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Intensity Compensation within Series of Images [chapter]

Grégoire Malandain, Eric Bardinet
2003 Lecture Notes in Computer Science  
This article addresses the problem of histogram matching in the context of medical image processing. Such a problem occurs while comparing two images of the same object, where intensity differences are due to different acquisition conditions. This can be compensated by histogram matching or equalization. To achieve this, we based our method on windowing techniques. This allows to match implicitly continuous probability density functions, yielding more robust results than the methods issued from discrete histograms.
doi:10.1007/978-3-540-39903-2_6 fatcat:ggds4vunkfhylakyvts3ddsgvi

Computing the Diameter of a Point Set [chapter]

Grégoire Malandain, Jean-Daniel Boissonnat
2002 Lecture Notes in Computer Science  
Given a finite set of points P in R d , the diameter of P is defined as the maximum distance between two points of P. We propose a very simple algorithm to compute the diameter of a finite set of points. Although the algorithm is not worst-case optimal, it appears to be extremely fast for a large variety of point distributions.
doi:10.1007/3-540-45986-3_18 fatcat:bm66z3ijhvavpipqlb445nni2m

Atlas-based delineation of lymph node levels in head and neck computed tomography images

Olivier Commowick, Vincent Grégoire, Grégoire Malandain
2008 Radiotherapy and Oncology  
Purpose: Radiotherapy planning requires accurate delineations of the tumor and of the critical structures. Atlas-based segmentation has been shown to be very efcient to automatically delineate brain critical structures. We therefore propose to construct an anatomical atlas of the head and neck region. Methods and Materials: Due to the high anatomical variability of this region, an atlas built from a single image as for the brain is not adequate. We address this issue by building a symmetric
more » ... s from a database of manually segmented images. First, we develop an atlas construction method and apply it to a database of 45 Computed Tomography (CT) images from patients with node-negative pharyngolaryngeal squamous cell carcinoma manually delineated for radiotherapy. Then, we qualitatively and quantitatively evaluate the results generated by the built atlas based on Leave-One-Out framework on the database. Results: We present qualitative and quantitative results using this atlas construction method. The evaluation was performed on a subset of 12 patients among the original CT database of 45 patients. Qualitative results depict visually well delineated structures. The quantitative results are also good, with an error with respect to the best achievable results ranging from 0.196 to 0.404 with a mean of 0.253. Conclusions: These results show the feasibility of using such an atlas for radiotherapy planning. Many perspectives are raised from this work ranging from extensive validation to the construction of several atlases representing sub-populations, to account for large inter-patient variabilities, and populations with node-positive tumors.
doi:10.1016/j.radonc.2008.01.018 pmid:18279984 fatcat:utdnq3fntfd5hjtaqqhto3c4qu

Tree Matching Applied to Vascular System [chapter]

Arnaud Charnoz, Vincent Agnus, Grégoire Malandain, Luc Soler, Mohamed Tajine
2005 Lecture Notes in Computer Science  
In this paper, we propose an original tree matching algorithm for intra-patient hepatic vascular system registration. The vascular systems are segmented from CT-Scan images acquired at different time, and then modeled as trees. The goal of this algorithm is to find common bifurcations (nodes) and vessels (edges) in both trees. Starting from the tree root, edges and nodes are iteratively matched. The algorithm works on a set of matching hypotheses which is updated to keep best matches. It is
more » ... st against topological modification, as the segmentation process can fail to detect some branches. Finally, this algorithm is validated on the Visible Human with synthetic deformations thanks to the simulator prototype developed at the INRIA which provides realistic deformations for liver and its vascular network.
doi:10.1007/978-3-540-31988-7_17 fatcat:f3pwwgb3efd7zkwphgqqjr2tum

Piecewise Affine Registration of Biological Images [chapter]

Alain Pitiot, Grégoire Malandain, Eric Bardinet, Paul M. Thompson
2003 Lecture Notes in Computer Science  
This manuscript tackles the registration of 2D biological images (histological sections or autoradiographs) to 2D images from the same or different modalities (e.g., histology or MRI). The process of acquiring these images typically induces composite transformations that can be modeled as a number of rigid or affine local transformations embedded in an elastic one. We propose a registration approach closely derived from this model. Given a pair of input images, we first compute a dense
more » ... y field between them with a block matching algorithm. A hierarchical clustering algorithm then automatically partitions this field into a number of classes from which we extract independent pairs of sub-images. Finally, the pairs of sub-images are, independently, affinely registered and a hybrid affine/non-linear interpolation scheme is used to compose the output registered image. We investigate the behavior of our approach under a variety of conditions, and discuss examples using real biomedical images, including MRI, histology and cryosection data.
doi:10.1007/978-3-540-39701-4_10 fatcat:kvyunrwtjzci3pb5l3p3snrify

