Multiscale vessel enhancement filtering

Frangi, Alejandro F.; Niessen, Wiro J.; Vincken, Koen L.; Viergever, Max A.

doi:10.1007/bfb0056195

Cited by 2,905 publications

(3,050 citation statements)

References 12 publications

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“…Image enhancement was performed using a Hessian matrixbased approach to increase the contrast of vessel structures. 21 Adaptive thresholding of the enhanced image was then implemented to obtain a binary representation of the vasculature (i.e., an equivalent image with all vessel pixels set to 1, and all other pixels set to 0). Morphologic image processing was applied as an additional noise removal step.…”

Section: Data Acquisition and Analysismentioning

confidence: 99%

Micro-Heterogeneity of Flow in a Mouse Model of Chronic Cerebral Hypoperfusion Revealed by Longitudinal Doppler Optical Coherence Tomography and Angiography

Srinivasan

Radhakrishnan

et al. 2015

J Cereb Blood Flow Metab

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Although microvascular dysfunction accompanies cognitive decline in aging, vascular dementia, and Alzheimer's disease, tools to study microvasculature longitudinally in vivo are lacking. Here, we use Doppler optical coherence tomography (OCT) and angiography for noninvasive, longitudinal imaging of mice with chronic cerebral hypoperfusion for up to 1 month. In particular, we optimized the OCT angiography method to selectively image red blood cell (RBC)-perfused capillaries, leading to a novel way of assessing capillary supply heterogeneity in vivo. After bilateral common carotid artery stenosis (BCAS), cortical blood flow measured by Doppler OCT dropped to half of baseline throughout the imaged tissue acutely. Microscopic imaging of the capillary bed with OCT angiography further revealed local heterogeneities in cortical flow supply during hypoperfusion. The number of RBC-perfused capillaries decreased, leading to increased oxygen diffusion distances in the days immediately after BCAS. Linear regression showed that RBC-perfused capillary density declined by 0.3% for a drop in flow of 1 mL/100 g per minute, and decreases in RBC-perfused capillary density as high as 25% were observed. Taken together, these results demonstrate the existence of local supply heterogeneity at the capillary level even at nonischemic global flow levels, and demonstrate a novel imaging method to assess this heterogeneity. Keywords: angiography; capillary recruitment; Doppler optical coherence tomography; hypoperfusion; vascular dementia INTRODUCTION Chronic cerebral hypoperfusion induced by small-artery occlusion or critical arterial stenosis is a pathophysiologic hallmark of vascular dementia. Histologically characterized by white matter changes and multifocal infarctions, chronic cerebral hypoperfusion is associated with cognitive decline. 1-3 Rodent models of chronic cerebral hypoperfusion that use common carotid artery stenosis or occlusion mimic many aspects of vascular cognitive impairment in patients, including decreased cerebral blood flow, inflammation and blood-brain barrier abnormalities, brain atrophy, white matter degeneration, decreased metabolism, as well as impaired working memory. 4 Bilateral common carotid artery occlusion has been widely used in the rat to model chronic cerebral hypoperfusion. 5 Recently, mouse bilateral common carotid artery stenosis (BCAS) models have emerged. 6 In these models, although the degree of hypoperfusion is correlated with the extent of ischemic lesions and neurologic impairment, 7 the magnitude of flow reductions after BCAS were moderate at best (~30 to 40%), 8 at least relative to classic ischemic thresholds of 80 to 85%, 9-11 and lasted only a few days before collateral development and recovery of flow. The lack of classic ischemia raises questions about the precise mechanism of tissue loss and cognitive impairment. Previous studies have used laser Doppler Journal of Cerebral Blood

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Section: Data Acquisition and Analysismentioning

confidence: 99%

Micro-Heterogeneity of Flow in a Mouse Model of Chronic Cerebral Hypoperfusion Revealed by Longitudinal Doppler Optical Coherence Tomography and Angiography

