Automated measurement of heterogeneity in CT images of healthy and diseased rat lungs using variogram analysis of an octree decomposition

BMC Medical Imaging

Volumn 14, Issue 1, 2014, Pages

  Jacob, Richard E ^a   Carson, James P ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

COPD; Disease detection; Emphysema; Lung imaging; Octree; Pulmonary; Variogram

Indexed keywords

ANIMAL; ARTICLE; COMPUTER ASSISTED DIAGNOSIS; COMPUTER ASSISTED TOMOGRAPHY; DISEASE MODEL; EMPHYSEMA; LUNG; MALE; METHODOLOGY; PATHOLOGY; RADIOGRAPHY; RAT; SENSITIVITY AND SPECIFICITY; SPRAGUE DAWLEY RAT; THREE DIMENSIONAL IMAGING;

ANIMALS; DISEASE MODELS, ANIMAL; EMPHYSEMA; IMAGING, THREE-DIMENSIONAL; LUNG; MALE; RADIOGRAPHIC IMAGE INTERPRETATION, COMPUTER-ASSISTED; RATS; RATS, SPRAGUE-DAWLEY; SENSITIVITY AND SPECIFICITY; TOMOGRAPHY, X-RAY COMPUTED;

EID: 84893818873     PISSN: None     EISSN: 14712342     Source Type: Journal    
DOI: 10.1186/1471-2342-14-1     Document Type: Article

References (40)

