ArticlePDF Available

Abstract and Figures

We deal with image processing applied to three-dimensional (3D) analysis of vascular morphology in magnetic resonance angiography (MRA) images. It is, above all, a state-of-the-art survey. Both filtering and segmentation techniques are discussed. We briefly describe our most recent contribution : an anisotropic non-linear filter which improves visualization of small blood vessels. Enhancement of small vessels is obtained by combining a directional L-filter applied according to the locally estimated orientation of image content and a 2D Laplacian orthogonal to this orientation.
Content may be subject to copyright.
Maciej Orkisz, Marcela Hernández-Hoyos, Philippe Douek, Isabelle Magnin
CREATIS, CNRS Research Unit (UMR 5515), affiliated to INSERM, Lyon, France
CREATIS INSA 502, 69621 Villeurbanne cedex, France,
Abstract We deal with image processing applied to three-dimensional (3D) analysis of
vascular morphology in magnetic resonance angiography (MRA) images. It is, above all, a state-of-the-
art survey. Both filtering and segmentation techniques are discussed. We briefly describe our most recent
contribution : an anisotropic non-linear filter which improves visualization of small blood vessels.
Enhancement of small vessels is obtained by combining a directional L-filter applied according to the
locally estimated orientation of image content and a 2D Laplacian orthogonal to this orientation.
Key words: 3D image processing, medical imaging, magnetic resonance angiography, image
enhancement, image segmentation
1. Introduction
Our work is motivated by diagnosis, treatment planning and follow-up of arterial diseases.
Atherosclerosis is the principal acquired affection of the arterial wall. Its consequences depend
on its localization and on the size of the vessel. They are of two natures : arterial lumen
obstruction (stenosis) and arterial wall vulnerability which may lead to excrescence
(aneurysm) and rupture. Diagnosis of these pathologies is greatly aided by imaging
techniques. There are several challenges concerning angiography images. They obviously
should clearly display the pathological artery segment. In the case of severe obstructions, the
physician also needs to assess the collateral vascularization, i.e. to see a network of thin
vessels around the diseased region. Qualitative assessment is usually done in two-dimensional
(2D) projection images. However, the choice and planning of pharmacological, intra-vascular
or surgical treatment depend on precise measurements such as length, different diameters and
section areas of the diseased segment. These quantitative measurements should take full
advantage of 3D information. The latter requirement, as well as the invasive character of the
conventional 2D X-ray digital subtraction angiography (DSA), are the reasons for which 3D
imaging techniques such as MRA and spiral computed tomography (CT) tend to replace DSA.
Like the medical objectives, image processing challenges are twofold : 1) vessel enhancement
and noise removal to improve the qualitative analysis, 2) 3D segmentation and quantification
for the sake of (semi-)automated measurements. Both tasks are difficult, due to the specificity
of the data. Questions how to enhance thin vessels and not to amplify noise, how to remove
1 This work is in the scope of the scientific topics of the PRC-GDR ISIS research group of the French
National Center for Scientific Research (CNRS).
noise and not to wipe out thin vessels, are still an issue. Similarly, most segmentation
techniques are designed for large and homogenous regions, while many blood vessels are not
thicker than 3 pixels, their structure is complex, with ramifications, and their intensity is often
relatively heterogeneous, due to partial volume effect, flow artifacts and other effects. In
section 2, an outline of the state of the art of the angiography image processing shall be given.
In section 3, our contribution in vessel enhancement field shall be presented.
2. State of the art
There is a rich literature about 2D DSA image enhancement and segmentation methods. Many
of them could be extended to 3D, but computational cost of these extensions would often be
prohibitive. Although some of these methods shall be cited hereafter, we will focus on the
techniques developed specifically for 3D MRA.
2.1. Filtering
We subdivide the filtering techniques into two categories : 1) techniques which try to
eliminate noise while conserving vessels, 2) techniques which try to enhance vessels while
avoiding noise amplification.
2.1.1. Smoothing
Isotropic low-pass filtering removes noise as well as thin vessels and hence is unsuited for
vascular images. Several authors proposed an anisotropic approach where local orientation of
structures is first estimated and filtering is locally done along this orientation so as to preserve
small vessels and not to blur boundaries of larger structures. This approach implies a two-
stage processing (1. orientation estimation, 2. filtering) and there are many possible
combinations of methods used at each stage. In [9], smoothing was carried out by anisotropic
diffusion in the direction of the least principal curvature. One of the methods proposed in [2]
applied a morphological operation of crest detection, using directional (linear) tools, and
selected the direction giving the strongest response. Another one selected the local orientation
from a set of discrete orientations (sticks), by choosing the stick with the smallest intensity
variance. In [14] a more robust criterion was proposed, which combined homogeneity within
the stick on the one hand and intensity difference between the neighboring sticks on the other
hand. In both cases, the median filter was then applied within the selected stick. In [7], the
local orientation was estimated using six 3D filters in quadrature. A low-pass filter was then
applied in the estimated direction for the purpose of smoothing, while a high-pass filter was
applied orthogonally to this direction for the purpose of enhancement.
