Abstract
High-resolution large datasets were acquired to improve the understanding of murine bone physiology. The purpose of this work is to present the challenges and solutions in segmenting and visualizing bone in such large datasets acquired using micro-CT scan of mice. The analyzed dataset is more than 50 GB in size with more than 6,000 2,048 × 2,048 slices. The study was performed to automatically measure the bone mineral density (BMD) of the entire skeleton. A global Renyi entropy (GREP) method was initially used for bone segmentation. This method consistently oversegmented skeletal region. A new method called adaptive local Renyi entropy (ALREP) is proposed to improve the segmentation results. To study the efficacy of the ALREP, manual segmentation was performed. Finally, a specialized high-end remote visualization system along with the software, VirtualGL, was used to perform remote rendering of this large dataset. It was determined that GREP overestimated the bone cross-section by around 30 % compared with ALREP. The manual segmentation process took 6,300 min for 6,300 slices while ALREP took only 150 min for segmentation. Automatic image processing with ALREP method may facilitate BMD measurement of the entire skeleton in a significantly reduced time, compared with manual process.
References
Feldkamp LA, et al: The direct examination of three-dimensional bone architecture in vitro by computed tomography. J Bone Miner Res 4:3–11, 1989
Patel V, et al: Self-calibration of a cone-beam micro-CT system. Med Phys 36:48, 2009
Ionita CN, et al: Cone-beam micro-CT system based on LabVIEW software. J Digit Imaging 21(3):296–305, 2008
Feldkamp LA, et al: Practical cone-beam algorithm. J Opt Soc Am 1:612–619, 1984
De Clerck NM, et al: Non-invasive high-resolution mCT of the inner structure of living animals. Microsc Anal 81:13–15, 2003
Postnov AA, et al: 3D in vivo X-ray microtomography of living snails. J Microsc 205:201, 2002
Postnov AA, et al: Quantitative analysis of bone mineral content by X-ray microtomography. Physiol Meas 24:165–167, 2003
Holdsworth DW, et al: Micro-CT in small animal and specimen imaging. Trends Biotechnol 20(8):S34–S39, 2002
Appleton CT et al: Forced mobilization accelerates pathogenesis: characterization of a preclinical surgical model of osteoarthritis. Arthritis Res Ther 9:R13, 2007
McErlain DD, et al: Study of subchondral bone adaptations in a rodent surgical model of OA using in vivo micro-computed tomography. Osteoarthr Cartil 16:458–469, 2008
Granton PV, et al: Rapid in vivo whole-body composition of rats using cone-beam micro-CT. J Appl Physiol 109(4):1162–1169, 2010
Kapur JN, et al: A new method for gray-level picture thresholding using the entropy of the histogram. Graph Models Image Process 29(3):273–285, 1985
Avizo®. http://www.vsg3d.com/avizo/overview Accessed on 19 Aug 2011
Yen JC, Chang FJ, Chang S: A new criterion for automatic multilevel thresholding. IEEE Trans Image Process 4(3):370–378, 1995
The VirtualGL Project. http://www.virtualgl.org. Accessed on 19 Aug 2011
Hui SK, Fairchild GR, Kidder LS, Sharma M, Bhattacharya M, Jackson S, Le C, Yee D: Skeletal remodeling following clinically relevant radiation-induced bone damage treated with zoledronic acid. Calcif Tissue Int 90:40–49, 2012
Hui SK, Khalil A, Zhang Y, Coghill K, Le C, Dusenbery K, Froelich J, Yee D, Downs L: Longitudinal assessment of bone loss from diagnostic computed tomography scans in gynecologic cancer patients treated with chemotherapy and radiation. Am J Obstet Gynecol 203(4):353.e1–7, 2010
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary materials
Below is the link to the electronic supplementary material.
(MOV 1.11 MB)
Rights and permissions
About this article
Cite this article
Chityala, R., Pudipeddi, S., Arensten, L. et al. Segmentation and Visualization of a Large, High-Resolution Micro-CT Data of Mice. J Digit Imaging 26, 302–308 (2013). https://doi.org/10.1007/s10278-012-9498-y
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10278-012-9498-y