VMTK Program that can be used for the 3d reconstruction of blood vessels
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generate 3D reconstruct 3D reconstruction mesh generation blood vessel

VMTK Description

Program that can be used for the 3d reconstruction of blood vessels VMTK is composed of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis in image-based blood vessel modeling. Here are some key features of "VMTK": Segmentation of vascular segments (or other anatomical structures) from medical images: · Gradient-based 3D level sets segmentation. A new gradient computation modality based on upwind finite differences allows the segmentation of small (down to 1.2 pixels/diameter) vessels. · Interactive level sets initialization based on the Fast Marching Method. This includes a brand new method for selecting a vascular segment comprised between two points automatically ignoring side branches, no parameters involved. Segmenting a complex vascular tract comes down to selecting the endpoints of a branch, letting level sets by attracted to gradient peaks with the sole advection term turned on, repeating the operation for all the branches and merging everything in a single model. Geometric analysis and surface data processing of 3D models of blood vessels (and tubular objects in general)((The key algorithms have been published on medical imaging journals. You can find a complete reference to publications at David Steinman's and Luca Antiga's homepages)): · Compute centerlines and maximal inscribed sphere radius of branching tubular structures given their polygonal surface representation · Split surface models into their constitutive branches based on centerline geometry · Compute centerline-based geometric quantities (such as bifurcation angles, planarity, symmetry, branch curvature, tortuosity) and surface-based geometric quantities (such as distance to centerlines, surface curvature, deviation from tangency to maximal inscribed spheres) · Robustly map branches to a rectangular parametric space · Generate rectangular patches based on the parametric mapping for statistical analysis of geometric and CFD data over populations. Scripts, I/O tools and simple algorithms to easily work with images and meshes: · Read and write a number of image, surface and volume mesh formats. Includes a DICOM series reader with auto-flipping capabilities, Netgen mesh format reader, libMesh xda mesh format writer, Tetgen mesh generator wrapper, FIDAP FDNEUT mesh format reader and writer and a Newtetr input file generator · Display images and meshes · Incapsulate several VTK classes and make them available as pipeable scripts e.g. Marching Cubes, surface smoothing, clipping, normal computation, (connectivity, subdivision, distance between surfaces, ICP registration) · Add cylindrical extensions to surface model boundaries as a preprocessing step for CFD simulations. · Generate boundary layers of prismatic elements with varying thickness for CFD What's New in This Release: · fixed bug in flow extension generation · improved surface remeshing · fixed Windows compilation issues · fixed 64-bit compilation issues · finally (thanks to the great initial contribution by Michalis and the later help by Hugo and Joppe) the Fluent export to msh files works correctly and it preserves boundary indicators correctly. This also allows to use vmtk meshes with OpenFOAM. · Dolfin and LifeV mesh writers fixed and improved · added radial basis function interpolation · added efficient modeling of tubes from centerlines + radius · included new vessel enhancement methods · fast vascular network analysis algorithm (see my PhD thesis) ported to vmtk · quadratic projection of linear meshes now does a complete check for negative Jacobians · added curved MPR class and script contributed by Hugo (along with vmtkimageshiftscale, vmtksurfacetransforminteractive and improvements to vmtksurfacetransform and vmtkimagereslice - check them out!) · centerline merging added · added extraction of bifurcation profiles · added tetrahedralization script for mixed meshes

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