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  • 1. Acosta, Oscar
    et al.
    Frimmel, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    Fenster, Aaron
    Ourselin, Sébastien
    Filtering and restoration of structures in 3D ultrasound images2007Inngår i: Proc. 4th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE , 2007, 888-891 s.Konferansepaper (Fagfellevurdert)
  • 2. Acosta, Oscar
    et al.
    Frimmel, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    Fenster, Aaron
    Salvado, Olivier
    Ourselin, Sébastien
    Pyramidal flux in an anisotropic diffusion scheme for enhancing structures in 3D images2008Inngår i: Medical Imaging 2008: Image Processing, Bellingham, WA, 2008, 691429:1-12 s.Konferansepaper (Fagfellevurdert)
  • 3.
    Afkham, Heydar Maboudi
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Ek, Carl Henrik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Datorseende och robotik, CVAP.
    Carlsson, Stefan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Datorseende och robotik, CVAP.
    Gradual improvement of image descriptor quality2014Inngår i: ICPRAM 2014 - Proceedings of the 3rd International Conference on Pattern Recognition Applications and Methods, 2014, 233-238 s.Konferansepaper (Fagfellevurdert)
    Abstract [en]

    In this paper, we propose a framework for gradually improving the quality of an already existing image descriptor. The descriptor used in this paper (Afkham et al., 2013) uses the response of a series of discriminative components for summarizing each image. As we will show, this descriptor has an ideal form in which all categories become linearly separable. While, reaching this form is not feasible, we will argue how by replacing a small fraction of these components, it is possible to obtain a descriptor which is, on average, closer to this ideal form. To do so, we initially identify which components do not contribute to the quality of the descriptor and replace them with more robust components. Here, a joint feature selection method is used to find improved components. As our experiments show, this change directly reflects in the capability of the resulting descriptor in discriminating between different categories.

  • 4.
    Agerskov, Niels
    et al.
    KTH, Skolan för teknik och hälsa (STH).
    Carrizo, Gabriel
    KTH, Skolan för teknik och hälsa (STH).
    Application for Deriving 2D Images from 3D CT Image Data for Research Purposes2016Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Karolinska University Hospital, Huddinge, Sweden, has long desired to plan hip prostheses with Computed Tomography (CT) scans instead of plain radiographs to save time and patient discomfort. This has not been possible previously as their current software is limited to prosthesis planning on traditional 2D X-ray images. The purpose of this project was therefore to create an application (software) that allows medical professionals to derive a 2D image from CT images that can be used for prosthesis planning.

    In order to create the application NumPy and The Visualization Toolkit (VTK) Python code libraries were utilised and tied together with a graphical user interface library called PyQt4. The application includes a graphical interface and methods for optimizing the images for prosthesis planning.

    The application was finished and serves its purpose but the quality of the images needs to be evaluated with a larger sample group. 

  • 5.
    Ahlander, Britt-Marie
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för kardiovaskulär medicin. Linköpings universitet, Medicinska fakulteten.
    Magnetic Resonance Imaging of the Heart: Image quality, measurement accuracy and patient experience2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Background: Non-invasive diagnostic imaging of atherosclerotic coronary artery disease (CAD) is frequently carried out with cardiovascular magnetic resonance imaging (CMR) or myocardial perfusion single photon emission computed tomography (MPS). CMR is the gold standard for the evaluation of scar after myocardial infarction and MPS the clinical gold standard for ischemia. Magnetic Resonance Imaging (MRI) is at times difficult for patients and may induce anxiety while patient experience of MPS is largely unknown.

    Aims: To evaluate image quality in CMR with respect to the sequences employed, the influence of atrial fibrillation, myocardial perfusion and the impact of patient information. Further, to study patient experience in relation to MRI with the goal of improving the care of these patients.

    Method: Four study designs have been used. In paper I, experimental cross-over, paper (II) experimental controlled clinical trial, paper (III) psychometric crosssectional study and paper (IV) prospective intervention study. A total of 475 patients ≥ 18 years with primarily cardiac problems (I-IV) except for those referred for MRI of the spine (III) were included in the four studies.

    Result: In patients (n=20) with atrial fibrillation, a single shot steady state free precession (SS-SSFP) sequence showed significantly better image quality than the standard segmented inversion recovery fast gradient echo (IR-FGRE) sequence (I). In first-pass perfusion imaging the gradient echo-echo planar imaging sequence (GREEPI) (n=30) had lower signal-to-noise and contrast–to-noise ratios than the steady state free precession sequence (SSFP) (n=30) but displayed a higher correlation with the MPS results, evaluated both qualitatively and quantitatively (II). The MRIAnxiety Questionnaire (MRI-AQ) was validated on patients, referred for MRI of either the spine (n=193) or the heart (n=54). The final instrument had 15 items divided in two factors regarding Anxiety and Relaxation. The instrument was found to have satisfactory psychometric properties (III). Patients who prior CMR viewed an information video scored significantly (lower) better in the factor Relaxation, than those who received standard information. Patients who underwent MPS scored lower on both factors, Anxiety and Relaxation. The extra video information had no effect on CMR image quality (IV).

    Conclusion: Single shot imaging in atrial fibrillation produced images with less artefact than a segmented sequence. In first-pass perfusion imaging, the sequence GRE-EPI was superior to SSFP. A questionnaire depicting anxiety during MRI showed that video information prior to imaging helped patients relax but did not result in an improvement in image quality.

