The Vascular Modeling Toolkit is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. VMTK can be used via its standalone interface, included as a Python or C++ library, or as an extension to the medical image processing platform 3D Slicer. By providing multiple user interfaces with various requirments of technical ability, VMTK aims to be usable by anyone with an interest in medical image processing; be they clinicians, researchers, industries, or educational institutions.
Tutorials, development instructions, and the general information is available at https://www.vmtk.org
- How to install VMTK.
- Learn how to open your dataset in vmtk, navigate into a 3D volume and set up your image for further processing.
- Learn how to use Pypes.
- Tutorials will guide you through the main features.
- Automatically generated python class references
- Automatically generated C++ class reference
- Screenshots from VMTK examples.
- Presentations about VMTK.
Gradient-based 3D level sets segmentation
Take a look into the Level Set Segmentation tutorial to learn how to reconstruct the 3D surface of a vascular segment from CT or MR images using level sets.
// Image segmentation vmtklevelsetsegmentation -ifile image_volume_voi.vti -ofile level_sets.vti //You can specify different parameters, for example: -levelsetsfile in order to start from an existing levelset segmentation -featureimagetype to change featureimage, for example the upwind modality -featurederivativesigma to use a Gaussian derivative convolution
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
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.
Take a look into the Computing Centerlines tutorial to learn how to compute centerlines of a vascular segment.
// Computing centerlines vmtkcenterlines -ifile foo.vtp -ofile foo_centerlines.vtp //Look the resulting centerlines vmtksurfacereader -ifile foo.vtp --pipe vmtkcenterlines --pipe vmtkrenderer --pipe vmtksurfaceviewer -opacity 0.25 --pipe vmtksurfaceviewer -i @vmtkcenterlines.o -array MaximumInscribedSphereRadius //Inspect the voronoi diagram vmtksurfacereader -ifile foo.vtp --pipe vmtkcenterlines --pipe vmtkrenderer --pipe vmtksurfaceviewer -opacity 0.25 --pipe vmtksurfaceviewer -i @vmtkcenterlines.voronoidiagram -array MaximumInscribedSphereRadius --pipe vmtksurfaceviewer -i @vmtkcenterlines.o
Centerlines are powerful descriptors of the shape of vessels and
are determined as weighted shortest paths traced between two extremal points.
In order to ensure that the final lines are in fact central, the paths cannot
lie anywhere in space, but are bound to run on the
Voronoi diagram of the vessel model,
considered as the place where the centers of maximal inscribed spheres are defined.
Centerlines are determined as the paths defined on Voronoi diagram sheets that minimize
the integral of the radius of
maximal inscribed spheres along the path, which is equivalent to finding the shortest paths in the radius metric.
Take a look into the Geometric analysis tutorial to learn how to analyze the 3D geometry of a vascular segment and into the Preparing a Surface for Meshing tutorial to learn how to prepare a surface for mesh generation.
// Generate a vtp file containing the data on the bifurcation vectors vmtksurfacereader -ifile foo.vtp --pipe vmtkcenterlines -seedselector openprofiles --pipe vmtkbranchextractor --pipe vmtkbifurcationreferencesystems --pipe vmtkbifurcationvectors -ofile foo_bv.vtp //Compute curvature and torsion vmtkcenterlinegeometry -ifile foo_cl.vtp -smoothing 1 -ofile foo_clgm.vtp //Smoothing a surface vmtksurfacesmoothing -ifile foo.vtp -passband 0.1 -iterations 30 -ofile foo_sm.vtp //Adding flow extensions vmtksurfacereader -ifile foo.vtp --pipe vmtkcenterlines -seedselector openprofiles --pipe vmtkflowextensions -adaptivelength 1 -extensionratio 20 -normalestimationratio 1 -interactive 0 --pipe vmtksurfacewriter -ofile foo_ex.vtp
Quantifying geometric features of the vascular segment,
those associated to
bifurcations, such as bifurcation planes
and bifurcation angles, and those associated to branches, such
curvature and torsion. Curvature and torsion are tightly linked
to the definition of the Frenet line frame, constituted by a tangent,
a normal and the binormal.
Increase surface smoothness prior to building the mesh.
Image segmentation can result in bumpy surfaces, especially if the
image quality is not high and one didn’t use any curvature term in level
Flow extensions are cylindrical extensions added to the
inlets and outlets of a model. They are important for ensuring that the
flow entering and leaving the computational domain is fully developed, so
that fully developed boundary conditions aren’t forcing the solution in the
Generating a mesh
Take a look into the Generating a Mesh tutorial to learn how to generate a mesh from a surface and into the Meshing based on centerlines tutorial to learn how to generate tetrahedral or mixed hexahedral meshes using vmtk coupled to Gmsh. Contributed by Emilie Marchandise, U. Louvain.
// generating a uniform element mesh vmtkmeshgenerator -ifile foo.vtp -ofile foo.vtu -edgelength 0.5 //Generating a radius-adaptive element mesh vmtksurfacereader -ifile foo.vtp --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -ofile foo.vtu //Adding a boundary layer vmtksurfacereader -ifile foo.vtp --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -boundarylayer 1 -ofile foo.vtu
remeshing is performed under the assumption that
the surface requires improvement before being used for CFD.
