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.
- SPM - Statistical Parametric Mapping
- APPIAN - automated software pipeline for analyzing PET images in conjunction with MRI
- NiftyPET - Python platform for PET/MR image reconstruction and analysis
- kinfitr - PET Kinetic Modelling using R
- Pypes - Python workflows for processing multimodal neuroimaging data
- LIFEx: textural and shape indices from PET, MR and CT images
- GraphPad Prism
- UCLA Tracer Kinetic Model Fitting Program
- Kinetic Imaging System (KIS) for microPET
- MunichHeart Cardiac Analysis Package
- SAKEV - Spectral analysis
- Metavol - a volume measurement tool for PET-CT
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 packages can be downloaded from seafile.utu.fi, Dropbox or OneDrive folder. TPCCLIB source codes are available in gitlab.utu.fi/vesoik/tpcclib. Library documentation can be found here, and list of applications in here. Instructions for installing the applications can be found here.
In addition, there are a few small CLI tools written in C# and Matlab:
Scripts for pre-processing input function data are available in gitlab.utu.fi/vesoik/inputbatch.
Human Emotion Systems Laboratory offers some of their software on their web page.
PET ERP is a management system for PET centres, containing PET scheduler, GMP compliant LIMS, stock management, and data management developed by Atostek.
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).
- Software development in TPC
- Command-line interface (CLI)
- PET simulators
- Drawing volumes-of-interest
- Software FAQ
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.
Funck T, Larcher K, Toussaint PJ, Evans AC, Thiel A. APPIAN: Automated Pipeline for PET Image Analysis. Front Neuroinform. 2018; 12: 64. doi: 10.3389/fninf.2018.00064.
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. doi: 10.1002/wics.1196.
Loening AM, Gambhir SS. AMIDE: a free software tool for multimodality medical image analysis. Mol Imaging 2003; 2(3): 131-137. doi: 10.1162/15353500200303133.
Markiewicz PJ, Ehrhardt MJ, Erlandsson K, Noonan PJ, Barnes A, Schott JM, Atkinson D, Arridge SR, Hutton BF, Ourselin S. NiftyPET: a high-throughput software platform for high quantitative accuracy and precision PET imaging and analysis. Neuroinformatics 2018; 16(1): 95-115. doi: 10.1007/s12021-017-9352-y.
Matheson GJ, Plavén-Sigray P, Tuisku J, Rinne J, Matuskey D, Cervenka S. Clinical brain PET research must embrace multi-centre collaboration and data sharing or risk its demise. Eur J Nucl Med Mol Imaging 2020; 47: 502-504. doi: 10.1007/s00259-019-04541-y.
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. doi: 10.1007/s10278-007-9056-1.
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. doi: 10.1016/j.ejrad.2010.05.004.
Savio AM, Schutte M, Graña M, Yakushev I. Pypes: workflows for processing multimodal neuroimaging data. Front Neuroinform. 2017; 11: 25. doi: 10.3389/fninf.2017.00025.
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. doi: 10.1016/j.cmpb.2013.03.016.
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. doi: 10.1016/j.neuroimage.2011.01.013.
Updated at: 2020-04-14
Created at: 2014-04-25
Written by: Vesa Oikonen