The AngioLab suite, part of the GIMIAS platform, allows the user to perform an entire workflow from medical images to morphological characterization of the aneurysm sac and parent vessels, virtual treatment and advanced visualization of fluid dynamic simulation results. These tools aim to assist the clinician in the assessment of aneurysm rupture risk and choosing the best treatment option for a specific patient.
AngioLab is meant to be used at the decision-making stage of the type of treatment to be undergone by a given patient. AngioLab provides additional information to the clinician by using the patient's medical images, such as aneurysm morphological characterization and simulation of various types of treatment. It includes the possibility to simulate and visualize the virtual treatment with minimally invasive techniques, such as stenting and coil embolization. These last two are called Virtual Stenting and Virtual Coiling, respectively. AngioLab also includes the necessary tools to perform virtual treatment of intracranial aneurysms, such as medical image segmentation, mesh editing tools and building centerlines and morphological characterization of intracranial aneurysms.
The suite is divided in two main workflows:
- Morphological Analysis
- Virtual Device Deployment
DICOM image viewing and PACS connection
This plugin can load medical images in DICOM format acquired from radiological examinations, from machines of different modalities, such as computed tomography angiography (CTA), magnetic resonance angiography (MRA), 3D rotational angiography (3DRA). This module is DICOM-compatible, and thus is prepared to work with integrated health information systems such as PACS.
AngioLab allows to set parameters and connect to a PACS (Picture Archive Communication System) and run the query operations, retrieve and send, using the communication protocol and the services provided by the DICOM Message Service Element (DIMSE). Depending on the configuration of the PACS server you want to connect to, others may also be required authentication parameters for each of the services you want to use through AngioLab. AngioLab allows you to search on the following fields: Patient Name, Patient ID, Patient Birth Date, Study ID and date of the study.
The display module allows three-dimensional reconstruction of high quality DICOM images interactively. In this manner allows display of images by multiplanar reformation, in view orthogonal cuts, cuts multiple views and volume rendering. The viewing window allows adjustment of the level of contrast and brightness, the display of images with all demographics, zoom and pan, rotation, selection of areas of interest (Regions of Interest - ROI). Volume rendering can be performed using standard techniques, such as Volume Raycast 3D Texture Mapping or volumetric image, together with a transfer function optimized for angiography images. The accuracy and speed of volume rendering can be adjusted enabling or disabling the acceleration of the Graphical Processing Unit (GPU) and the level of detail (Level of Details - LOD). Volume rendering includes the option of displaying the volumetric image with a 2D Texture Mapping technique which simulates the acquisition technique of X-ray, so as to obtain images similar to those obtained by fluoroscopy (see Figure 2).
Segmentation from a medical image is used to extract information about a structure or anatomy of interest to the clinician, in our case, is the 3D representation of the intracranial vessels.
The technique used in AngioLab consists of an algorithm based on geodesic active regions (GAR)  and is optimized for segmentation of vascular tissue through the standardization of image intensity . The GAR is a geometric deformable model that is governed by a power function where the internal force is defined by the local curvature of the surface to extract and combine external regional and gradient descriptors that drive the evolution of the model to the vascular limit. Regional descriptors are derived from a training set, which is a collection of images that have already been through manual segmentation and have a defined depth between what is background and what is blood vessel.
This technique uses different training sets, which enable segmentation of blood vessels from medical images from different modalities: 3DRA, CTA, MRA. Finally, the segmentation surface consists of a mesh composed of triangular elements (see Figure 4).
There are very few occasions when the GAR algorithm fails, but for these occasions an auxiliar segmentation algorithm has been added. This method is called Otsu and it performs a segmentation that depends on the histogram of gray levels of an image . The technique assumes that only two classes of voxels exist (the blood vessel and background) and calculates the optimum threshold separating those two classes. Generally, the segmentation from Otsu method is very crude and contains many flaws, therefore it should only be used when GAR segmentations fails.
Mesh editing tools
Depending on the quality of the image and the morphology of the patient's vessels, the mesh obtained with the automatic segmentation (GAR) may need some manual corrections. This may occur when, for example, there are arteries that fuse with the aneurysm or when the contrast has failed to completely fill the artery to be studied, to name a few (see Figure 5).
The tools availabl in AngioLab are:
- Global Tools (see Figure 6):
- Ring Cut: for cutting a vessel using a plane, perpendicular to the vessel, from a point selected by the user on the surface of the vessel.
- Holes Filling: allows to close all the holes on a surface or choose only a few to be closed.
