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

West JB: Pulmonary Pathophysiology. 1998, Philadelphia: Lippincott Williams & Wilkins, 5

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Glenny RW, Robertson HT: Fractal properties of pulmonary blood flow: characterization of spatial heterogeneity. J Appl Physiol. 1990, 69 (2): 532-545.

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.

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.

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. Edited by: Hoffman EA. 1995, Bellingham, WA: SPIE, 133-142. 2433

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.

Subramaniam K, Hoffman EA, Tawhai MH: Quantifying tissue heterogeneity using quadtree decomposition. Conf Proc IEEE Eng Med Biol Soc. 2012, 2012: 4079-4082.

Shephard MS, Georges MK: Automatic 3-dimensional mesh generation by the finite octree technique. Int J Numer Meth Eng. 1991, 32 (4): 709-749. 10.1002/nme.1620320406.

Zhang JH, Owen CB: Octree-based animated geometry compression. Comput Graph-Uk. 2007, 31 (3): 463-479. 10.1016/j.cag.2006.12.002.

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. 10.1007/BF00055001.

Zhang YJ, Bajaj C, Sohn BS: 3D finite element meshing from imaging data. Comput Method Appl M. 2005, 194 (48–49): 5083-5106.

Dua S, Kandiraju N, Chowriappa P: Region quad-tree decomposition based edge detection for medical images. Open Med Inform J. 2010, 4: 50-57.

Clark I, Harper WV: Practical Geostatistics 2000. 2000, Columbus, Ohio: Ecosse North America, LLC

Gringarten E, Deutsch CV: Variogram interpretation and modeling. Math Geol. 2001, 33 (4): 507-534. 10.1023/A:1011093014141.

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.

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.

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.

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.

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.

ImageJ. http://imagej.nih.gov/ij/ ,

ImageJ Plugins: 3D Toolkit. http://ij-plugins.sourceforge.net/plugins/3d-toolkit/index.html ,

Jackins CL, Tanimoto SL: Oct-trees and their use in representing three dimensional objects. Computer Graphics and Image Processing. 1980, 14 (3): 249-270. 10.1016/0146-664X(80)90055-6.

Schulz H, Mühle H: Respiration. The Laboratory Rat. Edited by: Krinke GJ. 2000, San Diego: Academic Press, 323-336.

Spencer H: Pathology of the Lung. Volume Volume 1. 1985, New York: Pergamon Press, 557-594. 4

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. Edited by: Metaxas D, Axel L, Szekely G. 2008, New York, NY: Springer, 322-330.

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, Nice, France: Springer, 86-93.

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-

Bohling GC: Introduction to Geostatistics. Kansas Geological Survey Open File Report no. 2007-26. 2007, 50-

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.

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.