Software for positron emission tomography

Comprehensive list of free software for image processing and analysis can be found from the site I do imaging. The author of the site, Andrew Crabb, organized and taught an excellent hands-on course at the XIII and XIV PET Symposium, and kindly shares the course material; please find the time to check out the contents!

Some software for PET image analysis are listed in instructions for drawing ROIs.

Software developed in TPC

Carimas™ can be used for cardiac analyses, and also as a general tool for image processing and data analysis, even for small animal studies.

Wide variety of tools with command-line interface (CLI) (TPCCLIB, written in C) for data processing and analysis are available for Windows, Linux, and macOS. Binary and source packages can be downloaded from seafile.utu.fi, Dropbox or OneDrive folder. Library documentation can be found here, and list of applications in here. Instructions for installing the applications on macOS can be found here.

Some CLI tools are not yet included in TPCCLIB, but are available in here. The C libraries (functional but deprecated) for these executables can be found here.

In addition, there are a few small CLI tools written in C# and Matlab:

Human Emotion Systems Laboratory offers some of their software on their web page.

PET ERP

PET ERP is a management system for PET centers, containing PET scheduler, GMP compliant LIMS, stock management, and data management developed by Atostek.

Licensing

Excluding Carimas, all other software developed in Turku PET Centre is free to use and OpenSource licensed, as recommended or requested by many publishers, including Nature (Eglen et al., 2017).


See also:



References

Eglen SJ, Marwick B, Halchenko YO, Hanke M, Sufi S, Gleeson P, Silver RA, Davison AP, Lanyon L, Abrams M, Wachtler T, Willshaw DJ, Pouzat C, Poline J-B. Toward standard practices for sharing computer code and programs in neuroscience. Nature Neurosci. 2017; 20(6): 770-773. doi: 10.1038/nn.4550.

Hawe D, Fernández FRH, O’Suilleabháin L, Huang J, Wolsztynski E, O’Sullivan F. Kinetic analysis of dynamic positron emission tomography data using open-source image processing and statistical inference tools. WIREs Comput Stat. 2012; 4: 316-322.

Loening AM, Gambhir SS. AMIDE: a free software tool for multimodality medical image analysis. Mol Imaging 2003; 2(3): 131-137.

Merisaari H, Tuisku J, Joutsa J, Hirvonen J, Tuominen L. Statistical Toolbox for automated brain PET data processing. 2014, Poster presentation. figshare.

Merisaari H. Batch processing with Matlab and in-house software. Powerpoint presentation in XIII Turku PET Symposium, 2014. figshare.

Muzic RF Jr, Cornelius S. COMKAT: compartmental model kinetic analysis tool. J Nucl Med. 2001; 42(4): 636-645.

Nagy P. Open Source in imaging informatics. J Digit Imaging 2007; 20(Suppl 1): 1-10.

Roberto de la Prieta (2012). Free Software for PET Imaging, Positron Emission Tomography - Current Clinical and Research Aspects, Dr. Chia-Hung Hsieh (Ed.), ISBN: 978-953-307-824-3, InTech. Available from here.

Ratib O, Rosset A, Heuberger J. Open Source software and social networks: disruptive alternatives for medical imaging. Eur J Radiol. 2011; 78: 259-265.

Veronese M, Rizzo G, Turkheimer FE, Bertoldo A. SAKE: a new quantification tool for positron emission tomography studies. Comput Methods Progr Biomed. 2013; 111: 199-213.

Tabelow K, Clayden JD, de Micheaux PL, Polzehl J, Schmid VJ, Whitcher B. Image analysis and statistical inference in neuroimaging with R. Neuroimage 2011; 55: 1686-1693.



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Created at: 2014-04-25
Updated at: 2017-09-01
Written by: Vesa Oikonen