2.1.2. Enhancement
Smoothed images are less noisy, than the original ones, but thin vessels often remain hardly
visible, because their initial intensities are low. To enhance them, each point's intensity can be
replaced by a parameter reflecting the anisotropy of the point's neighborhood. One feature of
the vessels is their continuity : image intensity and local orientation vary slowly along the
vessel. Starting from each point, a path having this property can be sought, and the parameter
can be set equal to the path length [10]. Designed for 2D DSA images, this algorithm would
however be too time consuming in 3D.
There were several attempts to characterize the anisotropic properties of the vascular images
by non-linear combinations of outputs of directional filters. In [4], a set of directional mean-
filters was used. The difference between the strongest and the weakest response was used as
anisotropy measure. Indeed, the mean intensity along a vessel should be larger than in
perpendicular directions. Directional derivatives can also be exploited. They should be close
to zero when calculated along a vessel, and should have large absolute values in orthogonal
directions. Various combinations of such filters were proposed in [5] [6].
Directional second derivatives can also be brought together in a Hessian matrix, so as to
exploit the matrix's eigenvectors and eigenvalues
3. Indeed, tubular structures should
give rise to
10 (the associated eigenvector is tangential to the vessel axis) and to |
3 (the associated eigenvectors lie within the plane locally orthogonal to the vessel).
Different combinations of these eigenvalues were proposed to enhance points likely to belong
to vessels. Moreover, if appropriately designed and applied at multiple scales, such
combinations should give the strongest response at one particular scale corresponding to the
vessel caliber [16], [13], [19]. Similar geometrical considerations concerning the principal
curvatures led to the use of the Weingarten matrix eigenvalues [11], [15]. However, a common
problem of the methods based on derivatives is their noise-sensitivity.
2.2. Segmentation
In spite of the advances in the image processing field, interactive thresholding is still the
unique segmentation tool used in the commercial medical image processing software
packages! However, several automated algorithms were developed in research laboratories to
improve segmentation reproducibility. Three principal approaches can be cited : automatic
adaptive thresholding, region-growing and vessel-tracking.
2.2.1. Adaptive thresholding
Usually an adaptive threshold is global and is based on image intensity histogram. In [3] the
threshold was calculated iteratively, starting from the image mean value
plus two standard
. At each iteration,
i and
i were recalculated after eliminating non-isolated
voxels above the current threshold. In [18] and [22], prior knowledge of the actual image
acquisition protocol was used to choose intensity distribution model and to deduce the
threshold from the histogram, by identifying the model's parameters. Uniform distribution of
vessel intensities was assumed. The threshold was set at the intersection between this
distribution and the background tissues distribution. The latter was modeled by Gaussians in
time-of-flight (TOF) MRA and by a Rician in phase-contrast (PC) MRA. In [20], the authors
also argued that the threshold should depend on the actual image acquisition protocol. They
suggested setting the threshold at 50% of the maximum vessel signal in the TOF MRA and
contrast-enhanced (CE) MRA, and at 10% in the PC MRA.
2.2.2. Seeded region-growing
Region-growing algorithms require an initial seed selection which usually is manual in
medical applications. New voxels are then agglomerated to the current region as far as they
satisfy a homogeneity criterion. The criterion often is an intensity threshold. The threshold
may vary along the vessel to adapt itself to local intensity statistics. In [1], the threshold was
set equal to max (
v), where
v and
b respectively were the intensity
mean values and standard deviations for voxels already classified as belonging to a vessel and
for the remaining ones within a small volume around a current voxel. In [26], the region-
growing of both vessel and background was carried out by competition, using two criteria
based on the histograms of intensity gradient and of maximum principal curvature. A
directional region-growing was proposed in [10]. Local orientations were first estimated for
each pixel, by seeking the discrete orientation maximizing the mean intensity within the
corresponding stick. New pixels were then agglomerated as far as their orientation agreed with
the seed's local orientation. A very interesting method for automated selection of seeds was
recently proposed in [27]. It exploits the depth map constructed during maximum intensity
projection (MIP). This map, considered as an image, is continuous within regions
corresponding to the vessels and presents strong discontinuities elsewhere. A continuity
measure calculated in this image is used to segment the 2D MIP image. Since depth of thus
obtained regions is known, they are used as seeds in 3D.
2.2.3. Vessel-tracking
The vessel-tracking algorithms in 3D images use (often implicitly) a generalized-cylinder
model, i.e. an association of an axis (centerline) and a surface (vessel wall). Two approaches
can be distinguished. The first one begins by the centerline extraction, then the vessel wall is
sought. In [11] [15] the centerline was obtained by chaining local maxima of the principal
curvature and no attempt was done to estimate the vessel wall position. An improved
continuity of the axis and its reduced noise-sensitivity was obtained in [23][24] using a B-
spline curve (snake). An energy function was designed to attract the snake towards local
maxima of an anisotropy measure based on the Hessian matrix eigenvalues. A B-spline
approximation (active surface) was also used for the vessel wall. The corresponding energy
was minimum when the surface was close to isosurface corresponding to an acquisition
protocol dependent threshold. In [25], the axis was extracted using inertia moments. The
actual vessel boundaries were not extracted. Instead, an estimate of the vessel radius along the
axis was deduced from the inertia moments.
