Transformation diffusion reconstruction of three-dimensional histology volumes from two-dimensional image stacks

Medical Image Analysis - Tập 38 - Trang 184-204 - 2017
Ramón Casero1, Urszula Siedlecka2, Elizabeth S. Jones2, Lena Gruscheski2, Matthew Gibb1, Jürgen E. Schneider3, Peter Kohl4, Vicente Grau1
1Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK
2Heart Science Centre, National Lung and Heart Institute, Imperial College London, Harefield UB9 6JH, UK
3BHF Experimental MR Unit, Division of Cardiovascular Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
4Institute for Experimental Cardiovascular Medicine, University Heart Centre Freiburg – Bad Krozingen, School of Medicine, University of Freiburg, Elsässer Str 2Q, 79110 Freiburg, Germany

Tài liệu tham khảo

Adler, 2012, Reconstruction of the human hippocampus in 3D from histology and high-resolution ex-vivo MRI, 294 Adler, 2014, Histology-derived volumetric annotation of the human hippocampal subfields in postmortem MRI, NeuroImage, 84, 505, 10.1016/j.neuroimage.2013.08.067 Alexa, 2002, Linear combination of transformations, 380 Ali, 1998, Registering coronal histological 2-D sections of a rat brain with coronal sections of a 3-D brain atlas using geometric curve invariants and B-spline representation, IEEE Trans. Med. Imaging, 17, 957, 10.1109/42.746628 Amunts, 2013, BigBrain: an ultrahigh-resolution 3D human brain model, Science, 340, 1472, 10.1126/science.1235381 Amunts, 2015, Architectonic mapping of the human brain beyond brodmann, Neuron, 88, 1086, 10.1016/j.neuron.2015.12.001 Annese, 2012, The importance of combining MRI and large-scale digital histology in neuroimaging studies of brain connectivity and disease, Front. Neuroinformatics, 6, 13, 10.3389/fninf.2012.00013 Arganda-Carreras, 2010, 3D reconstruction of histological sections: application to mammary gland tissue, Microsc. Res. Tech., 73, 1019, 10.1002/jemt.20829 Atkinson, 2014 Bardinet, 2002, Co-registration of histological, optical and MR data of the human brain Bloom, C., Blow, J., Muratori, C., 2004. Errors and Omissions in Marc Alexa's. “Linear Combination of Transformations”. Bub, 2010, Measurement and analysis of sarcomere length in rat cardiomyocytes in situ and in vitro, Am. J. Physiol. - Heart Circ. Physiol, 298, H1616, 10.1152/ajpheart.00481.2009 Burton, 2006, Three-dimensional models of individual cardiac histoanatomy: tools and challenges, Ann. N. Y. Acad. Sci., 1080, 301, 10.1196/annals.1380.023 Burton, 2014, Three-dimensional histology: tools and application to quantitative assessment of cell-type distribution in rabbit heart, Europace, 16, iv86, 10.1093/europace/euu234 Casero, 2016, Block-face imaging of wax-embedded tissue as a necessary step in the three-dimensional reconstruction of the heart structure, P1685 Casero, 2017, 3D histology reconstruction with external blockface reference Ceritoglu, 2010, Large deformation diffeomorphic metric mapping registration of reconstructed 3D histological section images and in vivo MR images, Front. Hum. Neurosci, 4 Choi, 2000, Injectivity conditions of 2D and 3D uniform cubic B-spline functions, Graph. Models, 62, 411, 10.1006/gmod.2000.0531 Chun, 2009, A simple regularizer for B-spline nonrigid image registration that encourages local invertibility, IEEE J. Sel. Top. Signal Process., 3, 159, 10.1109/JSTSP.2008.2011116 Cifor, 2011, Smoothness-guided 3-D reconstruction of 2-D histological images, NeuroImage, 56, 197, 10.1016/j.neuroimage.2011.01.060 Cifor, 2009, Smooth 3-D Reconstruction for 2-D Histological Images Feuerstein, 2011, Reconstruction of 3-D histology images by simultaneous deformable