MIA - A free and open source software for gray scale medical image analysis

Source Code for Biology and Medicine

Volumn 8, Issue , 2013, Pages

  Wollny, Gert ^a,c   Kellman, Peter ^e   Ledesma Carbayo, María Jesus ^a,c   Skinner, Matthew M ^b,d   Hublin, Jean Jaques ^b   Hierl, Thomas ^f  

^a UNIVERSIDAD POLITÉCNICA DE MADRID   (Spain)

^b MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^c BIOMATERIALES Y NANOMEDICINA CIBER BBN   (Spain)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

^e NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^f UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84885357120     PISSN: None     EISSN: 17510473     Source Type: Journal    
DOI: 10.1186/1751-0473-8-20     Document Type: Review

References (67)

1. Scilab Enterprises Scilab: Free and Open Source Software for Numerical Computation 2012, Scilab Enterprises: Orsay, http://www.scilab.org. [Access: 2013-06-05], Scilab Enterprises.
2. Schneider C, Rasband W, Eliceiri K. NIH image to ImageJ: 25 years of image analysis. Nat Methods 2012, 9(7):671-675. 10.1038/nmeth.2089, 22930834.
3. de Chaumont F, Dallongeville S, Chenouard N, Herve N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y, Lagache T, Dufour A, Olivo-Marin J. Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods 2012, 9(7):690-696. 10.1038/nmeth.2075, 22743774.
4. Chase DR. Garbage collection and other optimizations. PhD thesis 1988, http://hdl.handle.net/1911/16127. [Access: 2013-05-17].
5. Bradski G, Kaehler A. Learning OpenCV: Computer Vision with the OpenCV Library, 1st edition 2008
6. Yoo T, Ackerman MJ, Lorensen WE, Schroeder W, Chalana V, Aylward S, Metaxes D, Whitaker R. Engineering and algorithm design for an image processing API: a technical report on ITK - The insight toolkit. Medicine Meets Virtual Reality 2002, 586-592. AmsterdamL: IOS Press, Westwood J.
7. Bright W. C++ Compilation speed 2010, http://www.drdobbs.com/cpp/c-compilation-speed/228701711. [Access: 2013-05-17].
8. Woolrich M, Jbabdi S, Patenaude B, Chappell M, Makni S, Behrens T, Beckmann C, Jenkinson M, Smith S. Bayesian analysis of neuroimaging data in FSL. NeuroImage 2009, 45(1):173-186.
9. Lohmann G, Müller K, Bosch V, Mentzel H, Hessler S, Chen L, Zysset S, von Cramon DY. LIPSIA - a new software system for the evaluation of functional magnetic resonance images of the human brain. Computer Med Imaging Graph 2001, 25(6):449-457.
10. Klein S, Staring M, Murphy K, Viergever M, Pluim J. elastix: a toolbox for intensity based medical image registration. IEEE Trans Med Imaging 2010, 29:196-205.
11. Modat M, Ridgway GR, Taylor ZA, Lehmann M, Barnes J, Hawkes DJ, Fox NC, Ourselin S. Fast free-form deformation using graphics processing units. Comput Methods Prog Biomed 2010, 98(3):278-284.
12. Cardoso MJ. NiftySeg - Statistical segmentation and label fusion software package. http://niftyseg.sourceforge.net/. [Access: 2012-05-24].
13. Doria D, Staring M, Klein S. ITKTools. https://github.com/ITKTools/ITKTools. [Access: 2013-05-17].
14. Fedorov A, Beichel R, Kalpathy-Cramer J, Finet J, Fillion-Robin J-C, Pujol S, Bauer C, Jennings D, Fennessy F, Sonka M, Buatti J, Aylward SR, Miller JV, Pieper S, Kikinis R. 3D SLICER as an image computing platform for the quantitative imaging network. Magn Reson Imaging 2012, 30(9):1323-1341. 10.1016/j.mri.2012.05.001, 3466397, 22770690.
15. Tian J, Xue J, Dai Y, Chen J, Zheng J. A novel software platform for medial image processing and analyzing. IEEE Trans Med Imaging 2008, 12(6):800-811.
16. MeVisLab - medical image processing and visulaization. http://www.mevislab.de/. [Access: 2012-05-24].
17. Beck K. Test-Driven Development by Example 2003, Boston: Addison Wesley.
18. Everett F, Carter J. Implementation of the polar form of the Box-Muller transformation. 1994, ftp://ftp.taygeta.com/pub/c/boxmuller.c. [Access: 2012-01-22].
19. Thévenaz P, Blu T, Unser M. Interpolation revisited. IEEE Trans Med Imag 2000, 19(7):739-758.
20. Vandervoorde D, Josuttis NM. C++ Templates: The Complete Guide 2005, Boston: Addison Wesley.
