Inducing Vascular Grammars for Anomaly Classification in Brain Angiograms

Abstract As machine learning is used to make strides in med- ical diagnostics, few methods provide heuristics from which human doctors can learn directly. This work introduces a method for leveraging human observable structures, such as macro scale vascular formations, for producing assessments of medical conditions with rela- tively few training cases, and uncovering patterns that are potential diagnostic aids. The approach draws on shape grammars, a rule-based technique, pioneered in design and architecture, and accelerated through a re- cursive sub-graph mining algorithm. The distribution of rule instances in the data from which they are in- duced is then used as an intermediary representation en- abling common classification and anomaly detection ap- proaches to identify indicative rules with relatively small data sets. The method is applied to 7 Tesla time-of- flight (TOF) angiography MRI (n = 54) of human brain vasculature. The data were segmented and induced to generate representative grammar rules. Ensembles of rules were isolated to implicate vascular conditions reli- ably. This application demonstrates the power of auto- mated structured intermediary representations for as- sessing nuanced biological form relationships, and the strength of shape grammars, in particular for identify- ing indicative patterns in complex vascular networks.

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Mean-Subtraction Method for De-Shadowing of Tail Artifacts in Cerebral OCTA Images: A Proof of Concept

Materials ◽

10.3390/ma13092024 ◽

2020 ◽

Vol 13 (9) ◽

pp. 2024

Author(s):

Woo June Choi ◽

Bjorn Paulson ◽

Sungwook Yu ◽

Ruikang K. Wang ◽

Jun Ki Kim

Keyword(s):

Three Dimensional ◽

Volumetric Analysis ◽

Processing Technique ◽

Image Processing Technique ◽

Vascular Networks ◽

Simple Method ◽

Small Vessels ◽

Vascular Morphology ◽

Brain Vasculature ◽

Large Vessels

When imaging brain vasculature with optical coherence tomography angiography (OCTA), volumetric analysis of cortical vascular networks in OCTA datasets is frequently challenging due to the presence of artifacts, which appear as multiple-scattering tails beneath superficial large vessels in OCTA images. These tails shadow underlying small vessels, making the assessment of vascular morphology in the deep cortex difficult. In this work, we introduce an image processing technique based on mean subtraction of the depth profile that can effectively reduce these tails to better reveal small hidden vessels compared to the current tail removal approach. With the improved vascular image quality, we demonstrate that this simple method can provide better visualization of three-dimensional vascular network topology for quantitative cerebrovascular studies.

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Partially-parallel, susceptibility-weighted MR imaging of brain vasculature at 7 Tesla using sensitivity encoding and an autocalibrating parallel technique

2006 International Conference of the IEEE Engineering in Medicine and Biology Society ◽

10.1109/iembs.2006.259807 ◽

2006 ◽

Cited By ~ 6

Author(s):

Janine M. Lupo ◽

Suchandrima Banerjee ◽

Douglas Kelley ◽

Duan Xu ◽

Daniel B. Vigneron ◽

...

Keyword(s):

Mr Imaging ◽

7 Tesla ◽

Brain Vasculature ◽

Sensitivity Encoding ◽

Parallel Technique

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Partially-parallel, susceptibility-weighted MR imaging of brain vasculature at 7 Tesla using sensitivity encoding and an autocalibrating parallel technique

2006 International Conference of the IEEE Engineering in Medicine and Biology Society ◽

10.1109/iembs.2006.4397509 ◽

2006 ◽

Author(s):

Janine M. Lupo ◽

Suchandrima Banerjee ◽

Douglas Kelley ◽

Duan Xu ◽

Daniel B. Vigneron ◽

...

Keyword(s):

Mr Imaging ◽

7 Tesla ◽

Brain Vasculature ◽

Sensitivity Encoding ◽

Parallel Technique

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Assessment of middle cerebral artery diameter during hypocapnia and hypercapnia in humans using ultra-high-field MRI

Journal of Applied Physiology ◽

10.1152/japplphysiol.00651.2014 ◽

2014 ◽

Vol 117 (10) ◽

pp. 1084-1089 ◽

Cited By ~ 157

Author(s):

Jasper Verbree ◽

Anne-Sophie G. T. Bronzwaer ◽

Eidrees Ghariq ◽

Maarten J. Versluis ◽

Mat J. A. P. Daemen ◽

...

Keyword(s):

Middle Cerebral Artery ◽

Cerebral Artery ◽

Calibration Curve ◽

Transcranial Doppler ◽

7 Tesla ◽

Small Data ◽

Small Deviations ◽

Mri Scans ◽

Intracranial Arteries ◽

End Tidal

In the evaluation of cerebrovascular CO2 reactivity measurements, it is often assumed that the diameter of the large intracranial arteries insonated by transcranial Doppler remains unaffected by changes in arterial CO2 partial pressure. However, the strong cerebral vasodilatory capacity of CO2 challenges this assumption, suggesting that there should be some changes in diameter, even if very small. Data from previous studies on effects of CO2 on cerebral artery diameter [middle cerebral artery (MCA)] have been inconsistent. In this study, we examined 10 healthy subjects (5 women, 5 men, age 21–30 yr). High-resolution (0.2 mm in-plane) MRI scans at 7 Tesla were used for direct observation of the MCA diameter during hypocapnia, −1 kPa (−7.5 mmHg), normocapnia, 0 kPa (0 mmHg), and two levels of hypercapnia, +1 and +2 kPa (7.5 and 15 mmHg), with respect to baseline. The vessel lumen was manually delineated by two independent observers. The results showed that the MCA diameter increased by 6.8 ± 2.9% in response to 2 kPa end-tidal Pco2 (PetCO2) above baseline. However, no significant changes in diameter were observed at the −1 kPa (−1.2 ± 2.4%), and +1 kPa (+1.4 ± 3.2%) levels relative to normocapnia. The nonlinear response of the MCA diameter to CO2 was fitted as a continuous calibration curve. Cerebral blood flow changes measured by transcranial Doppler could be corrected by this calibration curve using concomitant PetCO2 measurements. In conclusion, the MCA diameter remains constant during small deviations of the PetCO2 from normocapnia, but increases at higher PetCO2 values.

