Volumetric feature extraction and visualization of tomographic molecular imaging.

Electron tomography is useful for studying large macromolecular complex within their cellular context. The associate problems include crowding and complexity. Data exploration and 3D visualization of complexes require rendering of tomograms as well as extraction of all features of interest. We present algorithms for fully automatic boundary segmentation and skeletonization, and demonstrate their applications in feature extraction and visualization of cell and molecular tomographic imaging. We also introduce an interactive volumetric exploration and visualization tool (Volume Rover), which encapsulates implementations of the above volumetric image processing algorithms, and additionally uses efficient multi-resolution interactive geometry and volume rendering techniques for interactive visualization.

[1]  Insung Ihm,et al.  Visualization-specific compression of large volume data , 2001, Proceedings Ninth Pacific Conference on Computer Graphics and Applications. Pacific Graphics 2001.

[2]  Martin Kraus,et al.  Hardware-accelerated volume and isosurface rendering based on cell-projection , 2000 .

[3]  Marko Subasic,et al.  Level Set Methods and Fast Marching Methods , 2003 .

[4]  Thomas S. Huang,et al.  Image processing , 1971 .

[5]  Jayant Shah,et al.  A common framework for curve evolution, segmentation and anisotropic diffusion , 1996, Proceedings CVPR IEEE Computer Society Conference on Computer Vision and Pattern Recognition.

[6]  W Hoppe,et al.  Three-dimensional reconstruction of individual negatively stained yeast fatty-acid synthetase molecules from tilt series in the electron microscope. , 1974, Hoppe-Seyler's Zeitschrift fur physiologische Chemie.

[7]  Chandrajit L. Bajaj,et al.  Error-bounded reduction of triangle meshes with multivariate data , 1996, Electronic Imaging.

[8]  D. Lee,et al.  Skeletonization via Distance Maps and Level Sets , 1995 .

[9]  Jerry L. Prince,et al.  Snakes, shapes, and gradient vector flow , 1998, IEEE Trans. Image Process..

[10]  Arne Stoschek,et al.  The architecture of active zone material at the frog's neuromuscular junction , 2001, Nature.

[11]  R. Glaeser.  Review: electron crystallography: present excitement, a nod to the past, anticipating the future. , 1999, Journal of structural biology.

[12]  Rüdiger Westermann,et al.  Efficiently using graphics hardware in volume rendering applications , 1998, SIGGRAPH.

[13]  Clara Franzini-Armstrong,et al.  Tomographic 3D Reconstruction of Quick-Frozen, Ca2+-Activated Contracting Insect Flight Muscle , 1999, Cell.

[14]  W. Baumeister,et al.  Macromolecular electron microscopy in the era of structural genomics. , 2000, Trends in biochemical sciences.

[15]  B. Alberts.  The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists , 1998, Cell.

[16]  Chandrajit L. Bajaj,et al.  Feature based volumetric video compression for interactive playback , 2002, Symposium on Volume Visualization and Graphics, 2002. Proceedings. IEEE / ACM SIGGRAPH.

[17]  A S Frangakis,et al.  Toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[18]  M. Heel,et al.  Single-particle electron cryo-microscopy: towards atomic resolution , 2000, Quarterly Reviews of Biophysics.

[19]  Manfred Auer,et al.  Three-dimensional electron cryo-microscopy as a powerful structural tool in molecular medicine , 2000, Journal of Molecular Medicine.

[20]  Jitendra Malik,et al.  Scale-Space and Edge Detection Using Anisotropic Diffusion , 1990, IEEE Trans. Pattern Anal. Mach. Intell..

[21]  Georgios Tziritas,et al.  Fast Marching to Moving Object Location , 1999, Scale-Space.

[22]  Zeyun Yu,et al.  Normalized Gradient Vector Diffusion and Image Segmentation , 2002, ECCV.

[23]  Gabriella Sanniti di Baja,et al.  Euclidean skeleton via centre-of-maximal-disc extraction , 1993, Image Vis. Comput..

[24]  A Leith,et al.  Sterecon--three-dimensional reconstructions from stereoscopic contouring. , 1996, Journal of structural biology.

[25]  R. Malladi,et al.  Segmentation of nuclei and cells using membrane related protein markers , 2001, Journal of microscopy.

[26]  Ching Y. Suen,et al.  Thinning Methodologies - A Comprehensive Survey , 1992, IEEE Trans. Pattern Anal. Mach. Intell..

[27]  Insung Ihm,et al.  3D RGB image compression for interactive applications , 2001, TOGS.

[28]  Jesse Freeman,et al.  in Morse theory, , 1999 .

[29]  J. Mccammon,et al.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. , 1999, Journal of structural biology.

[30]  Chandrajit L. Bajaj,et al.  Level set based Volumetric Anisotropic Diffusion for 3D Image Filtering , 2003 .

[31]  R. G. Hart.  Electron Microscopy of Unstained Biological Material: The Polytropic Montage , 1968, Science.

[32]  Y Li,et al.  Tinkerbell--a tool for interactive segmentation of 3D data. , 1997, Journal of structural biology.

