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Downloads
Software and Related Paper Download Links:
CCPi credit text is:
Code integrated within the Collaborative Computational Project in Tomographic Imaging (http://www.ccpi.ac.uk/) toolkits acknowledges the funding support by the EPSRC grants (EP/P02226X/1) 'Reconstruction Toolkit for Multichannel CT' and the network initiative (EP/M022498/1 from EP/J010456/1), as well as computational support by CoSeC, the Computational Science Centre for Research Communities.
Links to University of Manchester Research Software Engineering staff and computational facility within Research IT, should acknowledge this within papers and documents using the following wording:
https://research-it.manchester.ac.uk/acknowledging-research-it/
We have links to;
National Research Facility for Lab X-ray CT https://gow.epsrc.ukri.org/NGBOViewGrant.aspx?GrantRef=EP/T02593X/1
Fellowship: Inline virtual qualification from 3D X-ray imaging for high-value manufacturing; Llion Evans, Swansea University https://gtr.ukri.org/projects?ref=EP%2FR012091%2F1
CCPi CIL Core code and Flagship Frameworks
See project pages for the frameworks and exploitation of:
- CIL (Core Imaging Library) https://www.ccpi.ac.uk/CIL and
- Flagship (Reconstruction Toolkit for Multichannel CT; RT-MCT) https://www.ccpi.ac.uk/Flagship
Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
Poster for 2018 ToScA conference
Building and Testing service: (updated 4/2/2019)
- We use Jenkins instance at ANVIL service: https://anvil.softeng-support.ac.uk (maintained by STFC provided for UK academic community with SSO)
- General instruction about configuration of Jenkins and Github are at CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
- The build script and configuration is set as follow: Any commit to master branch is uploaded to anaconda channel ‘ccpi’; Commit tagged with a version (e.g. v10.0.3) is build and uploaded as production, i.e. user installs it by `conda install –c ccpi [ccpi-module]`; and Commit without tag is build and uploaded with ‘dev’ label. Can be installed by user with `conda install –c ccpi/label/dev [ccpi-module]`
Information about shared build script in the CIL docs https://cil.readthedocs.io/en/latest/buildandtestautomation.html
and sources at https://github.com/vais-ral/CCPi-VirtualMachine/blob/master/scripts/jenk...
1. CCPi Regularisation Toolkit
Code and examples: https://github.com/vais-ral/CCPi-Regularisation-Toolkit
Papers:
- Fully3D describing process and installation submitted/reviewed.
- Versatile regularisation toolkit for iterative image reconstruction with proximal splitting algorithms,” in the SPIE Digital Library as part of the proceedings of the 11072 conference. http://dx.doi.org/10.1117/12.2534289
- SoftX - Volume 9, January–June 2019, Pages 317-323 - https://www.sciencedirect.com/science/article/pii/S2352711018301912
2. CCPi Quantification
Old CCPi Plugins available:
3. CCPi Reconstruction
Barry Searle's repository has the code for iterative reconstruction. https://github.com/vais-ral/CCPi-Reconstruction
This includes CGLS, SIRT, MLEM (uses the Jacobs rays code that started life in David Szotten's code Tag https://github.com/vais-ral/CCPi-Reconstruction/releases/tag/v0.10.0
- old site has links to a package to use the iterative CGLS algorithm on data from XTek instruments is now available for 64 bit Windows systems. Please check the README file in the package if you are missing Windows dlls. http://ccpforge.cse.rl.ac.uk/gf/project/cgls/frs/
Daniil Kazantzev's repository for Iterative Reconstruction regualrisers https://github.com/dkazanc
- old site http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr/
4. CCPi Beamhardening Correction software and paper
The article on beam hardening is https://authors.elsevier.com/sd/article/S2352711018300360
Code available at https://github.com/vais-ral/CCPi-PreProcessing
5. CCPi-Flagship TomoPhantom software and paper
Software to generate 2D-4D analytical phantoms and their Radon transforms for image processing: Paper submitted to Software X
Code available at https://github.com/dkazanc/TomoPhantom
Zenodo link: https://zenodo.org/record/1288340#.XFhinvni7Lk
Elipsoid predecessor: Matlab Code for a 2D/3D Analytical Ellipsoid Phantom for Parallel-Ray CT https://zenodo.org/record/835417#.XFhjHPni7Lk
6. CCPi Loading nexus data
Into - Avizo (link)
Into - Paraview plugin for the NeXuS reader: https://github.com/vais-ral/CCPi-Quantification/blob/master/Wrappers/Par...
7. CCPi Associated Segmentation
SuRVoS segmentation system [Windows]
8. Digital Volume Correlation software
Link to Brian Bay's code and Catherine Disney's examplar with CCPi interface explanations. To APPEAR SOON
9. To Appear here
To Appear soon
10. Fellowship Laminography Code
Test code adn datasets: https://zenodo.org/record/2540509#.XFhh8_ni7Lk
11. Fellowship XCT Hacking code
Nikon X-Ray CT Machines running Inspect-X 2.2 (SP12) or earlier can be custom programmed using Visual Basic for Applications (VBA). Coding the machine in this way allows it to be used in a much wider scope than the "black-box" routines provided by Nikon. Many functionalities of the machine can be controlled, including the X-Ray source, the manipulator and image processing, allowing users to create routines that do (almost) whatever they desire.