In the second approach, named "virtual catheter", axis and boundaries are interdependent. At
each step, contours are sought in the plane orthogonal to the current axis orientation, the axis
position is re-estimated, the centerline is extended according to the corrected orientation, and
so on. In [8], the boundary points were sought radially starting from the current axis position
and taking into account the neighboring radii. The axis position was then corrected using the
contour's gravity center and the centerline was extended linearly. In [12], linear extension was
replaced by a B-spline approximation and the contour detection took into account the
neighboring slices to improve continuity. In [17], the local axis orientation was updated in a
more complex manner, using intersections between the vessel and eight straight lines equally
spaced around the axis and parallel to its current orientation. For the boundary detection in the
plane orthogonal to the axis, the authors suggested the use of active contours. Active contours
were also used in [13] for the same purpose. In [21], the boundaries were sought more
roughly, using a radial search of gradient maxima, starting from different candidate points.
The lengths of thus obtained radii were used to calculate a confidence coefficient for each
starting point and to select the point which was the likeliest to lie on the centerline. In [28], the
boundary search was improved. To obtain a closed contour in the initial coordinates the
algorithm sought the minimum cost path in polar coordinates, i.e. a line as straight and as
vertical as possible, passing through the points with the most negative gradient values.
3. Our contribution
We have already published our contribution in both fields : anisotropic non-linear smoothing
[14] and vessel-tracking [25]. Here we propose an operator designed to enhance small vessels
while limiting noise amplification. To this purpose we re-use the orientation estimation
technique described in [14] and our new operator replaces the median filter used in the
smoothing context. Let us briefly recall how the local orientation is estimated. It is selected
from a set of discrete orientations represented by "sticks". For the voxels located within
vessels, the "best-oriented" stick should locally be parallel to the vessel axis and it should be
(almost) entirely included either in the vessel or in the background, to ensure a good
homogeneity of the intensity within the stick. Consequently, some of the neighboring sticks
parallel to the central stick should belong to the same region as the central stick while the
other ones should be located outside this region. Hence the intensity within each of these
neighboring sticks should also be homogenous, but there should be a large intensity difference
between the central stick and the neighboring sticks lying outside the region it belongs to. Let
= {Sij: j = 0,1,…,n} be a set of n+1 parallel neighboring sticks for the i-th orientation,
where Si0 is the central stick. Let
ij be the intensity standard deviation for Sij and let gij be the
directional mean gradient between Sij and Si0. The averages respectively of
ij (j = 0,1,…,n)
and of |gij| (j = 1,…,n), shall be noted
. The best orientation is the one which
maximizes the following criterion :
HDi =
which simultaneously takes into account the intensity homogeneity along the sticks (weighted
by a coefficient
), and the intensity difference between the central stick and its neighbors.
Because of the mixed use of a homogeneity measure and of a difference measure, we called
this operator HD-filter.
3.1. Vessel enhancement operator
Knowing the local orientation it is possible to implement an enhancement scheme similar to
the one proposed in [7], i.e. to apply a kind of low-pass filter along this orientation and a high-
pass in the orthogonal plane. In fact, true low-pass filters (mean, Gaussian) give poor results
for very thin and tortuous vessels. Instead, we prefer using L-filters. Let us recall that these
filters are based on sorting the voxels in the increasing order of intensity : I1 IL, where L
is the number of voxels (in our case L is the length of the sticks). An L-filter is any linear
combination of thus sorted intensities, with coefficients ak depending on the rank k. When ak =
1/(2W+1) for k = k0 = (L+1)/2, k01,… k0W and ak = 0 for the remaining ranks, one obtains a
truncated mean. Note that W = 0 gives the conventional median filter. Let {moptj: j = 0,1,…,n}
be the truncated mean values for the considered set of sticks Sopt, opt is the orientation selected
by the HD operator. To obtain the enhancement effect we replace the initial intensity of the
central voxel in Sopt0 by :
f = (n+1)mopt0 - (mopt1 + …+m optn) (2)
It can be interpreted as combining mopt0 with a 2D Laplacian applied on the truncated mean
values. This combination can be weighted. Similarly, W can be tuned to choose a compromise
between smoothing and enhancement effect. Figures 1 and 2 were obtained using W = 0.
3.2. Results
This new operator was tested on CE MRA images from 9 patients. Such images are obtained
by acquiring two data volumes, one before and the other one after intravascular injection of a
contrast agent (gadolinium), and by subtracting the latter from the former. Ideally (without
motion artifacts) the subtraction should eliminate non-vascular tissues. In practice it also
amplifies noise. Due to a high computational cost of the 3D orientation estimation the tests
were carried out in 2D for MIP images.
Our method was compared with a conventional isotropic image enhancement technique which
consists in adding to the image its Laplacian. In the sequel the latter shall be referred to as
isotropic, while our operator shall be called anisotropic. The comparison was both qualitative
and quantitative. The qualitative inspection focused on the visibility of small vessels. The
quantitative comparison was based on contrast and noise measurements. An automatic vessel
tracking applied to user-selected vessel segments allowed us to measure the mean signal inside
and outside the vessels, as well as noise standard deviation in the vessels' vicinity. Let us note
that noise level is usually measured in an image region outside the patient's body. This choice
is not appropriate in the case of MRA images since the noise level depends on the local signal
level. The measurements were performed for 65 arterial segments of different diameters
ranging from 1 to 8 pixels and representing different vascular regions : from carotid arteries to
lower-limb arteries, including the abdominal aorta and its branchings.
