arXiv subjects

Jan Egger

Publications and source records attributed to Jan Egger.

100 records · Page 6Linked to original sources

arXiv2012

Template-Cut: A Pattern-Based Segmentation Paradigm

We present a scale-invariant, template-based segmentation paradigm that sets up a graph and performs a graph cut to separate an object from the background. Typically graph-based schemes distribute the nodes of the graph uniformly and equidistantly on the image, and use a regularizer to bias the cut towards a particular shape. The strategy of uniform and equidistant nodes does not allow the cut to prefer more complex structures, especially when areas of the object are indistinguishable from the background. We propose a solution by introducing the concept of a "template shape" of the target object in which the nodes are sampled non-uniformly and non-equidistantly on the image. We evaluate it on 2D-images where the object's textures and backgrounds are similar, and large areas of the object have the same gray level appearance as the background. We also evaluate it in 3D on 60 brain tumor datasets for neurosurgical planning purposes.

cs.CV↗

arXiv2012

Square-Cut: A Segmentation Algorithm on the Basis of a Rectangle Shape

We present a rectangle-based segmentation algorithm that sets up a graph and performs a graph cut to separate an object from the background. However, graph-based algorithms distribute the graph's nodes uniformly and equidistantly on the image. Then, a smoothness term is added to force the cut to prefer a particular shape. This strategy does not allow the cut to prefer a certain structure, especially when areas of the object are indistinguishable from the background. We solve this problem by referring to a rectangle shape of the object when sampling the graph nodes, i.e., the nodes are distributed nonuniformly and non-equidistantly on the image. This strategy can be useful, when areas of the object are indistinguishable from the background. For evaluation, we focus on vertebrae images from Magnetic Resonance Imaging (MRI) datasets to support the time consuming manual slice-by-slice segmentation performed by physicians. The ground truth of the vertebrae boundaries were manually extracted by two clinical experts (neurological surgeons) with several years of experience in spine surgery and afterwards compared with the automatic segmentation results of the proposed scheme yielding an average Dice Similarity Coefficient (DSC) of 90.97\pm62.2%.

cs.CV↗

arXiv2011

A Comparison of Two Human Brain Tumor Segmentation Methods for MRI Data

The most common primary brain tumors are gliomas, evolving from the cerebral supportive cells. For clinical follow-up, the evaluation of the preoperative tumor volume is essential. Volumetric assessment of tumor volume with manual segmentation of its outlines is a time-consuming process that can be overcome with the help of computerized segmentation methods. In this contribution, two methods for World Health Organization (WHO) grade IV glioma segmentation in the human brain are compared using magnetic resonance imaging (MRI) patient data from the clinical routine. One method uses balloon inflation forces, and relies on detection of high intensity tumor boundaries that are coupled with the use of contrast agent gadolinium. The other method sets up a directed and weighted graph and performs a min-cut for optimal segmentation results. The ground truth of the tumor boundaries - for evaluating the methods on 27 cases - is manually extracted by neurosurgeons with several years of experience in the resection of gliomas. A comparison is performed using the Dice Similarity Coefficient (DSC), a measure for the spatial overlap of different segmentation results.

cs.CV↗

arXiv2011

Ray-Based and Graph-Based Methods for Fiber Bundle Boundary Estimation

Diffusion Tensor Imaging (DTI) provides the possibility of estimating the location and course of eloquent structures in the human brain. Knowledge about this is of high importance for preoperative planning of neurosurgical interventions and for intraoperative guidance by neuronavigation in order to minimize postoperative neurological deficits. Therefore, the segmentation of these structures as closed, three-dimensional object is necessary. In this contribution, two methods for fiber bundle segmentation between two defined regions are compared using software phantoms (abstract model and anatomical phantom modeling the right corticospinal tract). One method uses evaluation points from sampled rays as candidates for boundary points, the other method sets up a directed and weighted (depending on a scalar measure) graph and performs a min-cut for optimal segmentation results. Comparison is done by using the Dice Similarity Coefficient (DSC), a measure for spatial overlap of different segmentation results.

cs.CV↗

arXiv2011

Aorta Segmentation for Stent Simulation

Simulation of arterial stenting procedures prior to intervention allows for appropriate device selection as well as highlights potential complications. To this end, we present a framework for facilitating virtual aortic stenting from a contrast computer tomography (CT) scan. More specifically, we present a method for both lumen and outer wall segmentation that may be employed in determining both the appropriateness of intervention as well as the selection and localization of the device. The more challenging recovery of the outer wall is based on a novel minimal closure tracking algorithm. Our aortic segmentation method has been validated on over 3000 multiplanar reformatting (MPR) planes from 50 CT angiography data sets yielding a Dice Similarity Coefficient (DSC) of 90.67%.