21. Jusottis NM. The C++ Standard Library 1999, Boston: Addison-Wesley.
22. Karlsson B. Beyond the C++ Standard Library: An Introduction to Boost 2005, Boston: Addison Wesley.
23. Rohlfing T, CRM J, Bluemke DA, Jacobs MA. Volume-preserving nonrigid registration of MR breast images using free-form deformation with an incompressibility constraint. IEEE Trans Med Imag 2003, 22:730-741.
24. Gamma E, Helm R, Johnson R, Vlissides J. Design Patterns: Elements of Reusable Object-Oriented Software 1994, Boston: Addison Wesley.
25. Troan EW. POPT - Parsing command line options. http://rpm5.org/files/popt/. [Access: 2012-05-24].
26. Prus V. BOOST Program Options. http://www.boost.org/libs/program_options. [Access: 2012-10-24].
27. Walsh N. DocBook 5: The Definitive Guide, 1.0.4 edition 2011, O'Reilly: Sebastopol.
28. Wollny G. Mia User Reference. 2012, http://mia.sourceforge.net/userref/index.html. [Access: 2013-05-24].
29. Rozental G. Boost Test Library http://www.boost.org/libs/test. [Access: 2012-10-24].
30. Wollny G, Ledesma-Carbayo MJ, Kellman P, Santos A. New Developments in Biomedical Engineering chap. On breathing motion compensation in myocardial perfusion imaging. In-Teh 2010: Vukovar, Croacia, 235-247.
31. Wollny G, Ledesma-Carbayo MJ, Kellman P, Santos A. Exploiting quasiperiodicity in motion correction of free-breathing myocardial perfusion MRI. IEEE Trans Med Imag 2010, 29(8):1516-1527.
32. Wollny G, Kellman P, Santos A, Ledesma-Carbayo MJ. Automatic motion compensation of free breathing acquired myocardial perfusion data by using independent component analysis. Med Image Anal 2012, 16(5):1015-1028. 10.1016/j.media.2012.02.004, 3372575, 22465078.
33. Pham DL, Prince JL. An adaptive fuzzy C-means algorithm for image segmentation in the presence of intensity inhomogeneities. Pattern Recognit Lett 1999, 20:57-68.
34. Wirzenius L, Oja J, Stafford S, Weeks A. Linux System Administrators Guide The Linux Documentation Project 2005 chap. 6.6 The buffer cache, http://www.tldp.org/LDP/sag/html/buffer-cache.html. [Access: 2013-05-17].
35. Stroustrup B. C++11 - the recently approved new ISO C++ standard. http://www.stroustrup.com/C++11FAQ.html 2012. [Access: 2013-10-21].
36. International Organization for Standardization S Geneva ISO/IEC 14882:2011: Information technology - Programming languages - C++. 2011, http://www.iso.org/iso/catalogue_detail.htm?csnumber=50372 [Access: 2013-08-07], International Organization for Standardization S Geneva.
37. Wollny G. MIA - tools for the processing of gray scale images. 2012, http://mia.sourceforge.net/. [Access: 2013-06-05].
38. Hsu LY, Groves DW, Aletras AH, Kellman P, Arai AE. A quantitative pixel-wise measurement of myocardial blood flow by contrast-enhanced first-pass CMR perfusion imaging: microsphere validation in dogs and feasibility study in humans. JACC Cardiovasc Imaging 2012, 5(2):154-166. 10.1016/j.jcmg.2011.07.013, 3460374, 22340821.
39. Jerosch-Herold M. Quantification of myocardial perfusion by cardiovascular magnetic resonance. J Cardiov Magn Reson 2010, 12(57). http://www.jcmr-online.com/content/12/1/57. [Access: 2013-08-07].
40. Milles J, van der Geest R, Jerosch-Herold M, Reiber J, Lelieveldt B. Fully automated motion correction in first-pass myocardial perfusion MR image sequences. IEEE Trans Med Imag 2008, 27(11):1611-1621.
41. Li C, Sun Y. Nonrigid registration of myocardial perfusion MRI using pseudo ground truth. Medical Image Computing and Computer-Assisted Intervention - MICCAI 2009 2009, 165-172. London, Berlin, Heidelberg: Springer-Verlag.
42. Xue H, Zuehlsdorff S, Kellman P, Arai A, Nielles-Vallespin S, Chefdhotel C, Lorenz CH, Guehring J. Unsupervised inline analysis of cardiac perfusion MRI. Medical Image Computing and Computer-Assisted Intervention - MICCAI 2009, Volume 5762/2009 of LNCS 2009, 741-749. Berlin, Heidelberg: Springer-Verlag.
43. Skinner M, Wood B, Boesch C, Olejniczak A, Rosas A, Smith T, Hublin JJ. Dental trait expression at the enamel-dentine junction of lower molars in extant and fossil hominoids. J Human Evol 2008, 54:173-186.
