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SCIRun
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SCIRun is a Problem Solving Environment (PSE), for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as the Power Apps: 
SCIRun 4.0 Release Notes
(4.0 released 10/27/08)
PowerApps
BioTensor
BioFEM
BioImage
These are examples of Power Apps; expansion packages for SCIRun that extend its capabilities for specific applications. They are included automatically when you download SCIRun. (PowerApps 4.0 for Windows, Linux, and Mac OSX now available.)
FusionViewer is included with Fusion.
NIH/NCRR Center for Integrative Biomedical Computing Acknowledgment
SCIRun, Seg3D, map3d, and the data sets provided on this web site are Open Source software projects that are principally funded through the SCI Institute's NIH/NCRR CIBC. [SCIRun License] For us to secure the funding that allows us to continue providing this software, we must have evidence of its utility. Thus we ask users of our software and data to acknowledge us in their publications and inform us of these publications. Please use one of the following acknowledgments and send us references to any publications, presentations, or successful funding applications that make use of the NIH/NCRR CIBC software or data sets we provide:
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SCIRun Citation: [bibtex citation] [Endnote citation] |
BioImage Citation: [bibtex citation] [Endnote citation] |
"This work was made possible in part by software from the NIH/NCRR Center for Integrative Biomedical Computing, P41-RR12553-07."
Video Overviews
The SCIRun Problem Solving environment
BioPSE Simulations: Dataflow and PowerApps
The BioImage PowerApp
The BioTensor PowerApp
"Introduction to SCIRun" class materials
Held at Northeastern University, August 2006
SCIRun Computational Workbench
- Rapid Prototyping
- Module Development Tools
- Extensible:
- Data Import/Export
- Algorithm Integration
Visual Programming
- Computational Steering
- Dataflow Interface
Modelling, Simulation and Visualization
- Model Construction and Manipulation
- Numerical Approximation and Solution of PDE's
- Scalar, Vector, and Tensor Field Visualization
High Level Utilities
- Scene Graph and Widget Libraries
- Math, Geometry, and Field Libraries
Low-Level Utilities
- Threads Management
- Memory Management
- Task Scheduling
SCIRun PowerApps
Historically, one of the major hurdles to SCIRun becoming a tool for the scientist or engineer has been SCIRun's dataflow interface. While visual programming is natural for computer scientists, who are accustomed to writing software and building algorithmic pipelines, it is overly cumbersome for application scientists. Even when a dataflow network implements a specific application (such as the forward bioelectric field simulation network provided with BioPSE and detailed in the BioPSE Tutorial), the user interface (UI) components of the network are presented to the user in separate UI windows, without any semantic context for their settings. Historically, there has not been a way to present the filename entries in their semantic context, for example to indicate that one entry should identify the electrodes input file and the other should identify the finite element mesh file.
With the 1.20 release of BioPSE/SCIRun, PowerApps were introduced. A PowerApp is a customized interface built atop a dataflow application network. The dataflow network controls the execution and synchronization of the modules that comprise the application, but the generic user interface windows are replaced with entries that are placed in the context of a single application-specific interface window.
PowerApps replace the multitude of generic dataflow user interface (UI) windows with a single customized interface. The most important controls from the dataflow interface are linked to contextually labeled variables on the PowerApp UI, while the other dataflow variables are assigned appropriate defaults, reducing the visual complexity and generic labels of the dataflow UI windows. the UI components are organized into logical groups and assists the user in smoothly progressing through the stages of the application.
There are currently four PowerApps available: BioFEM (for finite element problems); BioTensor (for post-processing and visualization of DWI MRI data); BioImage (for the processing and visualization of 3-dimensional data); and FusionViewer (for visualizing 3D scalar and vector magnetic fusion data).
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BioTensor
BioTensor is a program that processes and visualizes diffusion tensor images. It can read diffusion weighted images (DWIs), perform correction for a common class of distortions in echo-planar imaging, estimate tensors from DWIs, and visualize the diffusion tensor field. BioTensor's functionality is easily extended. Future versions will have expanded capabilities based on contributions from external collaborators and internal development.
Diffusion weighted imaging uses the diffusion of water molecules to probe the directional micro-structure of living tissue. A single diffusion weighted image generally measures diffusivity of water molecules along a particular direction. The amount of diffusion along a direction is detected by destructive interference of different phase signatures created by the magnetic gradient. A large set of DWIs along carefully chosen gradient directions permits estimation of a diffusion tensor that models the relationship between direction and diffusivity. The BioTensor application generates "diffusion tensor images" (DTIs) from DWIs. DTIs are three-dimensional fields of tensor values.
BioTensor Tutorial
BioFEM
BioFEM is a SCIRun PowerApp that computes the electric field in a volume produced by a set of dipoles. BioFEM computes a solution to the bioelectric field forward problem. BioFEM also computes voltage values at electrode positions, which can be compared with values recorded via ECG or EKG.
BioFEM Tutorial
BioImage
BioImage is a SCIRun PowerApp for processing and visualizing medical image volumes. With BioImage, users can directly load a variety of native data formats (e.g. DICOM, Analyze, VFF, NRRD, PICT) and can then apply processing algorithms to specify and enhance regions of interest within the volume (e.g. cropping, resampling, histogram equalization, median filtering, contrast / brightness). The BioImage visual interface allows users to interact with their data both in 2D "slice views" (powered by the ViewSlices module), as well as in a full 3D "volume rendering view" (powered by high-performance volume rendering modules). Users can seamlessly move between the 2D and 3D views to precisely control how different features of their data are displayed, and to gain both quantitative and qualitative insights into their data. All of these features are described in detail in our BioImage tutorial.
SCIRun License
SCIRun is available for free and open source under the MIT License
The MIT License Copyright (c) 2008 Scientific Computing and Imaging Institute, University of Utah. License for the specific language governing rights and limitations under Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