registration Fónyad, 2015, 3-dimensional digital reconstruction of the murine coronary system for the evaluation of chronic allograft vasculopathy, Diagn. Pathol., 10, 16, 10.1186/s13000-015-0248-6 Gaffling, 2015, A Gauss–Seidel iteration scheme for reference-free 3-D histological image reconstruction, IEEE Trans. Med. Imaging, 34, 514, 10.1109/TMI.2014.2361784 Gefen, 2003, Elastic 3-D alignment of rat brain histological images, IEEE Trans. Med. Imaging, 22, 1480, 10.1109/TMI.2003.819280 Gibb, 2012, Resolving the three-dimensional histology of the heart Gilbert, 2012, Visualization and quantification of whole rat heart laminar structure using high-spatial resolution contrast-enhanced MRI, Am. J. Physiol. Heart Circ. Physiol., 302, H287, 10.1152/ajpheart.00824.2011 Glocker, 2008, Dense image registration through MRFs and efficient linear programming, Med. Image Anal., 12, 731, 10.1016/j.media.2008.03.006 Gruscheski, 2015, Dual block-face imaging of wax-embedded whole heart on a motorized rotary microtome for improved serial two-dimensional histology stack acquisition, Proc. Physiol. Soc., 34 Guest, 1995, Automatic reconstruction of serial sections using the finite element method, Bioimaging, 3, 154, 10.1002/1361-6374(199512)3:4<154::AID-BIO2>3.0.CO;2-M Hartley, 2003 He, 1995, Three-dimensional reconstruction of the rubrocerebellar premotor network of the turtle, NeuroImage, 2, 21, 10.1006/nimg.1995.1005 Iglesias, 2015, Multi-atlas segmentation of biomedical images: a survey, Med. Image Anal., 24, 205, 10.1016/j.media.2015.06.012 Ju, 2006, 3D volume reconstruction of a mouse brain from histological sections using warp filtering, J. Neurosci. Methods, 156, 84, 10.1016/j.jneumeth.2006.02.020 Khimchenko, 2016, Extending two-dimensional histology into the third dimension through conventional micro computed tomography, NeuroImage, 139, 26, 10.1016/j.neuroimage.2016.06.005 Kim, 1997, Mutual information for automated unwarping of rat brain autoradiographs, NeuroImage, 5, 31, 10.1006/nimg.1996.0251 Klein, 2010, elastix: a toolbox for intensity-based medical image registration, IEEE Trans. Med. Imaging, 29, 196, 10.1109/TMI.2009.2035616 Machin, 1996, Computerized graphic imaging for three-dimensional representation: general principles and applications to embryo/fetal development, Int. Rev. Exp. Pathol., 36, 1 Magee, 2015, Histopathology in 3D: From three-dimensional reconstruction to multi-stain and multi-modal analysis, J. Pathol. Inform, 6, 10.4103/2153-3539.151890 Malandain, 2004, Fusion of autoradiographs with an MR volume using 2-D and 3-D linear transformations, NeuroImage, 23, 111, 10.1016/j.neuroimage.2004.04.038 Mansoori, 2007, An iterative method for registration of high-resolution cardiac histoanatomical and MRI images, 572 Mega, 1997, Mapping histology to metabolism: coregistration of stained whole-brain sections to premortem PET in Alzheimer's disease, NeuroImage, 5, 147, 10.1006/nimg.1996.0255 Moigne, 2011 Müller, 2014, Deformable reconstruction of histology sections using structural probability maps Narasimhan, 1999, Fourier's heat conduction equation: history, influence, and connections, Rev. Geophys., 37, 151, 10.1029/1998RG900006 Ourselin, 2001, Reconstructing a 3D structure from serial histological sections, Image Vis. Comput., 19, 25, 10.1016/S0262-8856(00)00052-4 Plank, 2009, Generation of histo-anatomically representative models of the individual heart: tools and application, Philos. Transact. A Math. Phys. Eng. Sci., 367, 2257 Pletcher, 2013, Computational fluid mechanics and heat transfer Reddy, 1996, An FFT-based technique for translation, rotation, and scale-invariant image