1. West JB. Pulmonary Pathophysiology 1998, Philadelphia: Lippincott Williams & Wilkins, 5.
2. Mets OM, De Jong PA, Van Ginneken B, Gietema HA, Lammers JW. Quantitative computed tomography in COPD: possibilities and limitations. Lung 2012, 190(2):133-145. 10.1007/s00408-011-9353-9, 3310986, 22179694.
3. Robertson HT, Buxton RB. Imaging for lung physiology: what do we wish we could measure?. J Appl Physiol 2012, 113(2):317-327. 10.1152/japplphysiol.00146.2012, 22582217.
4. Litmanovich D, Boiselle PM, Bankier AA. CT of pulmonary emphysema-current status, challenges, and future directions. Eur Radiol 2009, 19(3):537-551. 10.1007/s00330-008-1186-4, 18825385.
5. Chong D, Brown MS, Kim HJ, Van Rikxoort EM, Guzman L, McNitt-Gray MF, Khatonabadi M, Galperin-Aizenberg M, Coy H, Yang K, et al. Reproducibility of volume and densitometric measures of emphysema on repeat computed tomography with an interval of 1 week. Eur Radiol 2012, 22(2):287-294. 10.1007/s00330-011-2277-1, 22011903.
6. Uppaluri R, Mitsa T, Sonka M, Hoffman EA, McLennan G. Quantification of pulmonary emphysema from lung computed tomography images. Am J Respir Crit Care Med 1997, 156(1):248-254. 10.1164/ajrccm.156.1.9606093, 9230756.
7. Besir FH, Mahmutyazicioglu K, Aydin L, Altin R, Asil K, Gundogdu S. The benefit of expiratory-phase quantitative CT densitometry in the early diagnosis of chronic obstructive pulmonary disease. Diagn Interv Radiol 2012, 18(3):248-254.
8. Irion KL, Marchiori E, Hochhegger B, Porto Nda S, Moreira Jda S, Anselmi CE, Holemans JA, Irion PO. CT quantification of emphysema in young subjects with no recognizable chest disease. AJR Am J Roentgenol 2009, 192(3):W90-W96.
9. Reske AW, Busse H, Amato MB, Jaekel M, Kahn T, Schwarzkopf P, Schreiter D, Gottschaldt U, Seiwerts M. Image reconstruction affects computer tomographic assessment of lung hyperinflation. Intensive Care Med 2008, 34(11):2044-2053. 10.1007/s00134-008-1175-8, 18537024.
10. Yuan R, Mayo JR, Hogg JC, Pare PD, McWilliams AM, Lam S, Coxson HO. The effects of radiation dose and CT manufacturer on measurements of lung densitometry. Chest 2007, 132(2):617-623. 10.1378/chest.06-2325, 17573501.
11. Chen CC, Daponte JS, Fox MD. Fractal feature analysis and classification in medical imaging. IEEE Trans Med Imaging 1989, 8(2):133-142. 10.1109/42.24861, 18230510.
12. Glenny RW, Robertson HT. Fractal properties of pulmonary blood flow: characterization of spatial heterogeneity. J Appl Physiol 1990, 69(2):532-545.
13. Copley SJ, Giannarou S, Schmid VJ, Hansell DM, Wells AU, Yang GZ. Effect of aging on lung structure in vivo: assessment with densitometric and fractal analysis of high-resolution computed tomography data. J Thorac Imaging 2012, 27(6):366-371. 10.1097/RTI.0b013e31825148c9, 22487994.
14. Kido S, Ikezoe J, Naito H, Tamura S, Machi S. Fractal analysis of interstitial lung abnormalities in chest radiography. Radiographics 1995, 15(6):1457-1464. 10.1148/radiographics.15.6.8577968, 8577968.
15. Uppaluri R, Mitsa T, Galvin JR. Fractal analysis of high-resolution CT images as a tool for quantification of lung disease. Medical Imaging 1995: Physiology and Function from Multidimensional Images 1995, 133-142. Bellingham, WA: SPIE, Hoffman EA, 2433.
16. Kido S, Sasaki S. Fractal analysis for quantitative evaluation of diffuse lung abnormalities on chest radiographs: use of sub-ROIs. J Thorac Imaging 2003, 18(4):237-241. 10.1097/00005382-200310000-00005, 14561909.
17. Subramaniam K, Hoffman EA, Tawhai MH. Quantifying tissue heterogeneity using quadtree decomposition. Conf Proc IEEE Eng Med Biol Soc 2012, 2012:4079-4082.
18. Shephard MS, Georges MK. Automatic 3-dimensional mesh generation by the finite octree technique. Int J Numer Meth Eng 1991, 32(4):709-749.
19. Zhang JH, Owen CB. Octree-based animated geometry compression. Comput Graph-Uk 2007, 31(3):463-479.
20. Szeliski R, Lavallee S. Matching 3-D anatomical surfaces with non-rigid deformations using octree-splines. Int J Comput Vision 1996, 18(2):171-186.
21. Zhang YJ, Bajaj C, Sohn BS. 3D finite element meshing from imaging data. Comput Method Appl M 2005, 194(48-49):5083-5106.
22. Dua S, Kandiraju N, Chowriappa P. Region quad-tree decomposition based edge detection for medical images. Open Med Inform J 2010, 4:50-57. 2916208, 20694158.
23. Clark I, Harper WV. Practical Geostatistics 2000 2000, Columbus, Ohio: Ecosse North America, LLC.
24. Gringarten E, Deutsch CV. Variogram interpretation and modeling. Math Geol 2001, 33(4):507-534.
25. Keil F, Oros-Peusquens AM, Shah NJ. Investigation of the spatial correlation in human white matter and the influence of age using 3-dimensional variography applied to MP-RAGE data. Neuroimage 2012, 63(3):1374-1383. 10.1016/j.neuroimage.2012.07.034, 22836175.
26. Jacob RE, Minard KR, Laicher G, Timchalk C. 3D 3He diffusion MRI as a local in vivo morphometric tool to evaluate emphysematous rat lungs. J Appl Physiol 2008, 105(4):1291-1300. 10.1152/japplphysiol.90375.2008, 2576039, 18719237.
27. Jacob RE, Lamm WJ. Stable small animal ventilation for dynamic lung imaging to support computational fluid dynamics models. PLoS One 2011, 6(11):e27577. 10.1371/journal.pone.0027577, 3210813, 22087338.
28. Corley RA, Kabilan S, Kuprat AP, Carson JP, Minard KR, Jacob RE, Timchalk C, Glenny R, Pipavath S, Cox T, et al. Comparative computational modeling of airflows and vapor dosimetry in the respiratory tracts of rat, monkey, and human. Toxicol Sci 2012, 128(2):500-516. 10.1093/toxsci/kfs168, 3524950, 22584687.
29. Minard KR, Kuprat AP, Kabilan S, Jacob RE, Einstein DR, Carson JP, Corley RA. Phase-contrast MRI and CFD modeling of apparent (3)He gas flow in rat pulmonary airways. J Magn Reson 2012, 221:129-138. 3448557, 22771528.
30. ImageJ. http://imagej.nih.gov/ij/.
31. ImageJ Plugins: 3D Toolkit. http://ij-plugins.sourceforge.net/plugins/3d-toolkit/index.html.
32. Jackins CL, Tanimoto SL. Oct-trees and their use in representing three dimensional objects. Computer Graphics and Image Processing 1980, 14(3):249-270.
33. Schulz H, Mühle H. Respiration. The Laboratory Rat 2000, 323-336. San Diego: Academic Press, Krinke GJ.
34. Spencer H. Pathology of the Lung. Volume Volume 1 1985, 557-594. New York: Pergamon Press, 4.
35. El-Baz A, Gimel'farb G, Falk R, Holland T, Shaffer T. A new stochastic framework for accurate lung segmentation. Medical Image Computing and Computer-Assisted Intervention-MICCAI 2008, 322-330. New York, NY: Springer, Metaxas D, Axel L, Szekely G.
36. Abdollahi B, Soliman A, Civelek AC, Li XF, Gimel'farb G, El-Baz A. A novel 3D joint MGRF framework for precise lung segmentation. Third International Workshop MLMI: 2012 2012, 86-93. Nice, France: Springer.
37. El-Baz A, Beache GM, Gimel'farb G, Suzuki K, Okada K, Elnakib A, Soliman A, Abdollahi B. Computer-aided diagnosis systems for lung cancer: challenges and methodologies. Int J Biomed Imaging 2013, 2013:942353. 3570946, 23431282.
38. Bohling GC. Introduction to Geostatistics. Kansas Geological Survey Open File Report no. 2007-26 2007, 50.
39. Hsia CC, Hyde DM, Ochs M, Weibel ER. An official research policy statement of the American Thoracic Society/European Respiratory Society: standards for quantitative assessment of lung structure. Am J Respir Crit Care Med 2010, 181(4):394-418. 10.1164/rccm.200809-1522ST, 20130146.
40. Jacob RE, Carson JP, Gideon KM, Amidan BG, Smith CL, Lee KM. Comparison of two quantitative methods of discerning airspace enlargement in smoke-exposed mice. PLoS One 2009, 4(8):e6670. 10.1371/journal.pone.0006670, 2722737, 19688093.