube.com/channel/UCubfUe40LXvBs86UyKci0Fw)
aeva source code:
Kitware source code repository (https://gitlab.kitware.com/aeva)
aeva forum:
Forums (https://simtk.org/plugins/phpBB/indexPhpbb.php?group_id=1767 ) | |
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Registered: 2019-08-28 01:27 |
BlurLab -- 3D Microscopy Simulation Package
- BlurLab is an easy to use platform for generating simulated fluorescence microscopy data for use in mechanistic modeling visualization, image comparison, and hypothesis testing. The software accepts the 3D positions, intensities and labels of fluorescing objects that are produced by an underlying mechanistic model and transforms them into high quality simulated images. The program includes full 3D convolution with realistic (or even measured) point spread functions; inclusion of thermal, shot and custom noise spectra; simulations of mean and fully stochastic photobleacing; the ability to view scenes in wide-field and TIRF, and perform Z-slicing; and the ability to simulate FRAP experiments.
The software provides a platform for adjusting and saving these simulated images, as well as a number of helpful, semi-automated features to make image simulation easy and less error prone. | |
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Activity Percentile: 77.27 Registered: 2011-08-05 01:17 |
Fiber Tractography for Finite-Element Modeling of Transversely Isotropic Tissues
- This project demonstrates the process for fiber tractography of complex biological tissues with transverse isotropy, such as tendon and muscle. This is important for finite element studies of these tissues, as the fiber direction must be specified in the constitutive model. This project contains code, models, and data that can be used to reproduce the results of our publication on this technique. The supplied instructional videos will enable researchers to easily and efficiently apply this method to a variety of other tissues. The software used in the fiber tractography process and demonstrated in this project is Matlab, Autodesk Inventor (free for educators), and Autodesk Simulation CFD (free for educators). Full demonstrations and process instructions can be found in the 7 videos posted at https://vimeo.com/album/3414604:
Contents:
Chapter 1: Introduction (2:35)
This video introduces the CFD fiber tractography software pipeline
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Chapter 2: Supplementary materials code, models and data (20:21)
This video shows the shared models, code, and data posted online at simtk.org/m3lab_cfd4fea.
Chapter 3: Finite element simulations (5:38)
This video shows finite element simulations using the fiber mapping process.
Chapter 4: Iliacus example walkthrough (21:38)
This video shows the step-by-step process for fiber mapping the iliacus muscle (a hip flexor).
Chapter 5: Bflh example walkthrough (12:09)
This video shows the step-by-step process for fiber mapping the biceps femoris longhead muscle (a hamstring).
Chapter 6: Autodesk Inventor segmentation (9:09)
This video shows how to do segmentation of medical images in Autodesk Inventor in order to simplify the solid model for the CFD and FEA software.
Chapter 7: Curved inlet surfaces (6:28)
This video shows how to create curved inlet surfaces for use in Autodesk Simulation CFD. | |
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Activity Percentile: 35.23 Registered: 2015-05-28 18:52 |
3D visualization of spinal kinematics collected in 2D using Quantitative Fluoros
- 3D visualization of spinal kinematics collected in 2D using Quantitative Fluorosopy | |
Activity Percentile: 0.00 Registered: 2015-03-16 16:10 |
Investigating the effects of pelvic floor muscles during pregnancy
- Developing a risk predictive Model about how the pelvic floor muscles change during pregnancy and how they stretch during the delivery in order to identify and discover knowledge about these muscles to avoid damage during delivery. Which damage increases the risk of urinary incontinence or pelvic organ prolapse later in life. | |
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Registered: 2016-11-22 20:54 |
Cell Movement Simulation
- simulation of cell movements | |
Activity Percentile: 0.00 Registered: 2013-11-13 18:02 |
Muscle Fiber Analysis and Visualization with Diffusion Tensor Imaging
- This software allows users to attain functionally pertinent biological information about the fibrous structure of living muscle tissue using Diffusion Tensor Images (DTI). | |
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Activity Percentile: 0.00 Registered: 2006-04-10 22:45 |
Acetaminophen Induced Liver Injury
- The AILI project is a type of In-Silico Liver (ISL) project, which consists of a body of Java code used and reused for exploring hypothetical liver mechanisms. For AILI, the liver mechanisms are those that cause cellular damage, specifically necrosis, because of exposure to acetaminophen. Moreover, the model, a mouse analog, is used for virtual experimentation to explore and explain AILI phenomena, analogous to wet-lab experimentation. A recent addition to this project is studying the disconnect between in vitro and in vivo wet-lab experiments by comparing and contrasting virtual Mouse and Culture Analogs. | |
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Activity Percentile: 0.00 Registered: 2015-05-07 23:25 |
Neurogene: Elucidating apoptotic pathways in brain tumor models
- Genomics has brought many important discoveries and changes into science and medicine. The central dogma of molecular biology where "DNA makes RNA and RNA makes protein" is well established (yet controversial). Watson and Crick had originally proposed a double stranded model of DNA. This served as a useful foundation for further understanding and research. Throughout the years more investigations demonstrated that human evolution was far more complex than originally believed. There was originally a great deal of migration around the world causing some hereditary lineages to become isolated and others to become more robust.
