Abstract
Three dimensional microscopy images present significant potential to enhance biomedical studies. This paper presents an automated method for quantitative analysis of 3D primary vessel structures with histology whole slide images. With registered microscopy images of liver tissue, we identify primary vessels with an improved variational level set framework at each 2D slide. We propose a Vessel Directed Fitting Energy (VDFE) to provide prior information on vessel wall probability in an energy minimization paradigm. We find the optimal vessel cross-section associations along the image sequence with a two-stage procedure. Vessel mappings are first found between each pair of adjacent slides with a similarity function for four association cases. These bi-slide vessel components are further linked by Bayesian Maximum A Posteriori (MAP) estimation where the posterior probability is modeled as a Markov chain. The efficacy of the proposed method is demonstrated with 54 whole slide microscopy images of sequential sections from a human liver.
Chapter PDF
References
Foran, D.J., Chen, W., Yang, L.: Automated Image Interpretation Computer-assisted Diagnosis. Ana. Cell. Path. 34(6), 279–300 (2011)
Roberts, N., Magee, D., Song, Y., Brabazon, K., Shires, M., Crellin, D., Orsi, N.M., Quirke, R., Quirke, P., Treanor, D.: Toward Routine Use of 3D Histopathology as a Research Tool. Am. J. of Path. 180(5), 1835–1842 (2012)
Schwier, M., Hahn, H.K., Dahmen, U., Dirsch, O.: Reconstruction of Vessel Structures from Serial Whole Slide Sections of Murine Liver Samples. In: Proc. SPIE, Medical Imaging, vol. 8676 (2013)
Li, C., Huang, R., Ding, Z., Gatenby, C., Metaxas, D., Gore, J.: A Level Set Method for Image Segmentation in the Presence of Intensity Inhomogeneity With Application to MRI. IEEE Trans. Image Process. 20, 2007–2016 (2011)
Li, C., Kao, C., Gore, J.C., Ding, Z.: Implicit Active Contours Driven by Local Binary Fitting Energy. In: IEEE Comp. Vis. and Pat. Rec., pp. 1–7 (2007)
Frangi, A.F., Niessen, W.J., Vincken, K.L., Viergever, M.A.: Multiscale Vessel Enhancement Filtering. In: Wells, W.M., Colchester, A.C.F., Delp, S.L. (eds.) MICCAI 1998. LNCS, vol. 1496, pp. 130–137. Springer, Heidelberg (1998)
Ruifrok, A.C., Johnston, D.A.: Quantification of Histochemical Staining by Color Deconvolution. Anal. Quant. Cytol. Histol. 23, 291–299 (2001)
Li, C., Xu, C., Gui, C., Fox, M.D.: Distance Regularized Level Set Evolution and Its Application to Image Segmentation. IEEE TIP 19, 3243–3254 (2010)
Dantzig, G.B.: Linear Programming and Extensions. Princeton Press (1963)
Berclaz, J., Fleuret, F., Fua, P.: Multiple Object Tracking using Flow Linear Programming. In: Winter-PETS (2009)
Bise, R., Yin, Z., Kanade, T.: Reliable Cell Tracking by Global Data Association. In: ISBI (2011)
Vincent, L.: Morphological Grayscale Reconstruction in Image Analysis: Applications and Efficient Algorithms. IEEE TIP 2, 176–201 (1993)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Liang, Y. et al. (2015). A 3D Primary Vessel Reconstruction Framework with Serial Microscopy Images. In: Navab, N., Hornegger, J., Wells, W., Frangi, A. (eds) Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015. MICCAI 2015. Lecture Notes in Computer Science(), vol 9351. Springer, Cham. https://doi.org/10.1007/978-3-319-24574-4_30
Download citation
DOI: https://doi.org/10.1007/978-3-319-24574-4_30
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-24573-7
Online ISBN: 978-3-319-24574-4
eBook Packages: Computer ScienceComputer Science (R0)