44. Skinner M, Gunz P. The presence of accessory cusps in chimpanzee lower molars is consistent with a patterning cascade model of development. J Anat 2010, 217(3):245-253. 10.1111/j.1469-7580.2010.01265.x, 2972538, 20629983.
45. Skinner M, Skinner M, Boesch C. Developmental defects of the dental crown in chimpanzees from the Taï National Park, Côte D'Ivoire: coronal waisting. Am J Phys Anthropol 2012, 149(2):272-282. 10.1002/ajpa.22123, 22890693.
46. Skinner M, Gunz P, Wood B, Hublin JJ. Enamel-dentine junction (EDJ) morphology distinguishes the lower molars of Australopithecus africanus and Paranthropus robustus. J Human Evol 2008, 55(6):979-988.
47. Skinner M, Gunz P, Wood B, Hublin JJ. Discrimination of extant Pan species and subspecies using the enamel-dentine junction morphology of lower molars. Am J Phys Anthropol 2009, 140(2):234-243. 10.1002/ajpa.21057, 19382140.
48. Smith T, Kupczik K, Machanda Z, Skinner M, Zermeno J. Enamel thickness in Bornean and Sumatran orangutan dentitions. Am J Phys Anthropol 2012, 147(3):417-426. 10.1002/ajpa.22009, 22271572.
49. Felzenszwalb PF, Huttenlocher DP. Distance Transforms of Sampled Functions. Tech. rep. Cornell Computing and Information Science 2004, http://www.cs.brown.edu/~pff/dt/. [Access: 2013-01-22].
50. Popinet S. GTS - The GNU Triangulated Surfaces Library. http://gts.sourceforge.net. [Access: 2013-10-24].
51. Hierl T, Hemprich A. A novel modular retention system for midface distraction osteogenesis. Br J Oral Maxillofac Surg 2000, 38:623-626. 10.1054/bjom.2000.0469, 11092781.
52. Wollny G, Kruggel F. Computational cost of non-rigid registration algorithms based on fluid dynamics. IEEE Trans Med Imaging 2002, 11(8):946-952.
53. Wollny G, Kruggel F, Hierl T, Hendricks J. Assessment, validation, and visualisation of bony changes in crano-facial surgery. The 4th IASTED International Conference on Visualisation, Imaging, and Image Processing VIIP'04 2004, Calgary, Marbella: ACTA Press.
54. Hierl T, Wollny G, Hendricks J, Berti G, Schmidt JG, Fingberg J. Hemprich A: 3D-Analysis of soft tissue changes following maxillary distraction osteogenesis. Reconstruction of Soft Facial Parts 2005, Police and Research, Luchterhand Publishers, Buzug TM, Prüfer K, Sigl K, Bongartz J, Hering P, Willems G. Remagen.
55. Hierl T. Distraction Osteogeneis of the Facial Skeleton 2007, BC Decker Inc: chap. Lengthening the maxilla by distraction osteogenesis; Hamilton.
56. MIA GIT repository. https://sourceforge.net/p/mia/mia2/ci/master/tree/.
57. MIA bug tracking. https://sourceforge.net/p/mia/tickets/.
58. MIA discussion forums. https://sourceforge.net/p/mia/discussion/.
59. Tille A, Möller S, Hanke M, Halchenko Y. Debian Med - Integrated software environment for all medical purposes based on Debian GNU/Linux. Global Telemedicine and eHealth Updates: Knowledge Resources, Volume 4 2011, 12-12. Luxembourg: ISfTeH International Society for Telemedicine & eHealth, Jordanova M, Lievens F.
60. Wollny G. PPA for Medical Image Analyis. 2012, https://launchpad.net/~gert-die/+archive/ppa-mia. [Access: 2012-05-24].
61. The Free Software Foundation GNU General Public License. http://www.gnu.org/licenses/gpl.html. [Access:2013-05-20], The Free Software Foundation.
62. The Free Software Foundation Selling Free Software. http://www.gnu.org/philosophy/selling.html. [Access: 2012-05-20], The Free Software Foundation.
63. Kybic J, Unser M. Fast parametric elastic image registration. IEEE Trans Image Process 2003, 12(11):1427-1442. 10.1109/TIP.2003.813139, 18244700.
64. Christensen GE, RR D. Miller MI: Deformable templates using large deformation kinematics 1996, 5(10):1435-1447.
65. Galassi M, Davies J, Theiler J, Gough B, Jungman G, Alken P, Booth M, Rossi F. The GNU Scientific Library. http://www.gnu.org/software/gsl/ [Access: 2012-05-24].
66. Johnson SG. The NLopt nonlinear-optimization package. 2011, http://ab-initio.mit.edu/nlopt. [2012-05-24].
67. Ahmed MN, Yamany SM, Mohamed N, Farag AA, Moriarty T. A modified fuzzy C-means algorithm for bias field estimation and segmentation of MRI data. IEEE Trans. Med Imaging 2002, 21(3):193-198. 10.1109/42.996338, 11989844.