registration, IEEE Trans. Image Process., 5, 1266, 10.1109/83.506761 Roache, 1972 Roberts, 2012, Toward routine use of 3D histopathology as a research tool, Am. J. Pathol., 180, 1835, 10.1016/j.ajpath.2012.01.033 Rohlfing, 2012, Image similarity and tissue overlaps as surrogates for image registration accuracy: widely used but unreliable, IEEE Trans. Med. Imaging, 31, 153, 10.1109/TMI.2011.2163944 Rueckert, 2006, Diffeomorphic registration using B-splines Rusu, 2015, Framework for 3D histologic reconstruction and fusion with in vivo MRI: Preliminary results of characterizing pulmonary inflammation in a mouse model, Med. Phys, 42, 4822, 10.1118/1.4923161 Saalfeld, 2012, Elastic volume reconstruction from series of ultra-thin microscopy sections, Nat. Methods, 9, 717, 10.1038/nmeth.2072 Schmitt, 2006, Image Registration of Sectioned Brains, Int. J. Comput. Vis., 73, 5, 10.1007/s11263-006-9780-x Schoenberg, 1946, Contributions to the problem of approximation of equidistant data by analytic functions. Part A - On the problem of smoothing or graduation. A first class of analytic approximation formulae, Quart Appl Math, 4, 45, 10.1090/qam/15914 Schormann, 1995, Statistics of deformations in histology and application to improved alignment with MRI, IEEE Trans. Med. Imaging, 14, 25, 10.1109/42.370399 Schubert, 2016, 3D reconstructed cyto-, muscarinic M2 receptor, and fiber architecture of the rat brain registered to the Waxholm Space Atlas, Front. Neuroanat, 10, 10.3389/fnana.2016.00051 Shamonin, 2014, Fast parallel image registration on CPU and GPU for diagnostic classification of Alzheimer's disease, Front. Neuroinformatics, 7, 50 Siedlecka, 2013, Three-dimensional histological reconstruction of the heart guided by block-face imaging of wax-embedded tissue Siedlecka, 2013, Block-face imaging of wax-embedded tissue as a modality to aid three-dimensional histological reconstruction of the heart, p. PCD033 Siedlecka, 2017, Serial histology and blockface images Song, 2013, 3D reconstruction of multiple stained histology images, J. Pathol. Inform., 4, 7, 10.4103/2153-3539.109864 Stille, 2013, 3D reconstruction of 2D fluorescence histology images and registration with in vivo MR images: application in a rodent stroke model, J. Neurosci. Methods, 219, 27, 10.1016/j.jneumeth.2013.06.003 Streicher, 2000, Computer-based three-dimensional visualization of developmental gene expression, Nat. Genet., 25, 147, 10.1038/75989 Streicher, 1997, External marker-based automatic congruencing: a new method of 3D reconstruction from serial sections, Anat. Rec., 248, 583, 10.1002/(SICI)1097-0185(199708)248:4<583::AID-AR10>3.0.CO;2-L Thompson, 1996, A surface-based technique for warping three-dimensional images of the brain, IEEE Trans. Med. Imaging, 15, 402, 10.1109/42.511745 Timsari, 1999, Accurate registration of autoradiographic images of rat brain using a 3-D atlas, 285 Toga, 1994, High-resolution anatomy from in situ human brain, NeuroImage, 1, 334, 10.1006/nimg.1994.1018 Vercauteren, 2007, Diffeomorphic demons using ITK's finite difference solver hierarchy, Insight J., 1 Wirtz, S., Fischer, B., Modersitzki, J., Schmitt, O., 2004. Superfast elastic registration of histologic images of a whole rat brain for 3D reconstruction. pp. 328–334. doi:10.1117/12.534110. Xu, 2015, A method for 3D histopathology reconstruction supporting mouse microvasculature analysis, PLoS ONE, 10 Yarlagadda, 2010 Yushkevich, 2006, 3D mouse brain reconstruction from histology using a coarse-to-fine approach Zacur, 2014, Left-invariant riemannian geodesics on spatial transformation groups, SIAM J. Imaging Sci., 7, 1503, 10.1137/130928352