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Mia - A tool chain for Medical Image Analysis

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Synopsis

MIA is a collection of libraries and command line tools for the processing of gray scale images. The original version was developed at the Max-Planck-Institute of Human Cognitive and Brain Scienes as software accompanying the PhD thesis G. Wollny, "Analysis of changes in temporal series of medical images", PhD Thesis, University of Leipzig, 2003. Further development was done within the Department of Human Evolution at the Max-Planck-Institute for Evolutionary Anthropology. and at the ETSI Telecomunicación (UPM) within the group of Biomedical Image Technologies. Current development is done on a solely voluntary basis.

To continue reading please follow one of these links:

If you use this software for creating a publication, please reference it as

Wollny G, Kellman P, Ledesma-Carbayo M-J, Skinner MM, Hublin J-J, Hierl Th, "MIA - A Free and Open Source Software for Gray Scale Medical Image Analysis", Source Code for Biology and Medicine, 2013, 8:20

In addition, if you use specific algorithms, please reference the according article from the list below.

Publication list in BibTeX format

Christopher J. Dunmore, Gert Wollny, and Matthew M. Skinner, MIA-Clustering: a novel method for segmentation of paleontological material, PeerJ, 2018, DOI: 10.7717/peerj.4374.

Brett R. Cowan, Edward DiBella, Sancgeetha Kulaseharan, Devavrat Likhite, Nils Noorman, Lennart Tautz, Nicholas Tustison, Gert Wollny, Alistair A. Young, and Avan Suinesiaputra, "An Open Benchmark Challenge for Motion Correction of Myocardial Perfusion MRI", IEEE Journal of Biomedical and Health Informatics, 21(5), 2017, DOI:10.1109/JBHI.2016.2597145)

Gert Wollny, Isabel Casanova, Maria-Jesus Ledesma-Carbayo, , and Andres Santos. On post-acquisition
motion compensation for prostate perfusion analysis. bioRxiv - The preprint server for Biology, 2016.
DOI: 10.1101/037986.

Wollny G and Ledesma-Carbayo M-J, "Comparison of Linear and Non-linear 2D+T Registration Methods for DE-MRI Cardiac Perfusion Studies", In "Statistical Atlases and Computational Models of the Heart - Imaging and Modelling Challenges", 5th International Workshop, STACOM 2014, Held in Conjunction with MICCAI 2014, LNCS 8896 (Eds. Oscar Camara et al), 21-31, Boston, MA, USA, Sept 18, 2014, DOI:10.1007/978-3-319-14678-2_3. (preprint)

Wollny G and Kellman P, "Free breathing myocardial perfusion data sets for performance analysis of motion compensation algorithms", GigaScience, 2014, 3:23 DOI:10.1186/2047-217X-3-23

Wollny G, Kellman P, Ledesma-Carbayo M-J, Skinner MM, Hublin J-J, Hierl Th, "MIA - A Free and Open Source Software for Gray Scale Medical Image Analysis", Source Code for Biology and Medicine, 2013, 8:20, DOI:10.1186/1751-0473-8-20

G Wollny, M-J Ledesma-Carbayo and A Santos, ''MIA - A toolbox for Medical Image Analysis'', Workshop on Open-Source Medical Image Analysis Software, Barcelona, Spain, 2012 (abstract, poster)

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012, revised preprint, the final published version is available as DOI:10.1016/j.media.2012.02.004

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, Nonrigid Motion Compensation of Free Breathing Acquired Myocardial Perfusion Data, In Proc "Bildverarbeitung für die Medizin 2011", 84-88, Lübeck, Germany, March 20-22, 2011

Wollny, G., Ledesma-Carbayo, M.J., Kellman, P., Santos, A. "Exploiting Quasi-Periodicity in Motion Correction of Free-Breathing Myocardial Perfusion MRI". IEEE Trans. Med. Imaging, 29(8):1516-1527. Aug. 2010, doi: 10.1109/TMI.2010.2049270.

Wollny, G, Ledesma-Carbayo, MJ, Kellman, P and Santos, A "On Breathing Motion Compensation in Myocardial Perfusion Imaging", In New Developments in Biomedical Engineering, Domenico Campolo (Ed.), ISBN: 978-953-7619-57-2, InTech, doi:10.5772/7617

Wollny, G., Ledesma-Carbayo, M.J., Kellman, P., Santos, A. "Non-Rigid Motion Compensation in Free-Breathing Myocardial Perfusion Magnetic Resonance Imaging". Computers in Cardiology, 35:465-468. Bologna, Sep. 2008.

Wollny, G., Ledesma-Carbayo, M.J., Kellman, P., Santos, A. "A New Similarity Measure for Non-Rigid Breathing Motion Compensation of Myocardial Perfusion MRI". Proc 30th Annual International IEEE EMBS Conference, pp. 3389-3392. Vancouver, Aug. 2008, doi:10.1109/IEMBS.2008.4649933

G. Wollny, F. Kruggel, Th. Hierl, J. Hendricks., Assessment, validation, and visualisation of bony changes in crano-facial surgery, In Proceedings of The 4th IASTED International Conference on Visualisation, Imaging, and Image Processing VIIP'04, Marbella, Spain, September 2004, 2004

Wollny, G. and Kruggel, F., Computational cost of non-rigid registration algorithms based on fluid dynamics, IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002, doi:10.1109/TMI.2002.803113.

Wollny, G., On the Implementation of Non-Rigid Registration using Fluid Dynamics, Technical report

Publications that relate to the version 1 of the software

Some of the software used in these publications has not yet been ported to the new library.

Wollny, G., Tittgemeyer, M. and Kruggel, F., Segmentation of Vector Fields by Critical Point Analysis: Application to Brain Deformation, In Kasturi, R. and Laurendeau, D. and Suen, D.(Eds.), Proceedings of The 16th International Conference on Pattern Recognition, pp. 524-527, Quebec City, Canada, 2002, doi:10.1109/ICPR.2002.1044786.

Tittgemeyer, M., Wollny, G. and Kruggel, F.,Monitoring structural change in the brain: Application to neurodegeneration, In J. Sporring, W. Niessen and J. Weickert (Eds.), Proceedings of The International Workshop on Growth and Motion in 3D Medical Images, pp. 9-16, 3D Lab-University of Copenhagen,2002

Tittgemeyer, M., Wollny, G. and Kruggel, F., Visualizing deformation fields computed by nonlinear image registration, Computing and Visualization in Science, 5(1), pp. 45-51, 2002, The final version of the article is available at www.springerlink.com.

G. Wollny, "Analysis of changes in temporal series of medical images", PhD Thesis, University of Leipzig, 2003

Descombes, X., Kruggel, F., Wollny, G., Gertz, H..J., An object-based approach for detecting smallbrain lesions: Application to Virchow-Robin spaces, IEEE Transactions on Medical Imaging, 23(2), pp. 246-255, 2004, doi:10.1109/TMI.2003.823061

Additional information

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Wiki: An introduction and guide for Mia
Wiki: FAQ
Wiki: Tutorials