  • 6.
    Ahlander, Britt-Marie
    et al.
    Department of Radiology, Ryhov County Hospital, Jönköping.
    Maret, Eva
    Department of Radiology, Ryhov County Hospital, Jönköping / Department of Clinical Physiology, Karolinska University Hospital, Stockholm.
    Brudin, Lars
    Department of Clinical Physiology, Kalmar County Hospital, Kalmar.
    Starck, Sven-Åke
    Department of Natural Science and Biomedicine, School of Health Sciences, Jönköping University / Department of Oncology, Hospital Physics, Ryhov County Hospital, Jönköping.
    Engvall, Jan
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för kardiovaskulär medicin. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Medicinska fakulteten. Region Östergötland, Hjärt- och Medicincentrum, Fysiologiska kliniken US.
    An echo-planar imaging sequence is superior to a steady-state free precession sequence for visual as well as quantitative assessment of cardiac magnetic resonance stress perfusion2017Inngår i: Clinical Physiology and Functional Imaging, ISSN 1475-0961, E-ISSN 1475-097X, Vol. 37, nr 1, 52-61 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background To assess myocardial perfusion, steady-state free precession cardiac magnetic resonance (SSFP, CMR) was compared with gradient-echo–echo-planar imaging (GRE-EPI) using myocardial perfusion scintigraphy (MPS) as reference. Methods Cardiac magnetic resonance perfusion was recorded in 30 patients with SSFP and in another 30 patients with GRE-EPI. Timing and extent of inflow delay to the myocardium was visually assessed. Signal-to-noise (SNR) and contrast-to-noise (CNR) ratios were calculated. Myocardial scar was visualized with a phase-sensitive inversion recovery sequence (PSIR). All scar positive segments were considered pathologic. In MPS, stress and rest images were used as in clinical reporting. The CMR contrast wash-in slope was calculated and compared with the stress score from the MPS examination. CMR scar, CMR perfusion and MPS were assessed separately by one expert for each method who was blinded to other aspects of the study. Results Visual assessment of CMR had a sensitivity for the detection of an abnormal MPS at 78% (SSFP) versus 91% (GRE-EPI) and a specificity of 58% (SSFP) versus 84% (GRE-EPI). Kappa statistics for SSFP and MPS was 0·29, for GRE-EPI and MPS 0·72. The ANOVA of CMR perfusion slopes for all segments versus MPS score (four levels based on MPS) had correlation r = 0·64 (SSFP) and r = 0·96 (GRE-EPI). SNR was for normal segments 35·63 ± 11·80 (SSFP) and 17·98 ± 8·31 (GRE-EPI), while CNR was 28·79 ± 10·43 (SSFP) and 13·06 ± 7·61 (GRE-EPI). Conclusion GRE-EPI displayed higher agreement with the MPS results than SSFP despite significantly lower signal intensity, SNR and CNR.

  • 7.
    Ahlgren, Ulf
    et al.
    Umeå universitet, Medicinska fakulteten, Umeå centrum för molekylär medicin (UCMM).
    Kostromina, Elena
    Umeå universitet, Medicinska fakulteten, Umeå centrum för molekylär medicin (UCMM).
    Imaging the pancreatic beta cell: chapter 132011Inngår i: Type 1 diabetes: pathogenesis, genetics and immunotherapy / [ed] David Wagner, InTech, 2011Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    This book is a compilation of reviews about the pathogenesis of Type 1 Diabetes. T1D is a classic autoimmune disease. Genetic factors are clearly determinant but cannot explain the rapid, even overwhelming expanse of this disease. Understanding etiology and pathogenesis of this disease is essential. A number of experts in the field have covered a range of topics for consideration that are applicable to researcher and clinician alike. This book provides apt descriptions of cutting edge technologies and applications in the ever going search for treatments and cure for diabetes. Areas including T cell development, innate immune responses, imaging of pancreata, potential viral initiators, etc. are considered.

  • 8.
    Allalou, Amin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Methods for 2D and 3D Quantitative Microscopy of Biological Samples2011Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    New microscopy techniques are continuously developed, resulting in more rapid acquisition of large amounts of data. Manual analysis of such data is extremely time-consuming and many features are difficult to quantify without the aid of a computer. But with automated image analysis biologists can extract quantitative measurements and increases throughput significantly, which becomes particularly important in high-throughput screening (HTS). This thesis addresses automation of traditional analysis of cell data as well as automation of both image capture and analysis in zebrafish high-throughput screening. 

    It is common in microscopy images to stain the nuclei in the cells, and to label the DNA and proteins in different ways. Padlock-probing and proximity ligation are highly specific detection methods that  produce point-like signals within the cells. Accurate signal detection and segmentation is often a key step in analysis of these types of images. Cells in a sample will always show some degree of variation in DNA and protein expression and to quantify these variations each cell has to be analyzed individually. This thesis presents development and evaluation of single cell analysis on a range of different types of image data. In addition, we present a novel method for signal detection in three dimensions. 

    HTS systems often use a combination of microscopy and image analysis to analyze cell-based samples. However, many diseases and biological pathways can be better studied in whole animals, particularly those that involve organ systems and multi-cellular interactions. The zebrafish is a widely-used vertebrate model of human organ function and development. Our collaborators have developed a high-throughput platform for cellular-resolution in vivo chemical and genetic screens on zebrafish larvae. This thesis presents improvements to the system, including accurate positioning of the fish which incorporates methods for detecting regions of interest, making the system fully automatic. Furthermore, the thesis describes a novel high-throughput tomography system for screening live zebrafish in both fluorescence and bright field microscopy. This 3D imaging approach combined with automatic quantification of morphological changes enables previously intractable high-throughput screening of vertebrate model organisms.

  • 9.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Curic, Vladimir
    Pardo-Martin, Carlos
    Massachusetts Institute of Technology, USA.
    Yanik, Mehmet Fatih
    Massachusetts Institute of Technology, USA.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Approaches for increasing throughput andinformation content of image-based zebrafishscreens2011Inngår i: Proceeding of SSBA 2011, 2011Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Microscopy in combination with image analysis has emerged as one of the most powerful and informativeways to analyze cell-based high-throughput screening (HTS) samples in experiments designed to uncover novel drugs and drug targets. However, many diseases and biological pathways can be better studied in whole animals, particularly diseases and pathways that involve organ systems and multicellular interactions, such as organ development, neuronal degeneration and regeneration, cancer metastasis, infectious disease progression and pathogenesis. The zebrafish is a wide-spread and popular vertebrate model of human organfunction and development, and it is unique in the sense that large-scale in vivo genetic and chemical studies are feasible due in part to its small size, optical transparency,and aquatic habitat. To improve the throughput and complexity of zebrafish screens, a high-throughput platform for cellular-resolution in vivo chemical and genetic screens on zebrafish larvae has been developed at Yanik lab at Research Laboratory of Electronics, MIT, USA. The system loads live zebrafish from reservoirs or multiwell plates, positions and rotates them for high-speed confocal imaging of organs,and dispenses the animals without damage. We present two improvements to the described system, including automation of positioning of the animals and a novel approach for brightfield microscopy tomographic imaging of living animals.