cs.CV↗

arXiv2011

A Flexible Semi-Automatic Approach for Glioblastoma multiforme Segmentation

Gliomas are the most common primary brain tumors, evolving from the cerebral supportive cells. For clinical follow-up, the evaluation of the preoperative tumor volume is essential. Volumetric assessment of tumor volume with manual segmentation of its outlines is a time-consuming process that can be overcome with the help of segmentation methods. In this paper, a flexible semi-automatic approach for grade IV glioma segmentation is presented. The approach uses a novel segmentation scheme for spherical objects that creates a directed 3D graph. Thereafter, the minimal cost closed set on the graph is computed via a polynomial time s-t cut, creating an optimal segmentation of the tumor. The user can improve the results by specifying an arbitrary number of additional seed points to support the algorithm with grey value information and geometrical constraints. The presented method is tested on 12 magnetic resonance imaging datasets. The ground truth of the tumor boundaries are manually extracted by neurosurgeons. The segmented gliomas are compared with a one click method, and the semi-automatic approach yields an average Dice Similarity Coefficient (DSC) of 77.72% and 83.91%, respectively.

cs.CE↗

arXiv2011

Pituitary Adenoma Segmentation

Sellar tumors are approximately 10-15% among all intracranial neoplasms. The most common sellar lesion is the pituitary adenoma. Manual segmentation is a time-consuming process that can be shortened by using adequate algorithms. In this contribution, we present a segmentation method for pituitary adenoma. The method is based on an algorithm we developed recently in previous work where the novel segmentation scheme was successfully used for segmentation of glioblastoma multiforme and provided an average Dice Similarity Coefficient (DSC) of 77%. This scheme is used for automatic adenoma segmentation. In our experimental evaluation, neurosurgeons with strong experiences in the treatment of pituitary adenoma performed manual slice-by-slice segmentation of 10 magnetic resonance imaging (MRI) cases. Afterwards, the segmentations were compared with the segmentation results of the proposed method via the DSC. The average DSC for all data sets was 77.49% +/- 4.52%. Compared with a manual segmentation that took, on the average, 3.91 +/- 0.54 minutes, the overall segmentation in our implementation required less than 4 seconds.

cs.CE↗

arXiv2011

Evaluation of a Novel Approach for Automatic Volume Determination of Glioblastomas Based on Several Manual Expert Segmentations

The glioblastoma multiforme is the most common malignant primary brain tumor and is one of the highest malignant human neoplasms. During the course of disease, the evaluation of tumor volume is an essential part of the clinical follow-up. However, manual segmentation for acquisition of tumor volume is a time-consuming process. In this paper, a new approach for the automatic segmentation and volume determination of glioblastomas (glioblastoma multiforme) is presented and evaluated. The approach uses a user-defined seed point inside the glioma to set up a directed 3D graph. The nodes of the graph are obtained by sampling along rays that are sent through the surface points of a polyhedron. After the graph has been constructed, the minimal s-t cut is calculated to separate the glioblastoma from the background. For evaluation, 12 Magnetic Resonance Imaging (MRI) data sets were manually segmented slice by slice, by neurosurgeons with several years of experience in the resection of gliomas. Afterwards, the manual segmentations were compared with the results of the presented approach via the Dice Similarity Coefficient (DSC). For a better assessment of the DSC results, the manual segmentations of the experts were also compared with each other and evaluated via the DSC. In addition, the 12 data sets were segmented once again by one of the neurosurgeons after a period of two weeks, to also measure the intra-physician deviation of the DSC.

cs.CV↗

arXiv2011

A Semi-Automatic Graph-Based Approach for Determining the Boundary of Eloquent Fiber Bundles in the Human Brain

Diffusion Tensor Imaging (DTI) allows estimating the position, orientation and dimension of bundles of nerve pathways. This non-invasive imaging technique takes advantage of the diffusion of water molecules and determines the diffusion coefficients for every voxel of the data set. The identification of the diffusion coefficients and the derivation of information about fiber bundles is of major interest for planning and performing neurosurgical interventions. To minimize the risk of neural deficits during brain surgery as tumor resection (e.g. glioma), the segmentation and integration of the results in the operating room is of prime importance. In this contribution, a robust and efficient graph-based approach for segmentating tubular fiber bundles in the human brain is presented. To define a cost function, the fractional anisotropy (FA) is used, derived from the DTI data, but this value may differ from patient to patient. Besides manually definining seed regions describing the structure of interest, additionally a manual definition of the cost function by the user is necessary. To improve the approach the contribution introduces a solution for automatically determining the cost function by using different 3D masks for each individual data set.

cs.CV↗

arXiv2011

Glioblastoma Multiforme Segmentation in MRI Data with a Balloon Inflation Approach

Gliomas are the most common primary brain tumors, evolving from the cerebral supportive cells. For clinical follow-up, the evaluation of the preoperative tumor volume is essential. Volumetric assessment of tumor volume with manual segmentation of its outlines is a time-consuming process that can be overcome with the help of computer-assisted segmentation methods. In this paper, a semi-automatic approach for World Health Organization (WHO) grade IV glioma segmentation is introduced that uses balloon inflation forces, and relies on the detection of high-intensity tumor boundaries that are coupled by using contrast agent gadolinium. The presented method is evaluated on 27 magnetic resonance imaging (MRI) data sets and the ground truth data of the tumor boundaries - for evaluation of the results - are manually extracted by neurosurgeons.

cs.GR↗