Registration-based segmentation of murine 4D cardiac micro-CT data using symmetric normalization

Physics in Medicine and Biology

Volumn 57, Issue 19, 2012, Pages 6125-6145

  Clark, Darin ^a   Badea, Alexandra ^a   Liu, Yilin ^a   Johnson, G Allan ^a   Badea, Cristian T ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

C57BL/6 MICE; CARDIAC CHAMBERS; CARDIAC IMAGES; CARDIAC INDEXES; CARDIAC OUTPUT; CARDIAC PHASIS; CARDIO-VASCULAR DISEASE; DEFORMABLE REGISTRATION; DICE COEFFICIENT; EDGE-PRESERVING SMOOTHING; EJECTION FRACTION; IN-VIVO; LABEL PROPAGATION; LEFT ATRIUMS; LEFT VENTRICLES; MANUAL SEGMENTATION; MICRO CT; PRECLINICAL STUDIES; RIGHT VENTRICLE; STROKE VOLUMES; TEMPORAL RESOLUTION; TIME POINTS;

COMPUTERIZED TOMOGRAPHY; IMAGE SEGMENTATION; MAMMALS; PIPELINES; SYSTEMATIC ERRORS;

HEART;

ANIMAL; ARTICLE; C57BL MOUSE; FOUR DIMENSIONAL COMPUTED TOMOGRAPHY; HEART; IMAGE PROCESSING; IMAGE QUALITY; MALE; METHODOLOGY; MICRO-COMPUTED TOMOGRAPHY; MOUSE; RADIOGRAPHY;

ANIMALS; FOUR-DIMENSIONAL COMPUTED TOMOGRAPHY; HEART; IMAGE PROCESSING, COMPUTER-ASSISTED; MALE; MICE; MICE, INBRED C57BL; PHANTOMS, IMAGING; X-RAY MICROTOMOGRAPHY;

EID: 84866321601     PISSN: 00319155     EISSN: 13616560     Source Type: Journal    
DOI: 10.1088/0031-9155/57/19/6125     Document Type: Article

References (43)