The life cycle of a cell usually begins with division and continues with replication. However, errors in mitosis can cause a cell to undergo apoptosis or form into a tumor. Differentiating between the two final pathways may be critical in helping to guide cells towards a less destructive pathway for the host organism. The critical component has to do with the environment the cell is in. The cell receives information from the outside environment and adapts according to received stimuli.
This project has been conceived to leverage a team based approach for elucidating the underlying apoptotic pathways responsible for tumor lysis and cell death. Combining the current understanding of molecular dynamics, genomics, and contrast imaging agents to discover novel therapeutic targets and further the current understanding of tumor biology within the genomic era. | |
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Registered: 2010-03-17 09:26 |
Simple Immune System Response Agent Based Model
- This is a simple Agent Based Model of the immune response to a hypothetical wound. The model accompanies a Science News for Students article as a supplement to allow readers the opportunity to directly experiment with biological simulation. Adjust the strength of the immune response, the number of bacteria in the wound, the bacterial colony growth rate, and other parameters to view the time course of healing. | |
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Activity Percentile: 0.00 Registered: 2015-07-29 00:16 |
Agent-Based Model of Skeletal Muscle Injury, Inflammation, and Regeneration
- This model simulates the sterile inflammation process that follows a muscle injury (contusion, laceration, etc). The simulation tracks key inflammatory cells (neutrophils and macrophages), as well as their secretions and interactions with native muscle cells (muscle fibers, satellite cells, fibroblasts). | |
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Activity Percentile: 0.00 Registered: 2015-06-25 19:33 |
Specimen specific finite element model to study cruciate mechanics.
- This project will create a model for the anterior and posterior cruciate ligaments (ACL and PCL)from magnetic resonance imaging (MRI) images. This model will allow users to discover the stresses, strains, and displacements of the ACL and PCL that will result from varying forces applied at different positions on the knee. | |
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Registered: 2014-05-27 18:02 |
FEBio: Finite Elements for Biomechanics
- FEBio is a nonlinear finite element solver that is specifically designed for biomechanical applications. It offers modeling scenarios, constitutive models, and boundary conditions that are relevant to many research areas in biomechanics and biophysics. All features can be used together seamlessly, giving the user a powerful tool for solving 3D problems in computational biomechanics. The software is open-source, and pre-compiled executables for Windows, Mac OS X and Linux platforms are available.
Current modeling capabilities include:
* Large deformation quasi-static and dynamic structural mechanics analysis.
* Modeling of complex structures that contain a combination of deformable and rigid parts.
* Multiphasic modeling, where the solvent can contain any number of solutes that may undergo chemical reactions.
* Fluid mechanics analysis, both steady-state and transient
* Fluid-solid interaction (FSI), which combines the powerful solid and fluid solvers.
FEBio also supports a plugin framework that can be used to easily develop new features for FEBio, including new constitutive models, boundary conditions, and even entire new physics solvers.
For more information check out the FEBio website at http://www.febio.org | |
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Registered: 2007-09-14 16:08 |