Visual Analytics
11 May 2017
Yes
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Visual Analytics Group Software

No
 


The Visual Analytics and Imaging Systems group makes use of a number of Open Source and proprietary software packages, both in its own work and in providing services to the facilities and to the wider academic  community. The group develops extensions and plugins to some of these packages to enhance their capabilities and to provided access new software tools.  

                                                                                                                                                                                                                             

The main external software packages we currently work with are listed below, along with some of the contributions made to them: 

Software Overview
How to access
Avizo/AmiraAvizo is a commercial visualisation and analysis suite. It is used for CT image analysis by DLS and ISIS. Analysis methods include segmentation and mesh generation for CFD.  
VAIS has negotiated a site license for this software at RAL/DLS and provides first line support and training seminars. 
New analysis tools and file readers are provided as part of the CCPi project. Large memory machines and immersive 3D at RAL allow the full capabilities of Avizo to be used.
Site license available within STFC and DLS. Website: https://www.fei.com/software/amira-avizo/
ParaViewParaView is an Open Source visualisation tool based on VTK. It is a general purpose tool able to visualise image data, CFD/FEA data, particle  data, etc. Its particular strength is in parallel and remote visualisation suited to analysis in HPC systems.  CCPi image analysis plugins and readers are provided for ParaView. Immersive 3D and high end graphics machines are used to used to exploit this software at RAL.ParaView can be download from: www.paraview.org
ImageJ
ImageJ is one of the best know Open Source tools for image display and analysis. It is widely used with DLS and RCaH with CT data. CCPi analysis and reader plugins are available for this software.
The software can be downloaded from: https://fiji.sc
STiR - GadgetronSTiR is a package for analysis for PET medical image data, while Gadgetron is a package for reconstruction of MRI data. These two Open Source packages implement high quality algorithms to reconstruct medical images from these two separate modalities. CCP-PETMR is working to provide a framework that combines these two packages for joint reconstruction of PET-MR data.

Gadgetron is available from: https://gadgetron.github.io 

 

The software packages the VAIS has helped to develop include: 

 

SoftwareDescription
How to access
CIL Core Imaging Library
The Core Imaging library contains a set of algorithms related to CT image reconstruction and analysis that have been developed within the CCPi project. These are released as Open Source to allow further development and increased up take.
This software will be released in the near future. In the meantime some of the individual components are available separately.
PolyBHCBeam Hardening is a well known problem in CT analysis. This code, used in conjunction with special test hardware, allows correction based on fitting the effective energy response, using a method developed at QMUL.
An initial version of the software is available from: https://ccpforge.cse.rl.ac.uk/svn/tomo_bhc
Quantification Plugins
These plugins will form part of the CIL release. They offer a number of operations on CT image data such as accessible volume calculation and simple level based segmentation. This also includes a read for the NeXuS file format used by DLS. Versions are available for Avizo, ImageJ and ParaView.
Downloads are available from: https://www.ccpi.ac.uk/node/3
Reconstruction Plugins
These implement iterative reconstruction methods for CT analysis, including CGLS.
Downloads are available from: https://www.ccpi.ac.uk/node/3
SIRF
This software package is one of the main outcomes of CCP-PETMR and provides Python and Matlab interfaces to the STiR and Gadgetron packages mentioned above. The aim is to allow joint reconstruction of PET and MR images obtained by new scanners that combine both imaging techniques. This should increase the information obtained from a scan.Initial download is available from: https://www.ccppetmr.ac.uk/downloads


Contact: Fowler, Ronald (STFC,RAL,SC)