1. Avants B B, Epstein C L, Grossman M and Gee J C 2008 Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain Med. Image Anal. 12 26-41
2. Avants B B, Tustison N J, Song G, Cook P A, Klein A and Gee J C 2011a A reproducible evaluation of ANTs similarity metric performance in brain image registration Neuroimage 54 2033-44
3. Avants B B, Tustison N J, Wu J, Cook P A and Gee J C 2011b An open source multivariate framework for n-tissue segmentation with evaluation on public data Neuroinformatics 9 381-400
4. Badea C, Hedlund L W and Johnson G A 2004 Micro-CT with respiratory and cardiac gating Med. Phys. 31 3324-9
5. Badea C T, Fubara B, Hedlund L W and Johnson G A 2005 4-D micro-CT of the mouse heart Mol. Imaging 4 110-6
6. Badea C T, Hedlund L W, Mackel J F B, Lan M, Rockman H A and Johnson G A 2007 Cardiac micro-computed tomography for morphological and functional phenotyping of muscle LIM protein null mice Mol. Imaging 6 261-8
7. Badea C T, Johnston S, Johnson B, Lin M, Hedlund L W and Johnson G A 2008a A dual micro-CT system for small animal imaging Proc. SPIE 6913 691342
8. Badea C T, Johnston S M, Qi Y and Johnson G A 2011 4D micro-CT for cardiac and perfusion applications with view under sampling Phys. Med. Biol. 56 3351-69
9. Badea C T, Wetzel A W, Mistry N, Pomerantz S, Nave D and Johnson G A 2008b Left ventricle volume measurements in cardiac micro-CT: the impact of radiation dose and contrast agent Comput. Med. Imaging Graph. 32 239-50
10. Bartling S H, Stiller W, Grasruck M, Schmidt B, Peschke P, Semmler W and Kiessling F 2007 Retrospective motion gating in small animal CT of mice and rats Invest. Radiol. 42 704-14
11. Beg M F, Miller M I, Trouve A and Younes L 2005 Computing large deformation metric mappings via geodesic flows of diffeomorphisms Int. J. Comput. Vis. 61 139-57
12. Brau A C S, Hedlund L W and Johnson G A 2004 Cine magnetic resonance microscopy of the rat heart using cardiorespiratory-synchronous projection reconstruction J. Magn. Reson. Imaging 20 31-8
13. Bucholz E, Ghaghada K, Qi Y, Mukundan S and Johnson G A 2008 Four-dimensional MR microscopy of the mouse heart using radial acquisition and liposomal gadolinium contrast agent Magn. Reson. Med. 60 111-8
14. Bucholz E, Ghaghada K, Qi Y, Mukundan S, Rockman H A and Johnson G A 2010 Cardiovascular phenotyping of the mouse heart using a 4D radial acquisition and liposomal Gd-DTPA-BMA Magn. Reson. Med. 63 979-87
15. Clark D, Johnson G A and Badea C T 2012 Denoising of 4D cardiac micro-CT data using median-centric bilateral filtration Proc. SPIE 8314 83143Z
16. Contag P R 2002 Whole-animal cellular and molecular imaging to accelerate drug development Drug Discov. Today 7 555-62
17. Cootes T F, Beeston C, Edwards G J and Taylor C J 1999 A unified framework for atlas matching using active appearance models Proc. Information Processing in Medical Imaging pp 322-33
18. Drangova M, Ford N L, Detombe S A, Wheatley A R and Holdsworth D W 2007 Fast retrospectively gated quantitative four-dimensional (4D) cardiac micro computed tomography imaging of free-breathing mice Invest. Radiol. 42 85-94
19. Epstein F H 2007 MRI of left ventricular function J. Nucl. Cardiol. 14 729-44
20. Feldkamp L A, Davis L C and Kress J W 1984 Practical cone-beam algorithm J. Opt. Soc. Am. A 1 612-9
21. Francis J J and De Jager G 2003 The bilateral median filter Proc. 14th Annual Symp. of the Pattern Recognition Association of South Africa (Langebaan, South Africa,) ed F Nicolls pp 57-62 (available at http://www.prasa.org/ proceedings/2003/PRASA2003.pdf)
22. Frangi A F, Niessen W J and Viergever M A 2001 Three-dimensional modeling for functional analysis of cardiac images: a review IEEE Trans. Med. Imaging 20 2-25
23. Frangi A F, Rueckert D, Schnabel J A and Niessen W J 2002 Automatic construction of multiple-object three-dimensional statistical shape models: application to cardiac modeling IEEE Trans. Med. Imaging 21 1151-66
24. Ghaghada K B, Badea C T, Karumbaiah L, Fettig N, Bellamkonda R V, Johnson G A and Annapragada A 2011 Evaluation of tumor microenvironment in an animal model using a nanoparticle contrast agent in computed tomography imaging Acad. Radiol. 18 20-30
25. Haraokawa T, Kanza R E, Kido T, Higashino H, Mochizuki T and Shen Y 2004 Accuracy of LV volume assessment using cardiac MSCT (RSNA, Chicago)
26. Heijman E, Aben J P, Penners C, Niessen P, Guillaume R, Van Eys G, Nicolay K and Strijkers G J 2008 Evaluation of manual and automatic segmentation of the mouse heart from CINE MR images J. Magn. Reson. Imaging 27 86-93
27. Howles G P, Nouls J C, Qi Y and Johnson G A 2009 Rapid production of specialized animal handling devices using computer-aided design and solid freeform fabrication J. Magn. Reson. Imaging 30 466-71
28. Klein A et al 2009 Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration Neuroimage 46 786-802
29. Lapp R M, Lorenzo-Valdés M and Rueckert D 2004 3D/4D cardiac segmentation using active appearance models, non-rigid registration, and the insight toolkit Medical Image Computing and Computer-Assisted Intervention (MICCAI 2004) Lect. Notes Comput. Sci. 3216 419-26
30. Lorenzo-Valdés M, Sanchez-Ortiz G I, Elkington A G, Mohiaddin R H and Rueckert D 2004 Segmentation of 4D cardiac MR images using a probabilistic atlas and the EM algorithm Medical Image Computing and Computer-Assisted Intervention (MICCAI 2003) Med. Image Anal. 8 255-65
31. Lorenzo-Valdés M, Sanchez-Ortiz G I, Mohiaddin R and Rueckert D 2002 Atlas-based segmentation and tracking of 3D cardiac MR images using non-rigid registration Medical Image Computing and Computer-Assisted Intervention (MICCAI 2002) Lect. Notes Comput. Sci. 2488 642-50
32. Mukundan S Jr, Ghaghada K B, Badea C T, Kao C Y, Hedlund L W, Provenzale J M, Johnson G A, Chen E, Bellamkonda R V and Annapragada A 2006 A liposomal nanoscale contrast agent for preclinical CT in mice Am. J. Roentgenol. 186 300-7
33. Murphy K et al 2011 Evaluation of registration methods on thoracic CT: the EMPIRE10 challenge IEEE Trans. Med. Imaging 30 1901-20
34. Parker D L 1982 Optimal short scan convolution reconstruction for fanbeam CT Med. Phys. 9 254-7
35. Perperidis D, Bucholz E, Johnson G A and Constantinides C 2012 Morphological studies of the murine heart based on probabilistic and statistical atlases Comput. Med. Imaging Graph. 36 119-29
36. Peyrat J M, Delingette H, Sermesant M, Xu C and Ayache N 2010 Registration of 4D cardiac CT sequences under trajectory constraints with multichannel diffeomorphic demons IEEE Trans. Med. Imaging 29 1351-68
37. Sawall S, Bergner F, Lapp R, Mronz M, Karolczak M, Hess A and Kachelriess M 2011 Low-dose cardio-respiratory phase-correlated cone-beam micro-CT of small animals Med. Phys. 38 1416-24
38. Segars W P, Tsui B M W, Frey E C, Johnson G A and Berr S S 2004 Development of a 4-D digital mouse phantom for molecular imaging research Mol. Imaging Biol. 6 149-59
39. Suri J S 2000 Computer vision, pattern recognition and image processing in left ventricle segmentation: the last 50 years Pattern Anal. Appl. 3 209-42
40. Tomasi C and Manduchi R 1998 Bilateral filtering for gray and color images Proc. 1998 IEEE Int. Conf. on Computer Vision pp 839-46
41. Wiesmann F, Frydrychowicz A, Rautenberg J, Illinger R, Rommel E, Haase A and Neubauer S 2002 Analysis of right ventricular function in healthy mice and a murine model of heart failure by in vivo MRI Am. J. Physiol. Heart Circ. Physiol. 283 H1065-71
42. Wise R G, Huang C L, Gresham G A, Al-Shafei A I, Carpenter T A and Hall L D 1998 Magnetic resonance imaging analysis of left ventricular function in normal and spontaneously hypertensive rats J. Physiol. 513 873-87
43. Yushkevich P A, Piven J, Hazlett H C, Smith R G, Ho S, Gee J C and Gerig G 2006 User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability Neuroimage 31 1116-28