3D Coronary Vessel Tracking in X-Ray Projections [chapter]

Emmanuelle Poulain, Grégoire Malandain, Régis Vaillant
2017 Lecture Notes in Computer Science  
Fusing pre-operative CT angiography with per-operative angiographic and fluoroscopic images is considered by physicians as a potentially useful tool for improved guidance. To be adopted, this tool requires the development of tracking methods adapted to the deformations of the arteries caused by the cardiac motion. Here, we propose a 3D/2D temporal tracking of one coronary vessel, based on a spline deformation, using pairings with a controlled 2D stretching or contraction along the paired curves
more » ... and a preservation of the length of the 3D curve. Experiments were conducted on a database of 10 vessels from 5 distinct patients, with dedicated metrics assessing both the global registration and the local coherency of the position along the vessel. The proposed results demonstrate the efficiency of the proposed method, with an average standard deviation of 2 mm for the localization of landmarks.
doi:10.1007/978-3-319-59448-4_20 fatcat:6fcfqsusovcelocabypid32wdu

Coherent temporal extrapolation of labeled images

Gregoire Malandain, Gael Michelin
2017 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017)  
In developmental imaging, 3D+t series of microscopic images allow to follow the organism development at the cell level and have now became the standard way of imaging the development of living organs. Dedicated tools for cell segmentation in 3D images as well as cell lineage calculation from 3D+t sequences have been proposed to analyze these data. For some applications, it may be desirable to interpolate label images at intermediary time-points. However, the known methods do not allow to
more » ... handle the topological changes (ie cell. division). In the present work, we propose an extrapolation method that coherently deformed the label images to be interpolated.
doi:10.1109/isbi.2017.7950554 dblp:conf/isbi/MalandainM17 fatcat:z6qrkgdwfbhktgl6gxl36ahjha

Quantitative comparison of micro-vasculatures

Marion Linder, Cecile Duplaa, Thierry Couffinhal, Gregoire Malandain
2015 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)  
Angiogenesis is a key component of ontogenesis, but also of tumor development or in some pathology repair (i.e. ischemia). Deciphering the underlying mechanisms of vessel formation is of importance. We aimed at identifying and characterizing the genetic components that are involved in this development. This requires to compare the effect of each gene with respect to the others, hence appeals for quantitative comparisons. To that end, we propose then in this paper a methodology that first
more » ... rms a vascular image into a tree and second quantitatively analyze 3D vascular trees. Our preliminary experiments are conducted with images of the renal arterial network of different mutant mice. A first set of quantitative measurements are proposed that allow for group study.
doi:10.1109/isbi.2015.7163924 dblp:conf/isbi/LinderDCM15 fatcat:v6swmukp7nedflcqfd6ibnyrba

Systematized Calculation of Optimal Coefficients of 3-D Chamfer Norms [chapter]

Céline Fouard, Grégoire Malandain
2003 Lecture Notes in Computer Science  
Chamfer distances are widely used in image analysis, and many ways have been investigated to compute optimal chamfer mask coefficients. Unfortunately, these methods are not systematized: they have to be conducted manually for every mask size or image anisotropy. Since image acquisition (e.g. medical imaging) can lead to anisotropic discrete grids with unpredictable anisotropy value, automated calculation of chamfer mask coefficients becomes mandatory for efficient distance map computation. This
more » ... article presents a systematized calculation of these coefficients based on the automatic construction of chamfer masks of any size associated with a triangulation that allows to derive analytically the relative error with respect to the Euclidean distance, in any 3-D anisotropic lattice.
doi:10.1007/978-3-540-39966-7_20 fatcat:g7dgmldrrjc4zcvuomndg3t63e

Using consensus measures for atlas construction

Liliane Ramus, Gregoire Malandain
2009 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
Grégoire for the manually delineated database and for his expertise. K be the number of manual segmentations in our database and L the number of anatomical structures including the background.  ... 
doi:10.1109/isbi.2009.5193271 dblp:conf/isbi/RamusM09 fatcat:audz7gp5gbdjxhqvzj3xwtbwda