Srinivasan

Radhakrishnan

et al. 2015

J Cereb Blood Flow Metab

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“…Algorithms for segmentation of tumors and vessels combine intensitybased and morphological characteristics of given objects to identify them in source images. The basis of the algorithms is a multiscale filter, described in Frangi et al (1998), which detects local second-order structures based on the relationship between their eigenvalues. The filter distinguishes between linear (or cylindrical in 3D) and round (or spherical in 3D) structures, which can be used for detection of vessels and tumors, respectively.…”

Section: Automatic Segmentation Of Medical Imagesmentioning

confidence: 99%

Planning of Electroporation-Based Treatments Using Web-Based Treatment-Planning Software

et al. 2013

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Electroporation-based treatment combining high-voltage electric pulses and poorly permanent cytotoxic drugs, i.e., electrochemotherapy (ECT), is currently used for treating superficial tumor nodules by following standard operating procedures. Besides ECT, another electroporation-based treatment, nonthermal irreversible electroporation (N-TIRE), is also efficient at ablating deepseated tumors. To perform ECT or N-TIRE of deep-seated tumors, following standard operating procedures is not sufficient and patient-specific treatment planning is required for successful treatment. Treatment planning is required because of the use of individual long-needle electrodes and the diverse shape, size and location of deepseated tumors. Many institutions that already perform ECT of superficial metastases could benefit from treatmentplanning software that would enable the preparation of patient-specific treatment plans. To this end, we have developed a Web-based treatment-planning software for planning electroporation-based treatments that does not require prior engineering knowledge from the user (e.g., the clinician). The software includes algorithms for automatic tissue segmentation and, after segmentation, generation of a 3D model of the tissue. The procedure allows the user to define how the electrodes will be inserted. Finally, electric field distribution is computed, the position of electrodes and the voltage to be applied are optimized using the 3D model and a downloadable treatment plan is made available to the user.

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“…using the multi-scale "vesselness" measure of Frangi et al (1998). Of many suggested approaches for finding and detecting vessels, Lo et al (2010) is most similar to ours.…”

Section: Related Workmentioning

confidence: 52%

“…We follow the approach proposed by Frangi et al (1998), which is widely used in practice. MRI images typically do not contain isotropic voxels.…”

Section: Finding Tubular Structuresmentioning

confidence: 99%

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3d Reconstruction of Plant Roots From Mri Images

Schulz

Postma

Dusschoten

et al. 2012

Proceedings of the International Conference on Computer Vision Theory and Applications

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Abstract:We present a novel method for deriving a structural model of a plant root system from 3D Magnetic Resonance Imaging (MRI) data of soil grown plants. The structural model allows calculation of physiologically relevant parameters. Roughly speaking, MRI images show local water content of the investigated sample. The small, local amounts of water in roots require a relatively high resolution, which results in low SNR images. However, the spatial resolution of the MRI images remains coarse relative to the diameter of typical fine roots, causing many gaps in the visible root system. To reconstruct the root structure, we propose a three step approach: 1) detect tubular structures, 2) connect all pixels to the base of the root using Dijkstra's algorithm, and 3) prune the tree using two signal strength related thresholds. Dijkstra's algorithm determines the shortest path of each voxel to the base of the plant root, weighing the Euclidean distance measure by a multi-scale vesselness measure. As a result, paths running within good root candidates are preferred over paths in bare soil. We test this method using both virtually generated MRI images of Maize and real MRI images of Barley roots. In experiments on synthetic data, we show limitations of our algorithm with regard to resolution and noise levels. In addition we show how to use our reconstruction for root phenotyping on real MRI data of Barley roots in soil.

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Multiscale vessel enhancement filtering

Cited by 2,905 publications

References 12 publications

Micro-Heterogeneity of Flow in a Mouse Model of Chronic Cerebral Hypoperfusion Revealed by Longitudinal Doppler Optical Coherence Tomography and Angiography

Micro-Heterogeneity of Flow in a Mouse Model of Chronic Cerebral Hypoperfusion Revealed by Longitudinal Doppler Optical Coherence Tomography and Angiography

Planning of Electroporation-Based Treatments Using Web-Based Treatment-Planning Software

3d Reconstruction of Plant Roots From Mri Images

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