  • 10.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Wu, Yuelong
    Ghannad-Rezaie, Mostafa
    Eimon, Peter M.
    Yanik, Mehmet Fatih
    Automated deep-phenotyping of the vertebrate brain2017Inngår i: eLIFE, E-ISSN 2050-084X, Vol. 6, e23379Artikkel i tidsskrift (Fagfellevurdert)
  • 11.
    Andersson, Mats
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Burdakov, Oleg
    Linköpings universitet, Matematiska institutionen, Optimeringslära. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Zikrin, Spartak
    Linköpings universitet, Matematiska institutionen. Linköpings universitet, Tekniska högskolan.
    Global Search Strategies for Solving Multilinear Least-squares Problems2011Rapport (Annet vitenskapelig)
    Abstract [en]

    The multilinear least-squares (MLLS) problem is an extension of the linear least-squares problem. The difference is that a multilinearoperator is used in place of a matrix-vector product. The MLLS istypically a large-scale problem characterized by a large number of local minimizers. It originates, for instance, from the design of filter networks. We present a global search strategy that allows formoving from one local minimizer to a better one. The efficiencyof this strategy isillustrated by results of numerical experiments performed forsome problems related to the design of filter networks.

  • 12.
    Andersson, Mats
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Burdakov, Oleg
    Linköpings universitet, Matematiska institutionen, Optimeringslära. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Zikrin, Spartak
    Linköpings universitet, Matematiska institutionen, Matematik och tillämpad matematik. Linköpings universitet, Tekniska högskolan.
    Global search strategies for solving multilinear least-squares problems2012Inngår i: Sultan Qaboos University Journal for Science, ISSN 1027-524X, Vol. 17, nr 1, 12-21 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The multilinear least-squares (MLLS) problem is an extension of the linear leastsquares problem. The difference is that a multilinear operator is used in place of a matrix-vector product. The MLLS is typically a large-scale problem characterized by a large number of local minimizers. It originates, for instance, from the design of filter networks. We present a global search strategy that allows for moving from one local minimizer to a better one. The efficiency of this strategy is illustrated by results of numerical experiments performed for some problems related to the design of filter networks.

  • 13.
    Andersson, Mats
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Burdakov, Oleg
    Linköpings universitet, Matematiska institutionen, Optimeringslära. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Zikrin, Spartak
    Linköpings universitet, Matematiska institutionen. Linköpings universitet, Tekniska högskolan.
    Sparsity Optimization in Design of Multidimensional Filter Networks2013Rapport (Annet vitenskapelig)
    Abstract [en]

    Filter networks is a powerful tool used for reducing the image processing time, while maintaining its reasonably high quality.They are composed of sparse sub-filters whose low sparsity ensures fast image processing.The filter network design is related to solvinga sparse optimization problem where a cardinality constraint bounds above the sparsity level.In the case of sequentially connected sub-filters, which is the simplest network structure of those considered in this paper, a cardinality-constrained multilinear least-squares (MLLS) problem is to be solved. If to disregard the cardinality constraint, the MLLS is typically a large-scale problem characterized by a large number of local minimizers. Each of the local minimizers is singular and non-isolated.The cardinality constraint makes the problem even more difficult to solve.An approach for approximately solving the cardinality-constrained MLLS problem is presented.It is then applied to solving a bi-criteria optimization problem in which both thetime and quality of image processing are optimized. The developed approach is extended to designing filter networks of a more general structure. Its efficiency is demonstrated by designing certain 2D and 3D filter networks. It is also compared with the existing approaches.

  • 14.
    Andersson, Mats
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Adaptive Spatio-temporal Filtering of 4D CT-Heart2013Inngår i: Image Analyses: Image Processing, Computer Vision, Pattern Recognition, and Graphics / [ed] Joni-Kristian Kämäräinen, Markus Koskela, Berlin Heidelberg: Springer, 2013, 246-255 s.Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The aim of this project is to keep the x-ray exposure of the patient as low as reasonably achievable while improving the diagnostic image quality for the radiologist. The means to achieve these goals is to develop and evaluate an efficient adaptive filtering (denoising/image enhancement) method that fully explores true 4D image acquisition modes.

    The proposed prototype system uses a novel filter set having directional filter responses being monomials. The monomial filter concept is used both for estimation of local structure and for the anisotropic adaptive filtering. Initial tests on clinical 4D CT-heart data with ECG-gated exposure has resulted in a significant reduction of the noise level and an increased detail compared to 2D and 3D methods. Another promising feature is that the reconstruction induced streak artifacts which generally occur in low dose CT are remarkably reduced in 4D.

  • 15.
    Andersson, Thord
    et al.
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Läthén, Gunnar
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska högskolan.
    Lenz, Reiner
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska högskolan.
    Borga, Magnus
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Modified Gradient Search for Level Set Based Image Segmentation2013Inngår i: IEEE Transactions on Image Processing, ISSN 1057-7149, E-ISSN 1941-0042, Vol. 22, nr 2, 621-630 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Level set methods are a popular way to solve the image segmentation problem. The solution contour is found by solving an optimization problem where a cost functional is minimized. Gradient descent methods are often used to solve this optimization problem since they are very easy to implement and applicable to general nonconvex functionals. They are, however, sensitive to local minima and often display slow convergence. Traditionally, cost functionals have been modified to avoid these problems. In this paper, we instead propose using two modified gradient descent methods, one using a momentum term and one based on resilient propagation. These methods are commonly used in the machine learning community. In a series of 2-D/3-D-experiments using real and synthetic data with ground truth, the modifications are shown to reduce the sensitivity for local optima and to increase the convergence rate. The parameter sensitivity is also investigated. The proposed methods are very simple modifications of the basic method, and are directly compatible with any type of level set implementation. Downloadable reference code with examples is available online.

