694 research outputs found
Co-Segmentation Methods for Improving Tumor Target Delineation in PET-CT Images
Positron emission tomography (PET)-Computed tomography (CT) plays an important role in
cancer management. As a multi-modal imaging technique it provides both functional and anatomical
information of tumor spread. Such information improves cancer treatment in many ways. One
important usage of PET-CT in cancer treatment is to facilitate radiotherapy planning, for the information
it provides helps radiation oncologists to better target the tumor region. However, currently
most tumor delineations in radiotherapy planning are performed by manual segmentation, which
consumes a lot of time and work. Most computer-aided algorithms need a knowledgeable user to
locate roughly the tumor area as a starting point. This is because, in PET-CT imaging, some tissues
like heart and kidney may also exhibit a high level of activity similar to that of a tumor region. In
order to address this issue, a novel co-segmentation method is proposed in this work to enhance
the accuracy of tumor segmentation using PET-CT, and a localization algorithm is developed to
differentiate and segment tumor regions from normal regions. On a combined dataset containing
29 patients with lung tumor, the combined method shows good segmentation results as well as
good tumor recognition rate
Brain Tumor Detection and Segmentation in Multisequence MRI
Tato práce se zabĂ˝vá detekcĂ a segmentacĂ mozkovĂ©ho nádoru v multisekvenÄŤnĂch MR obrazech se zaměřenĂm na gliomy vysokĂ©ho a nĂzkĂ©ho stupnÄ› malignity. Jsou zde pro tento účel navrĹľeny tĹ™i metody. PrvnĂ metoda se zabĂ˝vá detekcĂ prezence částĂ mozkovĂ©ho nádoru v axiálnĂch a koronárnĂch Ĺ™ezech. Jedná se o algoritmus zaloĹľenĂ˝ na analĂ˝ze symetrie pĹ™i rĹŻznĂ˝ch rozlišenĂch obrazu, kterĂ˝ byl otestován na T1, T2, T1C a FLAIR obrazech. Druhá metoda se zabĂ˝vá extrakcĂ oblasti celĂ©ho mozkovĂ©ho nádoru, zahrnujĂcĂ oblast jádra tumoru a edĂ©mu, ve FLAIR a T2 obrazech. Metoda je schopna extrahovat mozkovĂ˝ nádor z 2D i 3D obrazĹŻ. Je zde opÄ›t vyuĹľita analĂ˝za symetrie, která je následována automatickĂ˝m stanovenĂm intenzitnĂho prahu z nejvĂce asymetrickĂ˝ch částĂ. TĹ™etĂ metoda je zaloĹľena na predikci lokálnĂ struktury a je schopna segmentovat celou oblast nádoru, jeho jádro i jeho aktivnà část. Metoda vyuĹľĂvá faktu, Ĺľe vÄ›tšina lĂ©kaĹ™skĂ˝ch obrazĹŻ vykazuje vysokou podobnost intenzit sousednĂch pixelĹŻ a silnou korelaci mezi intenzitami v rĹŻznĂ˝ch obrazovĂ˝ch modalitách. JednĂm ze zpĹŻsobĹŻ, jak s touto korelacĂ pracovat a pouĹľĂvat ji, je vyuĹľitĂ lokálnĂch obrazovĂ˝ch polĂ. Podobná korelace existuje takĂ© mezi sousednĂmi pixely v anotaci obrazu. Tento pĹ™Ăznak byl vyuĹľit v predikci lokálnĂ struktury pĹ™i lokálnĂ anotaci polĂ. Jako klasifikaÄŤnĂ algoritmus je v tĂ©to metodÄ› pouĹľita konvoluÄŤnĂ neuronová sĂĹĄ vzhledem k jejĂ známe schopnosti zacházet s korelacĂ mezi pĹ™Ăznaky. Všechny tĹ™i metody byly otestovány na veĹ™ejnĂ© databázi 254 multisekvenÄŤnĂch MR obrazech a byla dosáhnuta pĹ™esnost srovnatelná s nejmodernÄ›jšĂmi metodami v mnohem kratšĂm vĂ˝poÄŤetnĂm ÄŤase (v řádu sekund pĹ™i pouĹľitĂ˝ CPU), coĹľ poskytuje moĹľnost manuálnĂch Ăşprav pĹ™i interaktivnĂ segmetaci.This work deals with the brain tumor detection and segmentation in multisequence MR images with particular focus on high- and low-grade gliomas. Three methods are propose for this purpose. The first method deals with the presence detection of brain tumor structures in axial and coronal slices. This method is based on multi-resolution symmetry analysis and it was tested for T1, T2, T1C and FLAIR images. The second method deals with extraction of the whole brain tumor region, including tumor core and edema, in FLAIR and T2 images and is suitable to extract the whole brain tumor region from both 2D and 3D. It also uses the symmetry analysis approach which is followed by automatic determination of the intensity threshold from the most asymmetric parts. The third method is based on local structure prediction and it is able to segment the whole tumor region as well as tumor core and active tumor. This method takes the advantage of a fact that most medical images feature a high similarity in intensities of nearby pixels and a strong correlation of intensity profiles across different image modalities. One way of dealing with -- and even exploiting -- this correlation is the use of local image patches. In the same way, there is a high correlation between nearby labels in image annotation, a feature that has been used in the ``local structure prediction'' of local label patches. Convolutional neural network is chosen as a learning algorithm, as it is known to be suited for dealing with correlation between features. All three methods were evaluated on a public data set of 254 multisequence MR volumes being able to reach comparable results to state-of-the-art methods in much shorter computing time (order of seconds running on CPU) providing means, for example, to do online updates when aiming at an interactive segmentation.
