Oleg Lobachev
ABSTRACT
Histological serial sections allow for 3D representation of anatomical structures in microscopic to mesoscopic range. However, due to the nature of the acquisition, they suffer from severe anisotropy: 14-to-1 in a single average microscopic paraffin section. We present an interpolation method based on optical flow and show that standard interpolation methods are less suited for serial sections.
With our non-linear interpolation approach we are able to represent the "movement" of image parts that are of interest. This allows for better 3D reconstructions and further insights in microanatomy.
- Simon Baker, Daniel Scharstein, J. P. Lewis, Stefan Roth, Michael J. Black, and Richard Szeliski. 2011. A Database and Evaluation Methodology for Optical Flow. International Journal of Computer Vision 92, 1 (2011), 1--31. Google Scholar
Digital Library
- J. L. Barron, D. J. Fleet, and S. S. Beauchemin. 1994. Performance of optical flow techniques. International Journal of Computer Vision 12, 1 (1994), 43--77. Google ScholarDigital Library
- U. Baǧci and L. Bai. 2008. Registration of standardized histological images in feature space. In Proc. SPIE, Vol. 6914.Google Scholar
- Gary Bradski and Adrian Kaehler. 2008. Learning OpenCV: Computer vision with the OpenCV library. O'Reilly.Google Scholar
- T. Brox, A. Bruhn, N. Papenberg, and J. Weickert. 2004. High accuracy optical flow estimation based on a theory for warping. In European Conference on Computer Vision (ECCV) (LNCS 3024). Springer, 25--36. http://lmb.informatik.uni-freiburg.de//Publications/2004/Bro04aGoogle Scholar
- T. Brox and J. Malik. 2011. Large Displacement Optical Flow: Descriptor Matching in Variational Motion Estimation. IEEE Transactions on Pattern Analysis and Machine Intelligence 33, 3 (2011), 500--13. Google ScholarDigital Library
- Wilhelm Burger and Mark James Burge. 2009. Principles of digital image processing. Springer. Google ScholarDigital Library
- Albert Cardona, Stephan Saalfeld, Stephan Preibisch, Benjamin Schmid, Anchi Cheng, Jim Pulokas, Pavel Tomancak, and Volker Hartenstein. 2010. An Integrated Micro-and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy. PLOS Biology 8, 10 (10 2010), 1--17.Google Scholar
- Jonathan Chappelow, B. Nicolas Bloch, Neil Rofsky, Elizabeth Genega, Robert Lenkinski, William DeWolf, and Anant Madabhushi. 2011. Elastic registration of multimodal prostate MRI and histology via multiattribute combined mutual information. Med. Phys. 38, 4 (2011), 2005--18.Google ScholarCross Ref
- Amalia Cifor, Li Bai, and Alain Pitiot. 2011. Smoothness-guided 3-D reconstruction of 2-D histological images. NeuroImage 56, 1 (2011), 197--211.Google ScholarCross Ref
- Claude E Duchon. 1979. Lanczos filtering in one and two dimensions. Journal of Applied Meteorology 18, 8 (1979), 1016--22.Google ScholarCross Ref
- Jan Ehrhardt, René Werner, Dennis Säring, Thorsten Frenzel, Wei Lu, Daniel Low, and Heinz Handels. 2007. An optical flow based method for improved reconstruction of 4D CT data sets acquired during free breathing. Medical Physics 34, 2 (2007), 711--21.Google ScholarCross Ref
- Gunnar Farnebäck. 2003. Two-Frame Motion Estimation Based on Polynomial Expansion. In Image Analysis, Josef Bigun and Tomas Gustavsson (Eds.). 363--70. Google ScholarDigital Library
- Andriy Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Julien Finet, Jean-Christophe Fillion-Robin, Sonia Pujol, Christian Bauer, Dominique Jennings, Fiona Fennessy, Milan Sonka, et al. 2012. 3D Slicer as an image computing platform for the Quantitative Imaging Network. Magn. Reson. Imaging 30, 9 (2012), 1323--41.Google ScholarCross Ref
- J. M. Gijtenbeek, P. Wesseling, C. Maass, L. Burgers, and J. A. van der Laak. 2005. Three-dimensional reconstruction of tumor microvasculature: simultaneous visualization of multiple components in paraffin-embedded tissue. Angiogenesis 8, 4 (2005), 297--305.Google ScholarCross Ref
- E. Guest, E. Berry, R.A. Baldock, M. Fidrich, and M.A. Smith. 2001. Robust point correspondence applied to two- and three-dimensional image registration. IEEE T. Pattern Anal. Mach. Intell. 23, 2 (2001), 165--79. Google ScholarDigital Library