  • 16.
    Andersson, Thord
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Romu, Thobias
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Karlsson, Anette
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Norén, Bengt
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för radiologiska vetenskaper. Linköpings universitet, Medicinska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Region Östergötland, Diagnostikcentrum, Röntgenkliniken i Linköping.
    Forsgren, Mikael
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för radiologiska vetenskaper. Linköpings universitet, Medicinska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Region Östergötland, Centrum för kirurgi, ortopedi och cancervård, Radiofysikavdelningen US.
    Smedby, Örjan
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för radiologiska vetenskaper. Linköpings universitet, Medicinska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Region Östergötland, Diagnostikcentrum, Röntgenkliniken i Linköping.
    Kechagias, Stergios
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för kardiovaskulär medicin. Linköpings universitet, Medicinska fakulteten. Region Östergötland, Hjärt- och Medicincentrum, Magtarmmedicinska kliniken.
    Almer, Sven
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för neuro- och inflammationsvetenskap. Linköpings universitet, Medicinska fakulteten. Region Östergötland, Hjärt- och Medicincentrum, Magtarmmedicinska kliniken.
    Lundberg, Peter
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för radiologiska vetenskaper. Linköpings universitet, Medicinska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Region Östergötland, Centrum för kirurgi, ortopedi och cancervård, Radiofysikavdelningen US. Region Östergötland, Diagnostikcentrum, Röntgenkliniken i Linköping.
    Borga, Magnus
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Dahlqvist Leinhard, Olof
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för radiologiska vetenskaper. Linköpings universitet, Medicinska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Region Östergötland, Centrum för kirurgi, ortopedi och cancervård, Radiofysikavdelningen US.
    Consistent intensity inhomogeneity correction in water–fat MRI2015Inngår i: Journal of Magnetic Resonance Imaging, ISSN 1053-1807, E-ISSN 1522-2586, Vol. 42, nr 2, 468-476 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    PURPOSE:

    To quantitatively and qualitatively evaluate the water-signal performance of the consistent intensity inhomogeneity correction (CIIC) method to correct for intensity inhomogeneities METHODS: Water-fat volumes were acquired using 1.5 Tesla (T) and 3.0T symmetrically sampled 2-point Dixon three-dimensional MRI. Two datasets: (i) 10 muscle tissue regions of interest (ROIs) from 10 subjects acquired with both 1.5T and 3.0T whole-body MRI. (ii) Seven liver tissue ROIs from 36 patients imaged using 1.5T MRI at six time points after Gd-EOB-DTPA injection. The performance of CIIC was evaluated quantitatively by analyzing its impact on the dispersion and bias of the water image ROI intensities, and qualitatively using side-by-side image comparisons.

    RESULTS:

    CIIC significantly ( P1.5T≤2.3×10-4,P3.0T≤1.0×10-6) decreased the nonphysiological intensity variance while preserving the average intensity levels. The side-by-side comparisons showed improved intensity consistency ( Pint⁡≤10-6) while not introducing artifacts ( Part=0.024) nor changed appearances ( Papp≤10-6).

    CONCLUSION:

    CIIC improves the spatiotemporal intensity consistency in regions of a homogenous tissue type. J. Magn. Reson. Imaging 2014.

  • 17.
    Andersson, Thord
    et al.
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Romu, Thobias
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Norén, Bengt
    Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiologi. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Diagnostikcentrum, Röntgenkliniken i Linköping.
    Forsgren, Mikael
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiofysik. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Centrum för kirurgi, ortopedi och cancervård, Radiofysikavdelningen US.
    Smedby, Örjan
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiologi. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Diagnostikcentrum, Röntgenkliniken i Linköping.
    Almer, Sven
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Gastroenterologi och hepatologi. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Hjärt- och Medicincentrum, Endokrinmedicinska kliniken.
    Lundberg, Peter
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiofysik. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Centrum för kirurgi, ortopedi och cancervård, Radiofysikavdelningen US.
    Borga, Magnus
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Dahlqvist Leinhard, Olof
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiofysik. Linköpings universitet, Hälsouniversitetet.
    Self-calibrated DCE MRI using Multi Scale Adaptive Normalized Averaging (MANA)2012Inngår i: Proceedings of the annual meeting of the International Society for Magnetic Resonance in Medicine (ISMRM 2012), 2012, 2012Konferansepaper (Annet vitenskapelig)
  • 18.
    Angelopoulos, A.
    et al.
    -.
    Apostolakis, A.
    -.
    Aslanides, E.
    -.
    Backenstoss, G.
    -.
    Bargassa, P.
    -.
    Behnke, O.
    -.
    Benelli, A.
    -.
    Bertin, V.
    -.
    Blanc, F.
    -.
    Bloch, P.
    -.
    Danielsson, Mats
    KTH, Tidigare Institutioner, Fysik.
    K 0–K̄0 mass and decay-width differences: CPLEAR evaluation1999Inngår i: Physics Letters B, ISSN 0370-2693, E-ISSN 1873-2445, Vol. 471, nr 2, 332-338 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The CPT-violation parameters Re(δ) and Im(δ) determined recently by CPLEAR are used to evaluate the K0 mass and decay-width differences, as given by the difference between the diagonal elements of the neutral-kaon mixing matrix (M−iΓ/2). The results – GeV and GeV – are consistent with CPT invariance. The CPT invariance is also shown to hold within a few times 10−3–10−4 for many of the amplitudes describing neutral-kaon decays to different final states.