Fig. 1. Images of carotid arteries region : original (left) and enhanced by the anisotropic (middle) and
isotropic (right) operator.
Fig. 2. Images of abdominal aorta, renal and iliac arteries : original (left) and enhanced by the anisotropic
(middle) and isotropic (right) operator.
Visual inspection of figures 1 and 2 clearly shows that the arteries appear sharper after
application of both the isotropic and anisotropic operators. The conventional isotropic operator
however strongly amplifies noise, while our anisotropic operator produces a moderate noise
amplification. This qualitative impression was confirmed by the measurements. Indeed, on
average our anisotropic operator produced a significant improvement of the contrast (50,5 %)
and a smaller amplification of the noise standard deviation (41,5 %). This resulted in a
contrast-to-noise ratio improvement (11,7 %). The isotropic operator produced a similar
contrast enhancement (45 %) but noise level was strongly amplified (106,6 %) which led to a
contrast-to-noise ratio degradation (-26,3 %).
4. Conclusions
It is very difficult to enhance thin line-like objects and to avoid noise amplification. Our new
method using an L-filter applied along the vessels and a Laplacian applied in the plane locally
orthogonal to the vessel axis, seems to be a reasonable compromise. It strongly improves the
contrast while noise is moderately amplified. This method was successfully applied to
magnetic resonance angiography images in which it improved the visualization of small blood
vessels. It can therefore be used in practice to aid the assessment of collateral or peripheral
vascularization. However, it should not be used as preprocessing before stenosis diagnosis and
quantification, because vessel diameters are not necessarily preserved, especially near
bifurcations. Future work will focus on the computational cost reduction and on an application
of our operator to automated seed detection for the sake of segmentation.
Bibliographic references
[1] Hu X, Alperin N et al, Visualization of MR angiographic data with segmentation and volume-
rendering techniques, J Magn Reson Imaging, 1, 1991, 539-546.
[2] Vandermeulen D., Delaere D., Suetens P., Bosmans H., Marchal G. : Local filtering and global
optimization methods for 3D magnetic resonance angiography (MRA) image enhancement. Proc. SPIE
Vol. 1808, Visualization in Biomedical Computing, Chapel Hill NC (USA), 274-288.
[3] Du Y., Parker D.L. et al. : Contrast-to-noise-ratio measurements in three-dimensional magnetic
resonance angiography. Invest. Radiol., 28(11), 1004-1009.
[4] Chen H., Hale J. : An algorithm for MR angiography image enhancement. Magn. Reson. in Med., 33,
[5] Du Y.P., Parker D.L., Davis W.L. : Vessel enhancement filtering in three-dimensional MR
angiography. J. Magn. Reson. Imaging, 5, 151-157.
[6] Du Y.P., Parker D.L. : Digital vessel-enhancement filtering of 3D MR angiograms using long range
signal correlation. Int. Soc. Magn. Reson. in Med. Scientific Meeting, Nice (F), 581.
[7] Loock T., Westin C.F. et al. : Multidimensional adaptive filtering of 3D MRA data. Int. Soc. Magn.
Reson. in Med. Scientific Meeting, Nice (F), 716.
[8] Verdonck B., Bloch I. et al. : Blood vessel segmentation and visualization in 3D MRA and spiral CT
angiography. Comp. Assisted Radiol., Berlin (GER), (Elsevier), 177-182.
[9] Krissian K., Malandain G., Ayache N. : Directional anisotropic diffusion applied to segmentation of
vessels in 3D images. INRIA (F) research report # 3064.
[10] Kutka R., Stier S. : Extraction of line properties based on direction fields. IEEE Trans. MI, 15(1),
[11] Prinet V., Monga O., Ma S.D. : Extraction of vascular network in 3D images. Int. Conf. Image
Processing, Lausanne (CH), 307-310.
[12] Verdonck B., Bloch I. et al. : Accurate segmentation of blood vessels from 3D medical images. Int.
Conf. Image Processing, Lausanne (CH), 311-314.
[13] Lorenz C., Carlsen I.C. et al. : Multiscale line segmentation with automatic estimation of width,
contrast and tangential direction in 2D and 3D medical images. CVRMed, Grenoble (F), (Springer), 233-
[14] Orkisz M., Bresson C. et al. : Improved vessel visualization in MR angiography by non-linear
anisotropic filtering. Magn. Reson. in Med., 37, 914-919.
[15] Prinet V., Monga O., Rocchisani J.M. : Vessel representation in 2D and 3D angiograms. Comp.
Assisted Radiol., (Elsevier), 240-245.
[16] Sato Y., Nakajima S. et al. : 3-D multiscale line filter for segmentation and visualization of
curvilinear structures in medical images. CVRMed, Grenoble (F), (Springer), 213-222.
[17] Swift R.D., Ramaswamy K., Higgins W.E., Adaptive axes-generation algorithm for 3D tubular
structures. Int. Conf. Image Processing, Sta Barbara CA (USA), vol. 2, 136-139.