After the surface has been remeshed the volume is filled with
a combination of
We can heighten the
density of the mesh near the wall by generating
Mapping and patching
Take a look into the Mapping and patching tutorial to learn how to map the surface of a population of vessels onto the same parametric space and enable statistical analyses of surface-based quantities
// Longitudinal and circumferential metrics vmtkbranchmetrics -ifile aorta_clipped.vtp -centerlinesfile aorta_cl.vtp -abscissasarray Abscissas -normalsarray ParallelTransportNormals -groupidsarray GroupIds -centerlineidsarray CenterlineIds -tractidsarray TractIds -blankingarray Blanking -radiusarray MaximumInscribedSphereRadius -ofile aorta_clipped_metrics.vtp //Metrics mapping to branches vmtkbranchmapping -ifile aorta_clipped_metrics.vtp -centerlinesfile aorta_cl.vtp -referencesystemsfile aorta_cl_rs.vtp -normalsarray ParallelTransportNormals -abscissasarray Abscissas -groupidsarray GroupIds -centerlineidsarray CenterlineIds -tractidsarray TractIds -referencesystemsnormalarray Normal -radiusarray MaximumInscribedSphereRadius -blankingarray Blanking -angularmetricarray AngularMetric -abscissametricarray AbscissaMetric -ofile aorta_clipped_mapping.vtp //Patching of surface mesh and attributes vmtkbranchpatching -ifile aorta_clipped_mapping.vtp -groupidsarray GroupIds -longitudinalmappingarray StretchedMapping -circularmappingarray AngularMetric -longitudinalpatchsize 0.5 -circularpatches 12 -ofile aorta_clipped_patching.vtp
A common application is
mapping and patching of fluid dynamics variables,
such as wall shear stress
(WSS) or oscillatory shear index
on the surface mesh typically by means of a CFD simulation.
By construction of a harmonic function over each vascular segment, vmtkbranchmapping maps and stretches the longitudinal metric to correctly account for the presence of insertion regions at
bifurcations; the additional
StretchedMapping array is added to the surface.
Take a look into the Basic PypeS tutorial to learn how to effectively pipe vmtk scripts together, the Use PypeS Programmatically tutorial to learn how to interactively work with PypeS objects and into the Advanced PypeS tutorial to learn how to write your own PypeS modules.
vmtkmarchingcubes --help Creating vmtkMarchingCubes instance. Automatic piping vmtkmarchingcubes Parsing options vmtkmarchingcubes vmtkmarchingcubes : generate an isosurface of given level from a 3D image Input arguments: -id Id(int,1); default=0: script id -handle Self (self,1): handle to self -disabled Disabled (bool,1); default=0: disable execution and piping -i Image (vtkImageData,1): the input image -ifile ImageInputFileName(str,1): filename for the default Image Reader -array ArrayName (str,1): name of the array to work with -l Level(float,1); default=0.0: graylevel to generate the isosurface at -connectivity Connectivity (bool,1); default=0: only output the largest connected region of the isosurface -ofile SurfaceOutputFileName (str,1): filename for the default Surface writer Output arguments: -id Id (int,1); default= 0: script id -handle Self (self,1): handle to self -o Surface (vtkPolyData,1): the output surface
// We can use vmtkmarchingcubes as a stand-alone script by using the built-in I/O functionality vmtkmarchingcubes -ifile foo.vti -ofile foo.vtp //or we can build a pype that does the same thing vmtkimagereader -ifile foo.vti --pipe vmtkmarchingcubes --pipe vmtksurfacewriter -ofile foo.vtp @vmtkcenterlines.o -array MaximumInscribedSphereRadius //Say we want to read two images and extract a surface with Marching Cubes with a level of 20 for both. We can either write vmtkmarchingcubes -ifile foo1.vti -l 20 --pipe vmtkmarchingcubes -ifile foo2.vti -l 20 //or push the input argument -l along to the second vmtkmarchingcubes this way vmtkmarchingcubes -ifile foo1.vti -l@ 20 --pipe vmtkmarchingcubes -ifile foo2.vti
Writing classes implementing
algorithms and writing actual tools
to be used for everyday work are two distinct tasks.
Very often a well-designed object-oriented library ends up to be used in ever-growing collections of shell, Python or Tcl scripts or small C programs, each with its own argument parsing and I/O sections. Very often high-level code is duplicated to provide slightly different
functionality. On the other side, writing a GUI is a time-consuming task, and adding
new functionality requires time, which might deter experimentation.
PypeS goes in the
direction of providing a flexible
high-level code, both from the user’s
and from the developer’s points of view. The user wants to get things done minimizing
the work required and the amount of intermediate data generated. The coder wants to limit
the amount of code, she/he has to cut and paste (and maintain), and to quickly add new
functionality and make it interact with what she/he’s ever written before.
Development of VMTK is supported by Orobix Srl.