  • 19.
    Angelopoulos, Angelos
    et al.
    -.
    Locher, M P
    -.
    Markushin, V E
    -.
    Danielsson, Mats
    KTH, Tidigare Institutioner, Fysik.
    Dispersion relation analysis of the neutral kaon regeneration amplitude in carbon1999Inngår i: The European Physical Journal C-Particles and Fields, ISSN 434-6044, Vol. 10, nr 1, 19-25 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We apply a forward dispersion relation to the regeneration amplitude for kaon scattering on 12" style="position: relative;" tabindex="0" id="MathJax-Element-1-Frame" class="MathJax">12C using all available data. The CPLEAR data at low energies allow the determination of the net contribution from the subthreshold region which turns out to be much smaller than earlier evaluations, solving a long standing puzzle.

  • 20.
    Apostolakis, A.
    et al.
    -.
    Aslanides, E.
    -.
    Backenstoss, G.
    -.
    Bargassa, P.
    -.
    Behnke, O.
    -.
    Benelli, A.
    -.
    Bertin, V.
    -.
    Blanc, F.
    -.
    Bloch, P.
    -.
    Carlson, P.
    Danielsson, Mats
    KTH, Tidigare Institutioner, Fysik.
    Measurement of the energy dependence of the form factor f+ in K 0 e3 decay2000Inngår i: Physics Letters B, ISSN 0370-2693, E-ISSN 1873-2445, Vol. 473, nr 1, 186-192 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Neutral-kaon decays to πeν were analysed to determine the q2 dependence of the K0e3 electroweak form factor f+. Based on 365612 events, this form factor was found to have a linear dependence on q2 with a slope λ+=0.0245±0.0012stat±0.0022syst.

  • 21. Arvidsson, Anna
    et al.
    Sarve, Hamid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Johansson, Carina B.
    Comparing and visualizing titanium implant integration in rat bone using 2D and 3D techniques2015Inngår i: Journal of Biomedical Materials Research. Part B - Applied biomaterials, ISSN 1552-4973, E-ISSN 1552-4981, Vol. 103, nr 1, 12-20 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The aim was to compare the osseointegration of grit-blasted implants with and without a hydrogen fluoride treatment in rat tibia and femur, and to visualize bone formation using state-of-the-art 3D visualization techniques. Grit-blasted implants were inserted in femur and tibia of 10 Sprague-Dawley rats (4 implants/rat). Four weeks after insertion, bone implant samples were retrieved. Selected samples were imaged in 3D using Synchrotron Radiation-based CT (SRCT). The 3D data was quantified and visualized using two novel visualization techniques, thread fly-through and 2D unfolding. All samples were processed to cut and ground sections and 2D histomorphometrical comparisons of bone implant contact (BIC), bone area (BA), and mirror image area (MI) were performed. BA values were statistically significantly higher for test implants than controls (p<0.05), but BIC and MI data did not differ significantly. Thus, the results partly indicate improved bone formation at blasted and hydrogen fluoride treated implants, compared to blasted implants. The 3D analysis was a valuable complement to 2D analysis, facilitating improved visualization. However, further studies are required to evaluate aspects of 3D quantitative techniques, with relation to light microscopy that traditionally is used for osseointegration studies. (c) 2014 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 103B: 12-20, 2015.

  • 22.
    Avenel, Christophe
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Carlbom, Ingrid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Blur detection and visualization in histological whole slide images2015Inngår i: Proc. 10th International Conference on Mass Data Analysis of Images and Signals, Leipzig, Germany: IBaI , 2015Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Digital pathology holds the promise of improved workflow and also of the use of image analysis to extract features from tissue samples for quantitative analysis to improve current subjective analysis of, for example, cancer tissue. But this requires fast and reliable image digitization. In this paper we address image blurriness, which is a particular problem with very large images or tissue micro arrays scanned with whole slide scanners, since autofocus methods may fail when there is a large variation in image content. We introduce a method to detect, quantify and dis-play blurriness from whole slide images (WSI) in real-time. We describe a blurriness measurement based on an ideal high pass filter in the frequency domain. In contrast with other method our method does not require any prior knowledge of the image content, and it produces a continuous blurriness map over the entire WSI. This map can be displayed as an overlay of the original data and viewed at different levels of magnification with zoom and pan features. The computation time for an entire WSI is around 5 minutes on an average workstation, which is about 180 times faster than existing methods.

  • 23.
    Axelsson, Jan
    Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Radiofysik.
    Imlook4d: introducing an extendable research 4d analysis software2014Inngår i: XII Turku PET Symposium, 24-27 May 2014, Turku, Finland: the symposium of Nordic Association for Clinical Physics (NACP), 2014, 63-63 s.Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Imlook4d (http://www.dicom-port.com) is a free Matlab based graphical user interface (GUI) tool useful for static, dynamic and gated PET studies.  It supports reading and writing DICOM, Nifti, Analyze, ECAT.  The DICOM reader is orders of magnitude faster than the Matlab imaging toolbox.  Imlook4d requires no additional Matlab toolboxes.

    The main benefit with imlook4d is that it is easily extendable with scripts, accessing exported variables such as the image matrix (4D) and a region-of-interest (ROI) matrix.  Scripts are available via a menu in the imlook4d GUI, and can be used to manipulate the image-matrix and ROI data.  There is also a menu option to export and import these variables to the Matlab workspace for interactive manipulation, useful for one-off fixes or for script development.  There are presently about 30 scripts in categories such as ROI, Matrix, Header info etc.  There is also direct export to ImageJ [1] and import back from ImageJ, thus giving access to all tools available within ImageJ.

    Imlook4d has a built in volume-of-interest editor, with a brush tool for quick interactive ROI delineation, and via scripts, different ways of thresholding ROIs from parts of the image.  Time activity data is saved to a tab-delimited text file.