[18] Wilson D.L., Noble J.A., Segmentation of cerebral vessels and aneurysms from MR angiography
data. 15th Int. Conf. Information Processing in Med. Imaging, Poultney VT (USA), (Springer), 423-428.
[19] Frangi A.F., Niessen W.J. et al. : Multiscale vessel enhancement filtering. MICCAI, Cambridge MA
(USA), 130-137.
[20] Hoogeven R.M., Bakker C.J.G., Viergever M.A. : Limits to the accuracy of vessel diameter
measurement in MRA. J. Magn. Reson. Imaging, 8(6), 1228-1235.
[21] Wink O., Niessen W.J., Viergever M.A. : Fast quantification of abdobinal aortic aneurysms from
CTA volumes. MICCAI, Cambridge MA (USA), 138-145.
[22] Chung A.C.S., Noble J.A. : Statistical 3D vessel segmentation using a Rician distribution. MICCAI,
Cambridge (UK), (Springer), 82-89.
[23] Frangi A.F., Niessen W.J. et al. : Quantitation of vessel morphology from 3D MRA. MICCAI,
Cambridge (UK), (Springer) 358-367.
[24] Frangi A.F., Niessen W.J. et al. : Model-based quantitation of 3D Magnetic Resonance
Angiographic images. IEEE Trans. MI, 18(10), 946-956.
[25] Hernández-Hoyos M., Orkisz M. et al. : Inertia-based vessel axis extraction and stenosis
quantification in 3D MRA images. Comp. Assisted Radiol. & Surgery, Paris (F), (Elsevier), 189-193.
[26] Martinez-Pérez M.E., Hughes A.D. et al. : Retinal blood vessel segmentation by means of scale
space analysis and region growing. MICCAI, Cambridge (UK), (Springer), 90-97.
[27] Parker D.L., Chapman B.E. et al. : A novel segmentation and display technique : the depth buffer
segmentation (DBS) algorithm. 11th Int Workshop on Magn. Reson. Angio., Lund (S), 97.
[28] Wink O., Niessen W.J. et al. : Semi-automated quantification and segmentation of abdominal aorta
aneurysms from CTA volumes. Comp. Assisted Radiol. & Surgery, Paris (F), (Elsevier), 208-212.
... Hence, image denoising and vessel enhancement are useful both to improve the display and to help the segmentation. [6, 12] In MRA the vascular lumen usually appears brighter than the background, and can be visualized by means of the maximum intensity projection (MIP) technique. Ten years ago, when we initiated our first project in vascular image processing, MIP was the only widely available display mode capable of giving an overview of the vascularization. ...
... The filtering is performed according to the orientation φ that maximizes C(φ). We proposed a generic directional filter that can perform both denoising and enhancement weighted by appropriate parameters [12]. It computes a truncated mean values in each stick, then it combines them using the Laplacian-based scheme. ...
Full-text available
A synthesis of the authors' projects in the last decade, in the field of 3D vascular image processing, is provided. This work was motivated by the following applications: display improvement, extraction of geometrical measurements, acquisition optimization, stent-pose planning, phantom gener-ation, blood-flow simulations. The methods are often dependent on the imaging modality and/or on the anatomic region. They involve both: low-level models of intensity patterns and profiles, and higher-level models of cylindrical shapes. Amongst various algorithms used, recursive tracking and fast-marching level-sets are emphasized. Critical analysis of each model and algorithm is done. Problems that remain open, and perspectives associated with the progress of the image acquisition techniques, are listed.
... The second approach exploits the geometrical specificity of the vessels, in particular their orien- tation and tubular shape. Techniques that use this approach tend to use vessel-tracking [27][28][29][30][31] and (often implicitly) a generalized-cylinder model, i.e. an association of an axis (centerline) and a surface (vessel wall) [32][33]. Consequently, the segmentation process involves two tasks: centerline extraction and vessel contour detection in the planes perpendicular to the axis. ...
... The second approach exploits the geometric specificity of vessels, in particular the notions of orientation and tubular shape. Most of these approaches involve vessel tracking (27)(28)(29)(30)(31) and use (often implicitly) a generalized cylinder model, that is, an association between an axis (centerline) and a surface (vessel wall) (32,33). Consequently, the segmentation process involves two tasks: centerline extraction and vessel contour detection in the planes usually perpendicular to the axis. ...
... Discrete gradients have also been used. In [24], linelike orientation is first estimated using a set of discrete orientations. Then, instead of a classical low pass filter, an anisotropic filter is used to enhance curvilinear features. ...
Full-text available
The analysis of thin curvilinear objects in 3D images is a complex and challenging task. In this article, we introduce a new, nonlinear operator, called RORPO (Ranking Orientation Responses of Path Operators). Inspired by the multidirectional paradigm currently used in linear filtering for thin structure analysis, RORPO is built upon the notion of path operator from mathematical morphology. This operator, unlike most operators commonly used for 3D curvilinear structure analysis, is discrete, non-linear and non-local. From this new operator, two main curvilinear structure characteristics can be estimated: an intensity feature, that can be assimilated to a quantitative measure of curvilinearity; and a directional feature, providing a quantitative measure of the structure's orientation. We provide a full description of the structural and algorithmic details for computing these two features from RORPO, and we discuss computational issues.We experimentally assess RORPO by comparison with three of the most popular curvilinear structure analysis filters, namely Frangi Vesselness, Optimally Oriented Flux, and Hybrid Diffusion with Continuous Switch. In particular, we show that our method provides up to 8% more true positive and 50% less false positives than the next best method, on synthetic and real 3D images.