This project contains code developed at the University of Manchester for programming our Nikon Custom Bay. It contains training exercises for learning how to program the system, along with routines developed for simple circular scans, helical scans and interfacing with external devices via a USB-TTL connection.
Zenodo link: https://doi.org/10.5281/zenodo.1204087
Zenode link: New software protocols for enabling laboratory based temporal CT https://zenodo.org/record/1204088#.XFhiyvni7Lk
12. Fellowship Helical XCT
Implementing an exact algorithm for Helical CT:Removing the cone-beam artefacts https://zenodo.org/record/61409#.XFhj_Pni7Lk
A. DLS code: Tomographic data for testing, demonstrating, and developing methods of removing ring artifacts
Description and dataset: https://zenodo.org/record/1443568#.XFhiMPni7Lk
B. DLS code: Python implementation of distortion correction methods for X-ray tomography
Description: https://zenodo.org/record/1322720#.XFhicvni7Lk
Other Quantification, Reconstruction and Segmentation Tools
- Astra Toolbox, Matlab/Python/GPU based image reconstruction algorithms.
- Astra but for a neutron tomography (parallel beam), "tested the FBP and SIRT on the GPU and they were impressively fast"
- CASToR Project, Customizable and Advanced Software for Tomographic Reconstruction.
- Compressed Sensing algorithms.
- Computational Mechanics Software.
- EIDORS: Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software
- FSL, is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
- Gadgetron Software
- gVirtualXRay: Virtual X-Ray Imaging Library on GPU
- : IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections
- ;Mango, segmentation software.
- Matlab iradon, is always available.
- MIAKAT is a fully quantitative suite of analysis tools for PET neuroimaging data bringing together state of the art tools in a single user friendly software environment making it straightforward for novice or advanced imaging scientists to efficiently and accurately analyse their data..
- NIRFAST - modelling and reconstruction tools for near-infrared light transport in tissue.
- OpenMBIR, Project for Iterative Reconstruction.
- Operator Discretization Library (ODL), a python library for fast prototyping focusing on (but not restricted to) inverse problems.
- Pore3D at Elettra
- PyHST2 Hybrid distributed code for high speed,tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities
- Reactiv'IP Smart Image Processing - commercial 2d adn 3D imaging pipeline system.
- RooTrak Analysis of X-ray micro CT scans of roots in soil.
- Savu Python package to assist with reconstructing tomography data.
- scikit-image, a python collection of algorithms for image processing.
- Spiers, segmentation software.
- STIR PET/SPECT software.
- SPM, Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data.
- SYRMEP beamline of the Elettra synchrotron facility to perform the digital image processing required by parallel beam propagation-based phase contrast CT experiments.
- TauFactor, Tool to calculate tortuosity factor, volume fractions, surface areas and triple phase boundary densities from image based microstructural data.
- TIGRE Tomographic Iterative GPU-based Reconstruction toolbox from University of Bath
- ToMoBAR, TOmographic MOdel-BAsed Reconstruction software.
- Tomopy, Python based image reconstruction from ANL.
- TTK Topology Toolkit - includingc contour-maps https://topology-tool-kit.github.io/
- TomViz with a paper on the VTK format at: http://www.sciencedirect.com/science/article/pii/S2352711015000035
- TXM Wizard Toolbox for handling X-ray transmission image data collected using the Xradia TXM system.
- UFO multi-threaded, GPU-enabled and distributed data processing framework.
- X-AID iterative CT reconstruction software from MITOS.
- Xi-cam graphical environment for synchrotron data analysis, management, and visualization developed by the Advanced Light Source at Lawrence Berkeley National Laboratory.
Reminder software needs promoting so you our own code: Elsevier Original Software Publications
A metalink from USA is at: https://tomopedia.github.io/
Visualisation and Other tools
- Amira
- Aquila solution from XRE
- Avizo (VSG/FEI)
- Bitplane imaris software
- Blender
- BoneJ
- Cell Profiler
- Drishti
- Dragonfly from ORS is just released.
- DREAM.3D
- Hyperspy
- ImageJ
- IMARIS
- ZEISS ZEN Intellesis for Image Segmentation in Microscopy
- Interspectral
- InVesalius
- Molecular Maya Toolkit
- Occiput provides a Python library for image reconstruction and processing
- OpenIA
- Paraview
- RooTrak
- Simpleware
- 3DSlicer
- SuRVoS (Super-Region Volume Segmentation) Workbench for semi-automated segmentation of 3D image volumes
- syglass VR for
- TeraStitcher
- VG Studio Max
- vounwarp Python package for distortion correcting X-ray tomography
- Volview
- QUANT-CT from Berkeley
- ImaSim for Basic Education
Other Useful Tools:
- Photon Counting Toolkit (PcTK)
- RESOLUTE method (paper) for PET/MR brain pseudo-CT generation - paper at: http://iopscience.iop.org/article/10.1088/0031-9155/60/20/8047/meta and data at https://zenodo.org/record/1204197#.WrtEzfkRDLk
- Vega and Vega Lite
- Visualisation in R