IMAGE PROCESSING, SEGMENTATION AND MACHINE LEARNING MODELS TO CLASSIFY AND DELINEATE TUMOR VOLUMES TO SUPPORT MEDICAL DECISION
Techniques for processing and analysing images and medical data have become
the main’s translational applications and researches in clinical and pre-clinical
environments. The advantages of these techniques are the improvement of diagnosis
accuracy and the assessment of treatment response by means of quantitative biomarkers
in an efficient way. In the era of the personalized medicine, an early and
efficacy prediction of therapy response in patients is still a critical issue.
In radiation therapy planning, Magnetic Resonance Imaging (MRI) provides high
quality detailed images and excellent soft-tissue contrast, while Computerized
Tomography (CT) images provides attenuation maps and very good hard-tissue
contrast. In this context, Positron Emission Tomography (PET) is a non-invasive
imaging technique which has the advantage, over morphological imaging techniques,
of providing functional information about the patient’s disease.
In the last few years, several criteria to assess therapy response in oncological
patients have been proposed, ranging from anatomical to functional assessments.
Changes in tumour size are not necessarily correlated with changes in tumour
viability and outcome. In addition, morphological changes resulting from therapy
occur slower than functional changes. Inclusion of PET images in radiotherapy
protocols is desirable because it is predictive of treatment response and provides
crucial information to accurately target the oncological lesion and to escalate the
radiation dose without increasing normal tissue injury. For this reason, PET may be
used for improving the Planning Treatment Volume (PTV). Nevertheless, due to the
nature of PET images (low spatial resolution, high noise and weak boundary),
metabolic image processing is a critical task.
The aim of this Ph.D thesis is to develope smart methodologies applied to the
medical imaging field to analyse different kind of problematic related to medical
images and data analysis, working closely to radiologist physicians.
Various issues in clinical environment have been addressed and a certain amount
of improvements has been produced in various fields, such as organs and tissues
segmentation and classification to delineate tumors volume using meshing learning
techniques to support medical decision.
In particular, the following topics have been object of this study:
• Technique for Crohn’s Disease Classification using Kernel Support Vector
Machine Based;
• Automatic Multi-Seed Detection For MR Breast Image Segmentation;
• Tissue Classification in PET Oncological Studies;
• KSVM-Based System for the Definition, Validation and Identification of the
Incisinal Hernia Reccurence Risk Factors;
• A smart and operator independent system to delineate tumours in Positron
Emission Tomography scans;
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• Active Contour Algorithm with Discriminant Analysis for Delineating
Tumors in Positron Emission Tomography;
• K-Nearest Neighbor driving Active Contours to Delineate Biological Tumor
Volumes;
• Tissue Classification to Support Local Active Delineation of Brain Tumors;
• A fully automatic system of Positron Emission Tomography Study
segmentation.
This work has been developed in collaboration with the medical staff and
colleagues at the:
• Dipartimento di Biopatologia e Biotecnologie Mediche e Forensi
(DIBIMED), University of Palermo
• Cannizzaro Hospital of Catania
• Istituto di Bioimmagini e Fisiologia Molecolare (IBFM) Centro Nazionale
delle Ricerche (CNR) of CefalĂą
• School of Electrical and Computer Engineering at Georgia Institute of
Technology
The proposed contributions have produced scientific publications in indexed
computer science and medical journals and conferences. They are very useful in
terms of PET and MRI image segmentation and may be used daily as a Medical
Decision Support Systems to enhance the current methodology performed by
healthcare operators in radiotherapy treatments.