- Berthold K.P. Horn and Brian G. Schunck. 1981. Determining optical flow. Artificial Intelligence 17, 1 (1981), 185--203. Google ScholarDigital Library
- Tao Ju. 2004. Robust repair of polygonal models. ACM T. Graphic. 23, 3 (2004), 888--95. Google ScholarDigital Library
- Stephen L. Keeling and Wolfgang Ring. 2005. Medical Image Registration and Interpolation by Optical Flow with Maximal Rigidity. Journal of Mathematical Imaging and Vision 23, 1 (2005), 47--65. Google ScholarDigital Library
- R. Keys. 1981. Cubic convolution interpolation for digital image processing. IEEE Transactions on Acoustics, Speech, and Signal Processing 29, 6 (1981), 1153--60.Google ScholarCross Ref
- A. M. Khan, N. Rajpoot, D. Treanor, and D. Magee. 2014. A Nonlinear Mapping Approach to Stain Normalization in Digital Histopathology Images Using Image-Specific Color Deconvolution. IEEE T. Biomed. Eng. 61, 6 (2014), 1729--38.Google ScholarCross Ref
- T. M. Lehmann, C. Gonner, and K. Spitzer. 1999. Survey: interpolation methods in medical image processing. IEEE T. Med. Imaging 18, 11 (1999), 1049--75.Google ScholarCross Ref
- O. Lobachev, Ch. Ulrich, B. S. Steiniger, V. Wilhelmi, V. Stachniss, and M. Guthe. 2017. Feature-based multi-resolution registration of immunostained serial sections. Med. Image Anal. 35 (2017), 288--302.Google ScholarCross Ref
- William E. Lorensen and Harvey E. Cline. 1987. Marching cubes: A high resolution 3D surface construction algorithm. Comput. Graph. (ACM) 21, 4 (1987), 163--9. Google ScholarDigital Library
- Bruce D Lucas and Takeo Kanade. 1981. An iterative image registration technique with an application to stereo vision.. In International Joint Conference on Artificial Intelligence (IJCAI '81). 674--9. Google ScholarDigital Library
- Bin Ma, Lei Wang, Reinhard von Wasielewski, Werner Lindenmaier, and Kurt E. J. Dittmar. 2008. Serial sectioning and three-dimensional reconstruction of mouse Peyer's patch. Micron 39, 7 (2008), 967--75.Google ScholarCross Ref
- S. Ourselin, A. Roche, G. Subsol, X. Pennec, and N. Ayache. 2001. Reconstructing a 3D structure from serial histological sections. Image & Vision Comput. 19 (2001), 25--31. Issue 1--2.Google ScholarCross Ref
- E. Reinhard, M. Adhikhmin, B. Gooch, and P. Shirley. 2001. Color transfer between images. IEEE Comput. Graph. 21, 5 (2001), 34--41. Google ScholarDigital Library
- Jerome Revaud, Philippe Weinzaepfel, Zaid Harchaoui, and Cordelia Schmid. 2015. EpicFlow: Edge-Preserving Interpolation of Correspondences for Optical Flow. In Computer Vision and Pattern Recognition. 1164--72.Google Scholar
- Douglas S. Richardson and Jeff W. Lichtman. 2015. Clarifying Tissue Clearing. Cell 162, 2 (2015), 246--57.Google ScholarCross Ref
- D. Rueckert, L. I. Sonoda, C. Hayes, D. L G Hill, M. O. Leach, and D.J. Hawkes. 1999. Non-rigid registration using free-form deformations: application to breast MR images. IEEE Trans. Med. Imaging 18, 8 (1999), 712--21.Google ScholarCross Ref
- Stephan Saalfeld, Richard Fetter, Albert Cardona, and Pavel Tomancak. 2012. Elastic volume reconstruction from series of ultra-thin microscopy sections. Nat. Methods 9, 7 (2012), 717--20.Google ScholarCross Ref
- Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, et al. 2012. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 7 (2012), 676--82.Google ScholarCross Ref
- Julia A. Schnabel, Daniel Rueckert, Marcel Quist, Jane M. Blackall, Andy D. Castellano-Smith, Thomas Hartkens, Graeme P. Penney, Walter A. Hall, Haiying Liu, et al. 2001. A Generic Framework for Non-rigid Registration Based on Non-uniform Multi-level Free-Form Deformations. In MICCAI '01. Springer, 573--81. Google ScholarDigital Library
- A. Sotiras, C. Davatzikos, and N. Paragios. 2013. Deformable Medical Image Registration: A Survey. IEEE T. Med. Imaging 32, 7 (2013), 1153--90.Google ScholarCross Ref
- Birte Steiniger, Lars Rüttinger, and Peter J. Barth. 2003. The Three-dimensional Structure of Human Splenic White Pulp Compartments. J. Histochem. Cytochem. 51, 5 (2003), 655--63.Google ScholarCross Ref