- Local Tools (see Figure 7):
- Local surface editing: allows the selection of elements on a triangular surface mesh using different selection techniques (brush, unique triangle selection and sphere) for local editing operations (delete triangles, refine and smooth mesh).
After making the necessary corrections and edits, the result is a proper vascular model for the following steps: morphological analysis, building centerlines and virtual treatments.
Tools for building centerlines
This tool allows the creation of central lines from the vascular model surface mesh, as obtained from the previous mesh editing step.
This tool uses a specific algorithm for blood vessels which is based on the creation of central lines using a Voronoi diagram . The Voronoi diagram is used to define center points from the maximum inscribed spheres along a geometry which is, in this case, a blood vessel (see Figure 8). It is said that an inscribed sphere is maximum when it does not let other inscribed spheres to contain it. From these key central points, the shortest paths are defined between source points and target points. These paths are the centerlines.
The algorithms used are part of VMTK AngioLab (Vascular Modeling Toolkit) . This tool is especially necessary for the virtual treatment of an aneurysm with stent.
To perform a morphological analysis, it is necessary to extract a simplified geometry of the aneurysm and its closest vessels from the vascular model obtained during segmentation. Once this is obtained, the aneurysmal sac is isolated by a manual selection of the aneurysm neck.
From this simplified geometry, different measurements are calculated such as aspect ratio, non-sphericity index, aneurysm volume, aneurysm surface, surface of the aneurysm neck, width of the aneurysm neck (see Figure 9). The aspect ratio is a measurement that correlates the height of the aneurysm to the width of the aneurysm neck, while the non-sphericity factor relates the aneurysm volume with its area.
In addition to these measurements, the calculation of descriptors called dimensional invariant Zernike moments  is also performed. These descriptors are used to characterize the shape of the aneurysm and its nearby vessels, without depending on the orientation or scale of the geometry. This means that, to some level of detail, you could be able to rebuild the geometry from the descriptors.
The calculation of the Zernike moments is used to provide a comparison between the new patient's aneurysm with other aneurysms that have been treated previously, their geometric descriptors being stored in a database (see Figure 10) . Being able to list similar aneurysms, could offer further support to the clinician when making therapeutic decisions.
All descriptors are calculated automatically in real time and are easily stored in a database.
Also, you can refine your search depending on the location (near the posterior communicating artery, ophthalmic artery, etc.), and/or type of aneurysm (saccular or fusiform).
The stent deployment within the arterial geometry is performed by a method called 'Fast Virtual Stenting', developed by Larrabide et al . This technique is based on deformable models, where a partial differential equation of second order is used to deform a mesh under the effect of physical constraints such as the geometry, length and radius of the stent.
The Virtual Stenting technique requires as input the 3D model vessel segment and a centerline from which to deply the stent, with the restriction of the geometry patient's vasculature. The user can select a point on the centerline, marking the center from where the stent would be deployed for treating an aneurysm.
Once the stent is deployed, the user can view the initial and final position of the stent within the vascular geometry. IF the deploymetn wasn't satisfactory, the stent can be reployed to the desired position. The output of this module is a deployed stent mesh, which can be used for visual understanding of a paticular stent peplyment and flow simulations (see Figure 11).
In this tool, the geometries for the following stents are available: Neuroform (Boston Scientific), Enterprise (Cordis), SILK (Balt Extrusion) and PED (ev3).
Virtual Coiling is a dynamic route planning technique that mimics the insertion of coils into a three dimensional model of an aneurysm, giving plausible distribution of coils within a specific patient anatomy . Essentially, the technique involves the following steps:
- Insertion of coils, by moving the tip of the coil along an already established path, initializing an initial position and direction within the region where the coils are to be placed.
- Prohibits coil migration out of the aneurysmal area and coil crashes, for proper construction of the path.
- If the tip of the coil was trapped between other coils, the technique allows the removal of the coil tip to redirect the advance.
As a result, the Virtual Coiling is capable of obtaining a representation similar to the coils inserted in clinical practice that may be used for visual understanding of the treatment and flow simulations (see Figure 12).
AngioLab allows the user to visualize the coils within the aneurysm, try different numbers of coils within the aneurysm and know what percentage corresponds to a certain amount of coils.
AngioLab is capable of creating clinical reports with all the information that the user considers appropriate. This is possible either before, or after staring the analysis of the case. The report may include: text, tables (see Figure 13) and screenshots (see Figure 14).
Upon completion of the clinical analysis, the user can review the information that has been added to the report to decide what information is to be eliminated or added. You can also design the final look and print the report in PDF format.
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-  http://www.vmtk.org/Tutorials/Centerlines
-  http://www.vmtk.org
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