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Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis

Bioinformatics ◽

10.1093/bioinformatics/btaa461 ◽

2020 ◽

Vol 36 (Supplement_1) ◽

pp. i534-i541

Author(s):

Marwan Abdellah ◽

Nadir Román Guerrero ◽

Samuel Lapere ◽

Jay S Coggan ◽

Daniel Keller ◽

...

Keyword(s):

Visual Analysis ◽

Interactive Visualization ◽

Application Programming Interface ◽

Supplementary Information ◽

Vascular Networks ◽

Substantial Impact ◽

Domain Specific ◽

Brain Vasculature ◽

Application Programming ◽

Background Mode

Abstract Motivation Accurate morphological models of brain vasculature are key to modeling and simulating cerebral blood flow in realistic vascular networks. This in silico approach is fundamental to revealing the principles of neurovascular coupling. Validating those vascular morphologies entails performing certain visual analysis tasks that cannot be accomplished with generic visualization frameworks. This limitation has a substantial impact on the accuracy of the vascular models employed in the simulation. Results We present VessMorphoVis, an integrated suite of toolboxes for interactive visualization and analysis of vast brain vascular networks represented by morphological graphs segmented originally from imaging or microscopy stacks. Our workflow leverages the outstanding potentials of Blender, aiming to establish an integrated, extensible and domain-specific framework capable of interactive visualization, analysis, repair, high-fidelity meshing and high-quality rendering of vascular morphologies. Based on the initial feedback of the users, we anticipate that our framework will be an essential component in vascular modeling and simulation in the future, filling a gap that is at present largely unfulfilled. Availability and implementation VessMorphoVis is freely available under the GNU public license on Github at https://github.com/BlueBrain/VessMorphoVis. The morphology analysis, visualization, meshing and rendering modules are implemented as an add-on for Blender 2.8 based on its Python API (application programming interface). The add-on functionality is made available to users through an intuitive graphical user interface, as well as through exhaustive configuration files calling the API via a feature-rich command line interface running Blender in background mode. Supplementary information Supplementary data are available at Bioinformatics online.

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Flow driven robotic navigation of microengineered endovascular probes

Nature Communications ◽

10.1038/s41467-020-20195-z ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Lucio Pancaldi ◽

Pietro Dirix ◽

Adele Fanelli ◽

Augusto Martins Lima ◽

Nikolaos Stergiopulos ◽

...

Keyword(s):

The Body ◽

Medical Procedures ◽

Magnetic Actuation ◽

Vascular Networks ◽

Cross Sectional ◽

Hydrokinetic Energy ◽

Brain Vasculature ◽

Art Practices ◽

Iatrogenic Damage ◽

External Intervention

AbstractMinimally invasive medical procedures, such as endovascular catheterization, have considerably reduced procedure time and associated complications. However, many regions inside the body, such as in the brain vasculature, still remain inaccessible due to the lack of appropriate guidance technologies. Here, experimentally and through numerical simulations, we show that tethered ultra-flexible endovascular microscopic probes can be transported through tortuous vascular networks with minimal external intervention by harnessing hydrokinetic energy. Dynamic steering at bifurcations is performed by deformation of the probe head using magnetic actuation. We developed an endovascular microrobotic toolkit with a cross-sectional area that is orders of magnitude smaller than the smallest catheter currently available. Our technology has the potential to improve state-of-the-art practices as it enhances the reachability, reduces the risk of iatrogenic damage, significantly increases the speed of robot-assisted interventions, and enables the deployment of multiple leads simultaneously through a standard needle injection and saline perfusion.

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Tailoring microstructures of materials through biomimetics

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100148332 ◽

1993 ◽

Vol 51 ◽

pp. 500-501

Author(s):

Mehmet Sarikaya ◽

Ilhan A. Aksay

Keyword(s):

Chemical Properties ◽

Design And Synthesis ◽

Structure Sensitive ◽

Macro Scale ◽

Methods Of Synthesis ◽

Successive Level ◽

Engineering Materials ◽

Physical And Chemical ◽

And Chemical Properties ◽

Synthesis Of Materials

Biomimetics involves investigation of structure, function, and methods of synthesis of biological composite materials. The goal is to apply this information to the design and synthesis of materials for engineering applications.Properties of engineering materials are structure sensitive through the whole spectrum of dimensions from nanometer to macro scale. The goal in designing and processing of technological materials, therefore, is to control microstructural evolution at each of these dimensions so as to achieve predictable physical and chemical properties. Control at each successive level of dimension, however, is a major challenge as is the retention of integrity between successive levels. Engineering materials are rarely fabricated to achieve more than a few of the desired properties and the synthesis techniques usually involve high temperature or low pressure conditions that are energy inefficient and environmentally damaging.In contrast to human-made materials, organisms synthesize composites whose intricate structures are more controlled at each scale and hierarchical order.

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