    The principal-component (PC) based Hotelling filter is an integrated part of the program, which allows for interactive noise reduction without loss of quantitation [2].  A typical work flow for a dynamic data set is to turn on the filter for ROI delineation, and then there is the choice of turning it off for export of time-activity data.  Also the PC images can be used to draw ROIs on, which under some circumstances gives enhanced contrast.

    Calculation of parametric pharmacokinetic modelling images can be performed interactively, calculated slice by slice as the user scrolls through the volume.  Reference models for Patlak, Logan and Averaged Simple Flow Model [3]  applied on 15O-water are implemented, and it is relatively easy to implement other kinetic models.  Similarly, scripts have been developed for regional Patlak and Logan models on ROI data.

    [1] Rasband, WS, ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, http://imagej.nih.gov/ij/, 1997-2014

    [2] Axelsson J, Sörensen J, The 2D Hotelling filter - a quantitative noise-reducing principal-component filter for dynamic PET data, with applications in patient dose reduction. BMC Med Phys. 2013 Apr 10;13:1. doi: 10.1186/1756-6649-13-1.

    [3] Yoshida, K, Mullani, N and Gould KL, Coronary Flow and Flow Reserve by PET Simplified for Clinical Applications Using Rubidium-82 or Nitrogen-13-Ammonia, J Nucl Med 1996; 37:1701-1712

    Figure 1.  The imlook4d GUI with the user SCRIPTS menu selected.  The group of ROI scripts was further selected.  In the underlying image, a rough ROI is created.  

  • 24.
    Axelsson, Jan
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Radiofysik.
    Sörensen, Jens
    PET-center, Department of Radiology, Oncology and Radiation Sciences, Uppsala University, Uppsala, Sweden.
    The 2D Hotelling filter: a quantitativenoise-reducing principal-component filter fordynamic PET data, with applications in patientdose reduction2013Inngår i: BMC Medical Physics, ISSN 1756-6649, Vol. 13, nr 1Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: In this paper we apply the principal-component analysis filter (Hotelling filter) to reduce noise fromdynamic positron-emission tomography (PET) patient data, for a number of different radio-tracer molecules. Wefurthermore show how preprocessing images with this filter improves parametric images created from suchdynamic sequence.We use zero-mean unit variance normalization, prior to performing a Hotelling filter on the slices of a dynamictime-series. The Scree-plot technique was used to determine which principal components to be rejected in thefilter process. This filter was applied to [11C]-acetate on heart and head-neck tumors, [18F]-FDG on liver tumors andbrain, and [11C]-Raclopride on brain. Simulations of blood and tissue regions with noise properties matched to realPET data, was used to analyze how quantitation and resolution is affected by the Hotelling filter. Summing varyingparts of a 90-frame [18F]-FDG brain scan, we created 9-frame dynamic scans with image statistics comparable to 20MBq, 60 MBq and 200 MBq injected activity. Hotelling filter performed on slices (2D) and on volumes (3D) werecompared.Results: The 2D Hotelling filter reduces noise in the tissue uptake drastically, so that it becomes simple to manuallypick out regions-of-interest from noisy data. 2D Hotelling filter introduces less bias than 3D Hotelling filter in focalRaclopride uptake. Simulations show that the Hotelling filter is sensitive to typical blood peak in PET prior to tissueuptake have commenced, introducing a negative bias in early tissue uptake. Quantitation on real dynamic data isreliable. Two examples clearly show that pre-filtering the dynamic sequence with the Hotelling filter prior toPatlak-slope calculations gives clearly improved parametric image quality. We also show that a dramatic dosereduction can be achieved for Patlak slope images without changing image quality or quantitation.Conclusions: The 2D Hotelling-filtering of dynamic PET data is a computer-efficient method that gives visuallyimproved differentiation of different tissues, which we have observed improve manual or automated regionof-interest delineation of dynamic data. Parametric Patlak images on Hotelling-filtered data display improved clarity,compared to non-filtered Patlak slope images without measurable loss of quantitation, and allow a dramaticdecrease in patient injected dose.

  • 25. Azar, J.C.
    et al.
    Hamid Muhammed, Hamed
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik.
    Automated Tracking of the Carotid Artery in Ultrasound Image Sequences Using a Self Organizing Neural Network2010Inngår i: Proceedings of 20th International Conference on Pattern Recognition (ICPR 2010), Istanbul, Turkey, Istanbul, Turkey, 2010, 2548-2551 s.Konferansepaper (Fagfellevurdert)
    Abstract [en]

    An automated method for the segmentation and tracking of moving vessel walls in 2D ultrasound image sequences is introduced. The method was tested on simulated and real ultrasound image sequences of the carotid artery. Tracking was achieved via a self organizing neural network known as Growing Neural Gas. This topology-preserving algorithm assigns a net of nodes connected by edges that distributes itself within the vessel walls and adapts to changes in topology with time. The movement of the nodes was analyzed to uncover the dynamics of the vessel wall. By this way, radial and longitudinal strain and strain rates have been estimated. Finally, wave intensity signals were computed from these measurements. The method proposed improves upon wave intensity wall analysis, WIWA, and opens up a possibility for easy and efficient analysis and diagnosis of vascular disease through noninvasive ultrasonic examination.

  • 26.
    Azar, Jimmy
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion.
    Automated Tissue Image Analysis Using Pattern Recognition2014Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Automated tissue image analysis aims to develop algorithms for a variety of histological applications. This has important implications in the diagnostic grading of cancer such as in breast and prostate tissue, as well as in the quantification of prognostic and predictive biomarkers that may help assess the risk of recurrence and the responsiveness of tumors to endocrine therapy.

    In this thesis, we use pattern recognition and image analysis techniques to solve several problems relating to histopathology and immunohistochemistry applications. In particular, we present a new method for the detection and localization of tissue microarray cores in an automated manner and compare it against conventional approaches.