The future developments of this research concern the integration of data acquired
by image analysis with the managing and processing of big data coming from a wide
kind of heterogeneous sources
A Review of MRI Acute Ischemic Stroke Lesion Segmentation
Immediate treatment of a stroke can minimize long-term effects and even help reduce death risk. In the ischemic stroke cases, there are two zones of injury which are ischemic core and ischemic penumbra zone. The ischemic penumbra indicates the part that is located around the infarct core that is at risk of developing a brain infarction. Recently, various segmentation methods of infarct lesion from the MRI input images were developed and these methods gave a high accuracy in the extraction and detection of the infarct core. However, only some limited works have been reported to isolate the penumbra tissues and infarct core separately. The challenges exist in ischemic core identification are traditional approach prone to error, time-consuming and tedious for medical expert which could delay the treatment. In this paper, we study and analyse the segmentation algorithms for brain MRI ischemic of different categories. The focus of the review is mainly on the segmentation algorithms of infarct core with penumbra and infarct core only. We highlight the advantages and limitations alongside the discussion of the capabilities of these segmentation algorithms and its key challenges. The paper also devised a generic structure for automated stroke lesion segmentation. The performance of these algorithms was investigated by comparing different parameters of the surveyed algorithms. In addition, a new structure of the segmentation process for segmentation of penumbra is proposed by considering the challenges remains. The best accuracy for segmentation of infarct core and penumbra tissues is 82.1% whereas 99.1% for segmentation infarct core only. Meanwhile, the shortest average computational time recorded was 3.42 seconds for segmenting 10 slices of MR images. This paper presents an inclusive analysis of the discussed papers based on different categories of the segmentation algorithm. The proposed structure is important to enable a more robust and accurate assessment in clinical practice. This could be an opportunity for the medical and engineering sector to work together in designing a complete end-to-end automatic framework in detecting stroke lesion and penumbra
Semi Automatic Segmentation of a Rat Brain Atlas
A common approach to segment an MRI dataset is to use a standard atlas to identify different regions of interest. Existing 2D atlases, prepared by freehand tracings of templates, are seldom complete for 3D volume segmentation. Although many of these atlases are prepared in graphics packages like Adobe Illustrator® (AI), which present the geometrical entities based on their mathematical description, the drawings are not numerically robust. This work presents an automatic conversion of graphical atlases suitable for further usage such as creation of a segmented 3D numerical atlas. The system begins with DXF (Drawing Exchange Format) files of individual atlas drawings. The drawing entities are mostly in cubic spline format. Each segment of the spline is reduced to polylines, which reduces the complexity of data. The system merges overlapping nodes and polylines to make the database of the drawing numerically integrated, i.e. each location within the drawing is referred by only one point, each line is uniquely defined by only two nodes, etc. Numerous integrity diagnostics are performed to eliminate duplicate or overlapping lines, extraneous markers, open-ended loops, etc. Numerically intact closed loops are formed using atlas labels as seed points. These loops specify the boundary and tissue type for each area. The final results preserve the original atlas with its 1272 different neuroanatomical regions which are complete, non-overlapping, contiguous sub-areas whose boundaries are composed of unique polyline
Development and Application of Semi-automated ITK Tools Development and Application of Semi-automated ITK Tools for the Segmentation of Brain MR Images
Image segmentation is a process to identify regions of interest from digital images. Image segmentation plays an important role in medical image processing which enables a variety of clinical applications. It is also a tool to facilitate the detection of abnormalities such as cancerous lesions in the brain. Although numerous efforts in recent years have advanced this technique, no single approach solves the problem of segmentation for the large variety of image modalities existing today. Consequently, brain MRI segmentation remains a challenging task. The purpose of this thesis is to demonstrate brain MRI segmentation for delineation of tumors, ventricles and other anatomical structures using Insight Segmentation and Registration Toolkit (ITK) routines as the foundation. ITK is an open-source software system to support the Visible Human Project. Visible Human Project is the creation of complete, anatomically detailed, three-dimensional representations of the normal male and female human bodies. Currently under active development, ITK employs leading-edge segmentation and registration algorithms in two, three, and more dimensions. A goal of this thesis is to implement those algorithms to facilitate brain segmentation for a brain cancer research scientist
Semi-automated 18F-FDG PET segmentation methods for tumor volume determination in Non-Hodgkin lymphoma patients:a literature review, implementation and multi-threshold evaluation
In the treatment of Non-Hodgkin lymphoma (NHL), multiple therapeutic options are available. Improving outcome predictions are essential to optimize treatment. The metabolic active tumor volume (MATV) has shown to be a prognostic factor in NHL. It is usually retrieved using semi-automated thresholding methods based on standardized uptake values (SUV), calculated from 18F-Fluorodeoxyglucose Positron Emission Tomography (18F-FDG PET) images. However, there is currently no consensus method for NHL. The aim of this study was to review literature on different segmentation methods used, and to evaluate selected methods by using an in house created software tool. A software tool, MUltiple SUV Threshold (MUST)-segmenter was developed where tumor locations are identified by placing seed-points on the PET images, followed by subsequent region growing. Based on a literature review, 9 SUV thresholding methods were selected and MATVs were extracted. The MUST-segmenter was utilized in a cohort of 68 patients with NHL. Differences in MATVs were assessed with paired t-tests, and correlations and distributions figures. High variability and significant differences between the MATVs based on different segmentation methods (p < 0.05) were observed in the NHL patients. Median MATVs ranged from 35 to 211 cc. No consensus for determining MATV is available based on the literature. Using the MUST-segmenter with 9 selected SUV thresholding methods, we demonstrated a large and significant variation in MATVs. Identifying the most optimal segmentation method for patients with NHL is essential to further improve predictions of toxicity, response, and treatment outcomes, which can be facilitated by the MUST-segmenter
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