... L'idée de départ est qu'à partir de caractéristiques de la matrice des dérivées secondes des intensités des pixels, appelée matrice hessienne de l'image, il est possible de déterminer, en tout point, l'allure la plus probable d'uneéventuelle structure locale. Dans le cas 3D, la répartition sur l'axe réel des valeurs propres permet de discriminer les structures localement linéiques, planaires, volumiques, ou texturées et par la suite de filtrer et de segmenter les vaisseaux dans une reconstruction 3D [Orkisz et al., 2000]. La réduction au cas 2D de la méthode précédente donne un critère pour déterminer si une structure est localement linéique, planaire, ou texturée. ...
X-ray angiography is the mostly used imaging modality for the diagnosis of coronary arteries pathologies. Current clinical routine relies on a rough processing of X-ray projections. However, images have defects such as length foreshortening, magnification effect, and superimpositions. These difficulties impact diagnosis and therapeutical orientation. We propose to take advantage of a new angiography acquisition mode: the rotational mode, so that to produce tridimensional and dynamic models of the coronary tree. These models would allow to overcome the intrinsic defects of images. Our work is divided in three parts. First, a 3D multi-ocular reconstruction leads to a static model of coronary arteries centerlines, including the respiratory motion. Then, a 4D motion model of coronary arteries is computed over the entire cardiac cycle. Finally, knowledge of respiratory and cardiac motions is incorporated to perform the tomographic reconstruction of coronary arteries. We have tested our approach on a 22 patients database and have proposed new tools and clinical applications for these tridimensional and dynamic models. These diagnostic tools have been prototyped and will be involved in clinical studies.
... Discrete gradients are also used in tube-like detection. In [16], tube-like orientation is first estimated using a set of discrete orientations called "sticks". Then instead of a classical low pass filter, an anisotropic non-linear filter, the L-filter, is used to enhance tube-like features. ...
Conference Paper
Full-text available
Thin objects in 3D volumes, for instance vascular networks in medical imaging or various kinds of fibres in materials science, have been of interest for some time to computer vision. Particularly, tubular objects are everywhere elongated in one principal direction – which varies spatially – and are thin in the other two perpendicular directions. Filters for detecting such structures use for instance an analysis of the three principal directions of the Hessian, which is a local feature. In this article, we present a low-level tubular structure detection filter. This filter relies on paths, which are semi-global features that avoid any blurring effect induced by scale-space convolution. More precisely, our filter is based on recently developed morphological path operators. These require sampling only in a few principal directions, are robust to noise and do not assume feature regularity. We show that by ranking the directional response of this operator, we are further able to efficiently distinguish between blob, thin planar and tubular structures. We validate this approach on several applications, both from a qualitative and a quantitative point of view, demonstrating noise robustness and an efficient response on tubular structures.
... Instead, we drew our inspiration from the HD filter that was originally devised to improve the visualization of small vessels in MRA [32]. The first stage of the original HD filter estimated the local orientation of the vessel, while the second stage performed a directional smoothing or contrast enhancement [33]. Here, we are interested in the first stage that seeks, within a set of L different discrete orientations, the one that optimizes a criterion combining the longitudinal homogeneity (H) and the radial difference (D) of the image gray levels. ...
Full-text available
The long-term goal of our study is to understand the internal organization of the octocoral stem canals, as well as their physiological and functional role in the growth of the colonies, and finally to assess the influence of climatic changes on this species. Here we focus on imaging tools, namely acquisition and processing of three-dimensional high-resolution images, with emphasis on automated extraction of canal pathways. Our aim was to evaluate the feasibility of the whole process, to point out and solve - if possible - technical problems related to the specimen conditioning, to determine the best acquisition parameters and to develop necessary image-processing algorithms. The pathways extracted are expected to facilitate the structural analysis of the colonies, namely to help observing the distribution, formation and number of canals along the colony. Five volumetric images of Muricea muricata specimens were successfully acquired by X-ray computed tomography with spatial resolution ranging from 4.5 to 25 micrometers. The success mainly depended on specimen immobilization. More than [Formula: see text] of the canals were successfully detected and tracked by the image-processing method developed. Thus obtained three-dimensional representation of the canal network was generated for the first time without the need of histological or other destructive methods. Several canal patterns were observed. Although most of them were simple, i.e. only followed the main branch or "turned" into a secondary branch, many others bifurcated or fused. A majority of bifurcations were observed at branching points. However, some canals appeared and/or ended anywhere along a branch. At the tip of a branch, all canals fused into a unique chamber. Three-dimensional high-resolution tomographic imaging gives a non-destructive insight to the coral ultrastructure and helps understanding the organization of the canal network. Advanced image-processing techniques greatly reduce human observer's effort and provide methods to both visualize and quantify the structures of interest.