    We also present an unsupervised method for color decomposition based on modeling the image formation process while taking into account acquisition noise. The method is unsupervised and is able to overcome the limitation of specifying absorption spectra for the stains that require separation. This is done by estimating reference colors through fitting a Gaussian mixture model trained using expectation-maximization.

    Another important factor in histopathology is the choice of stain, though it often goes unnoticed. Stain color combinations determine the extent of overlap between chromaticity clusters in color space, and this intrinsic overlap sets a main limitation on the performance of classification methods, regardless of their nature or complexity. In this thesis, we present a framework for optimizing the selection of histological stains in a manner that is aligned with the final objective of automation, rather than visual analysis.

    Immunohistochemistry can facilitate the quantification of biomarkers such as estrogen, progesterone, and the human epidermal growth factor 2 receptors, in addition to Ki-67 proteins that are associated with cell growth and proliferation. As an application, we propose a method for the identification of paired antibodies based on correlating probability maps of immunostaining patterns across adjacent tissue sections.

    Finally, we present a new feature descriptor for characterizing glandular structure and tissue architecture, which form an important component of Gleason and tubule-based Elston grading. The method is based on defining shape-preserving, neighborhood annuli around lumen regions and gathering quantitative and spatial data concerning the various tissue-types.

  • 27.
    Azar, Jimmy
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Busch, Christer
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylär och morfologisk patologi.
    Carlbom, Ingrid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Histological Stain Evaluation for Machine Learning Applications2012Inngår i: Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention, 2012Konferansepaper (Fagfellevurdert)
  • 28.
    Azar, Jimmy
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Busch, Christer
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Carlbom, Ingrid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Microarray Core Detection by Geometric Restoration2012Inngår i: Analytical Cellular Pathology, ISSN 0921-8912, Vol. 35, nr 5-6, 381-393 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Whole-slide imaging of tissue microarrays (TMAs) holds the promise of automated image analysis of a large number of histopathological samples from a single slide. This demands high-throughput image processing to enable analysis of these tissue samples for diagnosis of cancer and other conditions. In this paper, we present a completely automated method for the accurate detection and localization of tissue cores that is based on geometric restoration of the core shapes without placing any assumptions on grid geometry. The method relies on hierarchical clustering in conjunction with the Davies-Bouldin index for cluster validation in order to estimate the number of cores in the image wherefrom we estimate the core radius and refine this estimate using morphological granulometry. The final stage of the algorithm reconstructs circular discs from core sections such that these discs cover the entire region of each core regardless of the precise shape of the core. The results show that the proposed method is able to reconstruct core locations without any evidence of localization error. Furthermore, the algorithm is more efficient than existing methods based on the Hough transform for circle detection. The algorithm's simplicity, accuracy, and computational efficiency allow for automated high-throughput analysis of microarray images.

  • 29.
    Azar, Jimmy C.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Simonsson, Martin
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Hast, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Image segmentation and identification of paired antibodies in breast tissue2014Inngår i: Computational & Mathematical Methods in Medicine, ISSN 1748-670X, E-ISSN 1748-6718, 647273:1-11 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Comparing staining patterns of paired antibodies designed towards a specific protein but toward different epitopes of the protein provides quality control over the binding and the antibodies' ability to identify the target protein correctly and exclusively. We present a method for automated quantification of immunostaining patterns for antibodies in breast tissue using the Human Protein Atlas database. In such tissue, dark brown dye 3,3'-diaminobenzidine is used as an antibody-specific stain whereas the blue dye hematoxylin is used as a counterstain. The proposed method is based on clustering and relative scaling of features following principal component analysis. Our method is able (1) to accurately segment and identify staining patterns and quantify the amount of staining and (2) to detect paired antibodies by correlating the segmentation results among different cases. Moreover, the method is simple, operating in a low-dimensional feature space, and computationally efficient which makes it suitable for high-throughput processing of tissue microarrays.

  • 30.
    Azar, Jimmy
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Simonsson, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Hast, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Automated Classification of Glandular Tissue by Statistical Proximity Sampling2015Inngår i: International Journal of Biomedical Imaging, ISSN 1687-4188, E-ISSN 1687-4196, 943104Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Due to the complexity of biological tissue and variations in staining procedures, features that are based on the explicit extraction of properties from subglandular structures in tissue images may have difficulty generalizing well over an unrestricted set of images and staining variations. We circumvent this problem by an implicit representation that is both robust and highly descriptive, especially when combined with a multiple instance learning approach to image classification. The new feature method is able to describe tissue architecture based on glandular structure. It is based on statistically representing the relative distribution of tissue components around lumen regions, while preserving spatial and quantitative information, as a basis for diagnosing and analyzing different areas within an image. We demonstrate the efficacy of the method in extracting discriminative features for obtaining high classification rates for tubular formation in both healthy and cancerous tissue, which is an important component in Gleason and tubule-based Elston grading. The proposed method may be used for glandular classification, also in other tissue types, in addition to general applicability as a region-based feature descriptor in image analysis where the image represents a bag with a certain label (or grade) and the region-based feature vectors represent instances.

  • 31.
    Bae, Sang Won
    et al.
    Kyonggi University, Suwon, South Korea.
    Korman, Matias
    Tohoku University, Sendai, Japan.
    Mitchell, Joseph SB
    Stony Brook University, New York, USA.
    Okamoto, Yoshio
    The University of Electro-Communications, Tokyo, Japan.
    Polishchuk, Valentin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Kommunikations- och transportsystem. Linköpings universitet, Tekniska fakulteten.
    Wang, Haitao
    Utah State University, Utah, USA.
    Computing the $ L_1 $ Geodesic Diameter and Center of a Polygonal Domain2016Inngår i: Leibniz International Proceedings in Informatics, ISSN 1868-8969, E-ISSN 1868-8969, Vol. 47, 14:1-14:14 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    For a polygonal domain with h holes and a total of n vertices, we present algorithms that compute the L1 geodesic diameter in O(n2+h4) time and the L1 geodesic center in O((n4+n2h4) (n)) time, where (·) denotes the inverse Ackermann function. No algorithms were known for these problems before. For the Euclidean counterpart, the best algorithms compute the geodesic diameter in O(n7.73) or O(n7(h+log n)) time, and compute the geodesic center in O(n12+) time. Therefore, our algorithms are much faster than the algorithms for the Euclidean problems. Our algorithms are based on several interesting observations on L1 shortest paths in polygonal domains.