- B. S. Steiniger, S. Bubel, W. Böckler, K. Lampp, A. Seiler, B. Jablonski, M. Guthe, and V. Stachniss. 2013. Immunostaining of Pulpal Nerve Fibre Bundle/Arteriole Associations in Ground Serial Sections of Whole Human Teeth Embedded in Technovit®9100. Cells Tissues Organs 198, 1 (2013), 57--65.Google ScholarCross Ref
- Birte S. Steiniger, Anja Seiler, Katrin Lampp, Verena Wilhelmi, and Vitus Stachniss. 2014a. B lymphocyte compartments in the human splenic red pulp: capillary sheaths and periarteriolar regions. Histochem. Cell Biol. 141, 5 (2014), 507--18.Google ScholarCross Ref
- Birte S. Steiniger, Vitus Stachniss, Verena Wilhelmi, Anja Seiler, Katrin Lampp, Andreas Neff, Michael Guthe, and Oleg Lobachev. 2016. Three-dimensional arrangement of human bone marrow microvessels revealed by immunohistology in undecalcified sections. PLOS ONE 11, 12 (12 2016), 1--25.Google Scholar
- Birte S. Steiniger, Verena Wilhelmi, Anja Seiler, Katrin Lampp, and Vitus Stachniss. 2014b. Heterogeneity of stromal cells in the human splenic white pulp. Fibroblastic reticulum cells, follicular dendritic cells and a third superficial stromal cell type. Immunol. 143, 3 (2014), 462--77.Google ScholarCross Ref
- D. Sun, S. Roth, and M. J. Black. 2010. Secrets of optical flow estimation and their principles. In 2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. 2432--9.Google Scholar
- Gabriel Taubin. 1995. A signal processing approach to fair surface design. In Proceedings of the 22nd annual conference on Computer graphics and interactive techniques. ACM, 351--8. Google ScholarDigital Library
- P. Thevenaz, T. Blu, and M. Unser. 2000. Interpolation revisited. IEEE T. Med. Imaging 19, 7 (2000), 739--58.Google ScholarCross Ref
- J.-P. Thirion. 1998. Image matching as a diffusion process: an analogy with Maxwell's demons. Med. Image Anal. 2, 3 (1998), 243--60.Google ScholarCross Ref
- Christine Ulrich, Oleg Lobachev, Birte S. Steiniger, and Michael Guthe. 2014. Imaging the Vascular Network of the Human Spleen from Immunostained Serial Sections. In Visual Computing for Biology and Medicine (VCBM '14), Ivan Viola, Katja Buehler, and Timo Ropinski (Eds.). EG. Google ScholarDigital Library
- Tao Wan, B. Nicolas Bloch, Shabbar Danish, and Anant Madabhushi. 2013. A novel point-based nonrigid image registration scheme based on learning optimal landmark configurations. In Medical Imaging 2013: Image Processing (Proc. SPIE 8669). 866934-866934-12.Google Scholar
- Yiwen Xu, J. Geoffrey Pickering, Zengxuan Nong, Eli Gibson, John-Michael Arpino, Hao Yin, and Aaron D. Ward. 2015. A Method for 3D Histopathology Reconstruction Supporting Mouse Microvasculature Analysis. PLoS ONE 10, 5 (05 2015), 1--24.Google Scholar
- C. W. Zitnick, N. Jojic, and Sing Bing Kang. 2005. Consistent segmentation for optical flow estimation. In International Conference on Computer Vision (ICCV '05). IEEE, 1308--15. Google ScholarDigital Library
Index Terms
- Compensating anisotropy in histological serial sections with optical flow-based interpolation
Recommendations
Robust registration of Mouse brain slices with severe histological artifacts
ICVGIP '16: Proceedings of the Tenth Indian Conference on Computer Vision, Graphics and Image ProcessingBrain mapping research is facilitated by first aligning digital images of mouse brain slices to standardized atlas framework such as the Allen Reference Atlas (ARA). However, conventional processing of these brain slices introduces many histological ...
Computerized methodology for micro-CT and histological data inflation using an IVUS based translation map
A framework for the inflation of micro-CT and histology data using intravascular ultrasound (IVUS) images, is presented. The proposed methodology consists of three steps. In the first step the micro-CT/histological images are manually co-registered with ...
Co-registration of in vivo human MRI brain images to postmortem histological microscopic images
Certain features such as small vascular lesions seen in human MRI (Magnetic Resonance Imaging) are detected reliably only in postmortem histological samples by microscopic imaging. Co-registration of these microscopically detected features to their ...
Comments