... The second approach exploits the geometrical specificity of the vessels, in particular their orien- tation and tubular shape. Techniques that use this approach tend to use vessel-tracking [27][28][29][30][31] and (often implicitly) a generalized-cylinder model, i.e. an association of an axis (centerline) and a surface (vessel wall) [32][33]. Consequently, the segmentation process involves two tasks: centerline extraction and vessel contour detection in the planes perpendicular to the axis. ...
Magnetic resonance angiography (MRA) is a medical imaging modality used to reveal the shape of vessels for diagnosis and therapeutic purposes. This technique receives much attention because it is non-invasive and provides three-dimensional (3D) data sets as opposed to the planar or two-dimensional (2D) projections of conventional x-ray digital subtraction angiography (DSA) [1-7]. Like DSA, contrast-enhanced MRA (CE MRA) uses contrast agents to enhance the vascular lumen. The term post-processing refers to a vast number of image manipulation techniques that facilitate the assessment of arterial and venous structures at an independent console. It refers to all operations from data transfer and image visualization to automatic quantification of vessel lesions. For accurate image interpretation, knowledge of the available image processing tools is mandatory. A varietyof reformatting techniques are now available, and it is advantageous to be well versed in as many of these as possible. Each technique has its own strengths and weaknesses,which can lead to pitfalls and artifacts in inexperienced hands. The main challenges for MRA image processing include proper visualization of vessel lumen, optimized thresholding of vessel-to-background image contrast, and arterial-venous separation. The most widely available methods for post-processing MRA data sets are multiplanar reformatting (MPR), maximum-intensity projection (MIP), subvolume MIP, surface-rendering (SR), volumerendering (VR) and virtual intraluminal endoscopy (VIE). This article will focus on the three main areas of the MRA post-processing systems: data handling, image visualization and vascular analysis (Fig. 1).
... One of them consists in defining: 1) a set of discrete line segments, often called "sticks", centred on a current voxel (volume element, i.e. 3D image point) and having various orientations and 2) a "vesselness" criterion calculated for each stick and used to deduce a kind of "probability" that the central voxel belongs to a vessel and/or to estimate the local orientation of the vessel. Criteria based on such measures as mean intensity [6,27], intensity variance [51], directional second derivatives of the intensity [10,11] and on their combinations [36,37] have been proposed. An example of such a criterion can be cited from [36]: ...
Full-text available
In image processing, models are used to improve robustness of algorithms by introducing a priori knowledge. Deformable models, frequently used in the field of medical images, are described by means of energy functionals with data attachment terms and regularising terms. The regularising terms express constraints relating to the expected shapes. The expected shape of a blood vessel segment in 3D images obtained by Magnetic Resonance Imaging or by helicoidal Computed Tomography is often implicitly described by a generalised cylinder model, i.e. an association of an axis (vessel centreline) and a surface (vessel boundary). In this context, the data attachment terms involve, for candidate points, a measure of the likelihood of being located on the centreline or on the boundary. Such a measure can use models reflecting low-level local photometrical properties of the brightness patterns. This presentation will give an overview of the recently used models and will be illustrated by the authors' contribution. 5. INTRODUCTION Three-dimensional (3D) imaging techniques, namely computed tomography angiography (CTA) and magnetic resonance angiography (MRA), meet a growing success in diagnosis, treatment planning and follow-up of vascular pathologies. These techniques provide rich anatomical information which is not directly available with standard 2D X-ray digital subtraction angiography (DSA). Moreover, MRA is not invasive for the patient. However, due to limitations of contrast agent quantity and of image acquisition time, the current 3D images are relatively noisy and small blood vessels appear poorly contrasted. Their legible visualisation as well as reproducible quantification of the vascular pathologies such as stenosis and aneurysm, require appropriate image processing techniques capable to cope with these difficulties. An improved visualisation can be obtained by an adequate filtering or image enhancement technique capable of distinguishing thin vessels from noise. However, the key operation for both visualisation (namely surface rendering) and quantification is image segmentation, i.e. separating the vascular structures from the surrounding tissues. It is well-known that robustness of image segmentation techniques dealing with noisy and poorly contrasted data, can be improved when exploiting a priori knowledge. This prior knowledge of the characteristics of the objects to be segmented and/or of the imaging process is usually introduced by means of a model. In the field of the vascular images, several levels of models are used. The highest level describes branching structures and includes anatomical knowledge of
L'objectif de cette thèse est la segmentation d'images vasculaires tridimensionnelles obtenues par résonance magnétique.L'application clinique visée est la quantification de sténoses artérielles. Nous proposons une méthode de segmentation diviséeen deux étapes : extraction de l'axe central du vaisseau et détection des contours sur les plans localement perpendiculaires àl'axe.Notre principale contribution est la méthode d'extraction automatique de la ligne centrale du vaisseau, basée sur unmodèle de squelette extensible dont la croissance est régie par l'analyse multi-échelle du tenseur d'inertie. Cette analyse nousfournit des informations sur l'orientation, le diamètre et la forme locale du vaisseau en chaque point de l'axe. Ceci nous permetde proposer un mécanisme de reconstruction approximative du vaisseau à l'aide d'un volume binaire composé d'une successionde sphéroïdes centrés sur l'axe, orientés selon l'orientation locale du vaisseau et adaptés à la taille locale du vaisseau. Sur lamême base théorique, nous proposons une méthode de détection semi-automatique de bifurcations artérielles. Le traitementrécursif des bifurcations détectées vise à aborder la problématique de l'extraction de l'arbre vasculaire entier.Le calcul des paramètres de sténose s'appuie sur l'extraction de contours planaires. Pour ce faire, nous avons implémentédeux algorithmes : le premier basé sur l’extraction d’iso-contours à seuil adaptatif et le deuxième sur un modèle de contouractif à longueur normalisée. Ces algorithmes ont été implémentés dans un logiciel convivial appelé MARACAS (MAgneticResonance Angiography Computer ASsisted analysis) qui a été soumis à une validation pré-clinique portant sur 6 fantômesvasculaires et sur des données cliniques de 27 patients.