[33]  Valerio Pascucci,et al.  Contour trees and small seed sets for isosurface traversal , 1997, SCG '97.

[34]  John F. Canny,et al.  A Computational Approach to Edge Detection , 1986, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[35]  Arthur W. Toga,et al.  Efficient Skeletonization of Volumetric Objects , 1999, IEEE Trans. Vis. Comput. Graph..

[36]  Reiner Hegerl,et al.  Towards automatic electron tomography , 1992 .

[37]  J A Sethian,et al.  A fast marching level set method for monotonically advancing fronts. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[38]  S. Osher,et al.  Geometric Level Set Methods in Imaging, Vision, and Graphics , 2011, Springer New York.

[39]  Olaf Kübler,et al.  Hierarchic Voronoi skeletons , 1995, Pattern Recognit..

[40]  Zeyun Yu,et al.  Anisotropic vector diffusion in image smoothing , 2002, Proceedings. International Conference on Image Processing.

[41]  S J Young,et al.  A flexible environment for the visualization of three-dimensional biological structures. , 1996, Journal of structural biology.

[42]  James A. Sethian,et al.  A real-time algorithm for medical shape recovery , 1998, Sixth International Conference on Computer Vision (IEEE Cat. No.98CH36271).

[43]  W Baumeister,et al.  Electron tomography of molecules and cells. , 1999, Trends in cell biology.

[44]  N. Volkmann,et al.  Quantitative fitting of atomic models into observed densities derived by electron microscopy. , 1999, Journal of structural biology.

[45]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[46]  William E. Lorensen,et al.  The Transfer Function Bake-Off , 2001, IEEE Computer Graphics and Applications.

[47]  B F McEwen,et al.  The relevance of dose-fractionation in tomography of radiation-sensitive specimens. , 1995, Ultramicroscopy.

[48]  Martin Kraus,et al.  Hardware-accelerated volume and isosurface rendering based on cell-projection , 2000, Proceedings Visualization 2000. VIS 2000 (Cat. No.00CH37145).

[49]  Georgios Tziritas,et al.  Moving object localisation using a multi-label fast marching algorithm , 2001, Signal Process. Image Commun..

[50]  D A Agard,et al.  Automated microscopy for electron tomography. , 1992, Ultramicroscopy.

[51]  R. Ellis.  Macromolecular crowding : obvious but underappreciated , 2022 .

[52]  James A. Sethian,et al.  Level Set Methods and Fast Marching Methods , 1999 .

[53]  J. Frank.  Electron Tomography , 1992, Springer US.

[54]  Valerio Pascucci,et al.  Visualization of scalar topology for structural enhancement , 1998, Proceedings Visualization '98 (Cat. No.98CB36276).

[55]  Alfred M. Bruckstein,et al.  Skeletonization via Distance Maps and Level Sets , 1995, Comput. Vis. Image Underst..

[56]  Niels Volkmann,et al.  A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. , 2002, Journal of structural biology.

[57]  J R Kremer,et al.  Computer visualization of three-dimensional image data using IMOD. , 1996, Journal of structural biology.

[58]  Yee-Hong Yang,et al.  Skeletonisation: An electrostatic field-based approach , 1998, Pattern Analysis and Applications.

[59]  M Marko,et al.  Three-dimensional transmission electron microscopy and its application to mitosis research. , 1999, Methods in cell biology.

[60]  Valerio Pascucci,et al.  Fast isocontouring for improved interactivity , 1996, VVS '96.

[61]  S Birmanns,et al.  Using situs for flexible and rigid-body fitting of multiresolution single-molecule data. , 2001, Journal of structural biology.

[62]  Grégoire Malandain,et al.  Euclidean skeletons , 1998, Image Vis. Comput..

[63]  Joachim Weickert,et al.  Anisotropic diffusion in image processing , 1996 .

[64]  Junaed Sattar.  Snakes , Shapes and Gradient Vector Flow , 2022 .

[65]  Bruce Alberts,et al.  The Cell as a Collection Overview of Protein Machines: Preparing the Next Generation of Molecular Biologists , 1998 .

[66]  Valerio Pascucci,et al.  The contour spectrum , 1997, Proceedings. Visualization '97 (Cat. No. 97CB36155).

[67]  A S Frangakis,et al.  Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. , 2001, Journal of structural biology.

[68]  Zeyun Yu,et al.  Image segmentation using gradient vector diffusion and region merging , 2002, Object recognition supported by user interaction for service robots.

[69]  Jinho Lee.  The Transfer Function BakeOff , 2001 .

[70]  Joachim Frank,et al.  Electron tomographic and other approaches for imaging molecular machines , 2001, Current Opinion in Neurobiology.

[71]  M Marko,et al.  The Emergence of Electron Tomography as an Important Tool for Investigating Cellular Ultrastructure , 2001, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[72]  Achilleas S Frangakis,et al.  Segmentation of two- and three-dimensional data from electron microscopy using eigenvector analysis. , 2002, Journal of structural biology.