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:

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: 

  1. Fully3D describing process and installation submitted/reviewed.
  2. 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
  3. SoftX - Volume 9, January–June 2019, Pages 317-323 - https://www.sciencedirect.com/science/article/pii/S2352711018301912

2. CCPi Quantification

Old CCPi Plugins available:

Avizo Plugins: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/frs/?action=FrsReleaseBrowse...
Paraview Plugins: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/frs/?action=FrsReleaseBrowse...
ImageJ Plugins: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/frs/?action=FrsReleaseBrowse...
EP Plugins: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/frs/?action=FrsReleaseBrowse...

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

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

    Other Useful Tools:

    Linked Tools:

    Data Format