Conference Paper
Full-text available
We present a method for retinal blood vessel segmentation based upon the scale-space analysis of the first and second derivative of the intensity image which gives information about its topology and overcomes the problem of variations in contrast inherent in these images. We use the local maxima over scales of the magnitude of the gradient and the maximum principal curvature as the two features used in a region growing procedure. In the first stage, the growth is constrained to regions of low gradient magnitude. In the final stage this constraint is relaxed to allow borders between regions to be defined. The algorithm is tested in both red-free and fluorescein retinal images.
Conference Paper
Full-text available
Three dimensional magnetic resonance angiographic images (3D MRA) are routinely inspected using maximum intensity projections (MIP). However, accuracy of stenosis estimates based on projections is limited. Therefore, a method for quantitative 3D MRA is introduced. Linear vessel segments are modeled with a central vessel axis curve coupled to a vessel wall surface. First, the central vessel axis is determined. Subsequently, the vessel wall is segmented using knowledge of the acquisition process. The user interaction to initialize the model is performed in a 3D setting. The method is validated on a carotid bifurcation phantom and also illustrated on patient data. 1
For a variety of reasons, small vessels have low signal intensity in magnetic resonance angiography. When the vessel signal intensity is lower than the signal intensity of background tissues, these vessels tend not to be visible on maximum-intensity-projection images. The authors developed a nonlinear second-difference spatial filtering technique that enhances the details of small vessels while suppressing both noise and uniform background tissue. Two similar nonlinear second-difference filters are presented and compared with the linear Laplacian second-difference filter. To evaluate the performance of these Filters, they were applied to intracranial three-dimensional time-of-flight MR angiographic data and the results compared with the vessel enhancement obtained with a simple second-difference Laplacian filter and with magnetization transfer contrast (MTC) techniques. The comparisons demonstrated that nonlinear filtering and MTC techniques result in similar improvement in small-vessel visibility and apparent continuity, A quantitative comparison demonstrated that the improvement in the contrast-to-noise ratio is much greater with the nonlinear filters than the Laplacian filter.
In this presentation, we discuss the visualization of cerebral blood vessels in 3-D MR angiography images. Two techniques for an improved visualization are investigated: 3-D non- linear morphological filters that enhance the contrast of blood-vessel-like structures and a global stochastic optimization framework incorporating shape constraints. The resulting filtered images are combined into a novel hybrid volume rendering visualization method for the integrated viewing of brain structures and cerebral vasculature.
Novel image processing and computer graphics techniques were developed to create three-dimensional (3D) models of vasculature from magnetic resonance (MR) angiographic images of the head or neck. Region growing was used to produce a mask that isolated the vascular signal in the MR angiographic data. The masked images were subjected to gradient-shaded volume rendering to create 3D views of the vasculature. The computer-derived model of intracranial vasculature was then merged with a 3D model of brain parenchyma derived from a set of MR images. The combined display of vascular and gyral anatomy may be useful for neurosurgical planning.
A new multi-scale segmentation technique for line-like structures in 2D and 3D medical images is presented. It is based on normalized first and second derivatives and on the eigenvector analysis of the hessian matrix. Application areas are the segmentation and tracking of bloodvessels, electrodes, catheters and other line-like objects. It allows for the estimation of the local diameter, the longitudinal direction and the contrast of the vessel and for the distinction between edge-like and line-like structures. The method is applicable as automatic 2D and 3D line-filter, as well as for interactive algorithms that are based on local direction estimation. A 3D line-tracker has been constructed that uses the estimated longitudinal direction as step-direction. After extraction of the centerline, the hull of the structure is determined by a 2D active-contour algorithm, applied in planes, orthogonal to the longitudinal line-direction. The procedure results in a stack of contours allowing quantitative crosssection area determination and visualization by means of a triangulation based rendering.
Conference Paper
A method is presented which aids the clinician in obtaining quantitative measurements of an abdominal aortic aneurysm from a CTA volume. These measurements are needed in the preoperative evaluation of candidates for minimally invasive aneurysmal repair. The user initializes starting points in the iliac artery. Subsequently, an iterative tracking procedure outlines the central lumen line in the aorta and the iliac arteries. Quantitative measurements on vessel morphology are performed in the planes perpendicular to the vessel axis. The entire process is performed in less than one minute on a standard workstation. In addition to the presentation of the calculated measures, a 3D view of the vessels is generated. This allows for interactive inspection of the vasculature and the tortuosity of the vessels.