3-D chamfer distances and norms in anisotropic grids

Céline Fouard, Grégoire Malandain
2005 Image and Vision Computing  
Chamfer distances are widely used in image analysis and many authors have investigated the computation of optimal chamfer mask coefficients. Unfortunately, these methods are not systematized: calculations have to be conducted manually for every mask size or image anisotropy. Since image acquisition (e.g. medical imaging) can lead to discrete anisotropic grids with unpredictable anisotropy value, automated calculation of chamfer mask coefficients becomes mandatory for efficient distance map
more » ... tations. This article presents an automatic construction for chamfer masks of arbitrary sizes. This allows, first, to derive analytically the relative error with respect to the Euclidean distance, in any 3-D anisotropic lattice, and second, to compute optimal chamfer coefficients. In addition, the resulting chamfer map verifies discrete norm conditions. q
doi:10.1016/j.imavis.2004.06.009 fatcat:ogycvf5rurd3fdhz7oxpdlia7m

3D Coronary Vessel Tree Tracking in X-Ray Projections [chapter]

Emmanuelle Poulain, Grégoire Malandain, Régis Vaillant
2019 Lecture Notes in Computer Science  
CTA angiography brings potentially useful information for guidance in an interventional procedure. It comes with the challenge of registering this 3D modality to the projection of the coronary arteries which are deforming with the cardiac motion. A tree-spline i.e. a tree with a spline attached to each edge and shared control points between these points describes a 3D coronary tree and is able to represent its deformation along the time. We combine this description with a registration algorithm
more » ... operating between the tree-spline and the angiographic projection of the coronary tree. It starts by the estimation of a rigid transformation for the iso cardiac phase time followed by a non-rigid deformation of the tree driven by the pairings formed between the projection of the edges of the tree-spline and the observed x-ray projection of the coronary arteries. The pairings are built taking into account the tree topology consistency. Anatomical constraints of length preservation is enforced when deforming the arteries. The proposed approach has been evaluated with clinical data issued from ten different clinical cases which enabling to form twenty three different experimental conditions. Encouraging results have been obtained.
doi:10.1007/978-3-030-21949-9_42 fatcat:kb4lgcgu3vdvvgsezjzcrqpw34

Using Frankenstein's Creature Paradigm to Build a Patient Specific Atlas [chapter]

Olivier Commowick, Simon K. Warfield, Grégoire Malandain
2009 Lecture Notes in Computer Science  
Conformal radiotherapy planning needs accurate delineations of the critical structures. Atlas-based segmentation has been shown to be very efficient to delineate brain structures. It would therefore be very interesting to develop an atlas for the head and neck region where 7 % of the cancers arise. However, the construction of an atlas in this region is very difficult due to the high variability of the anatomies. This can generate segmentation errors and over-segmented structures in the atlas.
more » ... o overcome this drawback, we present an alternative method to build a template locally adapted to the patient's anatomy. This is done first by selecting in a database the images that are the most similar to the patient on predefined regions of interest, using on a distance between transformations. The first major contribution is that we do not compute every patient-to-image registration to find the most similar image, but only the registration of the patient towards an average image. This method is therefore computationally very efficient. The second major contribution is a novel method to use the selected images and the predefined regions to build a "Frankenstein's creature" for segmentation. We present a qualitative and quantitative comparison between the proposed method and a classical atlas-based segmentation method. This evaluation is performed on a subset of 58 patients among a database of 105 head and neck CT images and shows a great improvement of the specificity of the results.
doi:10.1007/978-3-642-04271-3_120 fatcat:p46byf5ltzg7pd6shnoox3hbiq

Piecewise affine registration of biological images for volume reconstruction

Alain Pitiot, Eric Bardinet, Paul M. Thompson, Grégoire Malandain
2006 Medical Image Analysis  
When an external reference is available, anatomical information can be exploited to guide the registration process (Malandain et al., 2004) .  ...  In Malandain et al. (2004) , the reconstruction process was additionally guided by an external anatomical reference (MRI) to further approximate the anatomical ground truth.  ... 
doi:10.1016/ pmid:15963755 fatcat:qwss2qjzifasnaegdk3gycgece


2002 International journal of computational geometry and applications  
doi:10.1142/s0218195902001006 fatcat:2lzs4jgr6bdlzaruhxajbw34mu
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