  • 32.
    Baeza Ortega, José Antonio
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Combined Visualization of Intracardiac Blood Flow and Wall Motion Assessed by MRI2011Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    MRI is a well known and widely spread technique to characterize cardiac pathologies due to its high spatial resolution, its accessibility and its adjustable contrast among soft tissues.

    In attempt to close the gap between blood flow, myocardial movement and the cardiac fucntion, researching in the MRI field addresses the quantification of some of the most relevant blood and myocardial parameters.

    During this proyect a new tool that allows reading, postprocessing, quantifying and visualizing 2D motion sense MR data has been developed. In order to analyze intracardiac blood flow and wall motion, the new tool quantifies velocity, turbulent kinetic energy, pressure and strain.

    In the results section the final tool is presented, describing the visualization modes, which represent the quantified parameters both individually and combined; and detailing auxiliary tool features as masking, thresholding, zooming, and cursors.

    Finally, thecnical aspects as the convenience of two dimensional examinations to create compact tools, and the challenges of masking as part of the relative pressure calculation, among others, are discussed; ending up with the proposal of some future developments.

  • 33.
    Bagheri, Maryam
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för cellbiologi. Linköpings universitet, Medicinska fakulteten.
    Rezakhani, Arjang
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för cellbiologi. Linköpings universitet, Medicinska fakulteten.
    Roghani, Mehrdad
    Neurophysiology Research Center, Shahed University, Iran.
    Joghataei, Mohammad T.
    Iran University of Medical Science, Iran.
    Mohseni, Simin
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för cellbiologi. Linköpings universitet, Medicinska fakulteten.
    Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes2015Inngår i: Journal of Visualized Experiments, ISSN 1940-087X, E-ISSN 1940-087X, nr 106, e53113- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify their functional and structural properties, a condition called reactive astrogliosis. Here, a protocol for assessment of the morphological properties of astrocytes is presented. This protocol includes quantification of 12 different parameters i.e. the surface area and volume of the tissue covered by an astrocyte (astrocyte territory), the entire astrocyte including branches, cell body, and nucleus, as well as total length and number of branches, the intensity of fluorescence immunoreactivity of antibodies used for astrocyte detection, and astrocyte density (number/1,000 mu m(2)). For this purpose three-dimensional (3D) confocal microscopic images were created, and 3D image analysis software such as Volocity 6.3 was used for measurements. Rat brain tissue exposed to amyloid beta(1-40) (A beta(1-40)) with or without a therapeutic intervention was used to present the method. This protocol can also be used for 3D morphometric analysis of other cells from either in vivo or in vitro conditions.

  • 34. Bajić, Buda
    et al.
    Lindblad, Joakim
    Sladoje, Nataša
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    An evaluation of potential functions for regularized image deblurring2014Inngår i: Image Analysis and Recognition: Part I, Springer Berlin/Heidelberg, 2014, 150-158 s.Konferansepaper (Fagfellevurdert)
  • 35.
    Banaem, Hossein Y.
    et al.
    Tehran University of Medical Sciences, Iran.
    Ahmadian, Alireza
    Tehran University of Medical Sciences, Iran.
    Saberi, Hooshangh
    Tehran University of Medical Sciences, Iran.
    Daneshmehr, Alireza
    Univiversity of Tehran, Iran.
    Khodadad, Davood
    Tehran University of Medical Sciences, Iran.
    Brain tumor modeling: glioma growth and interaction with chemotherapy2011Inngår i: Proc. SPIE 8285, International Conference on Graphic and Image Processing (ICGIP 2011), SPIE - International Society for Optical Engineering, 2011, 82851MKonferansepaper (Fagfellevurdert)
    Abstract [en]

    In last decade increasingly mathematical models of tumor growths have been studied, particularly on solid tumors which growth mainly caused by cellular proliferation. In this paper we propose a modified model to simulate the growth of gliomas in different stages. Glioma growth is modeled by a reaction-advection-diffusion. We begin with a model of untreated gliomas and continue with models of polyclonal glioma following chemotherapy. From relatively simple assumptions involving homogeneous brain tissue bounded by a few gross anatomical landmarks (ventricles and skull) the models have been expanded to include heterogeneous brain tissue with different motilities of glioma cells in grey and white matter. Tumor growth is characterized by a dangerous change in the control mechanisms, which normally maintain a balance between the rate of proliferation and the rate of apoptosis (controlled cell death). Result shows that this model closes to clinical finding and can simulate brain tumor behavior properly.

  • 36.
    Baranowski, Jacek
    et al.
    Linköping Heart Centre, University Hospital, Linköping University.
    Ahn, Henrik
    Linköping Heart Centre, University Hospital, Linköping University.
    Freter, Wolfgang
    Linköping Heart Centre, University Hospital, Linköping University.
    Nielsen, Niels-Erik
    Linköping Heart Centre, University Hospital, Linköping University.
    Nylander, Eva
    Linköping Heart Centre, University Hospital, Linköping University.
    Janerot-Sjöberg, Birgitta
    Linköping Heart Centre, University Hospital, Linköping University.
    Sandborg, Michael
    Linköping Heart Centre, University Hospital, Linköping University.
    Wallby, Lars
    Linköping Heart Centre, University Hospital, Linköping University.
    Echo-guided presentation of the aortic valve minimises contrast exposure in transcatheter valve recipients2011Inngår i: Catheterization and cardiovascular interventions, ISSN 1522-1946, E-ISSN 1522-726X, Vol. 77, nr 2, 272-275 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    OBJECTIVES: We have developed a method using transthoracic echocardiography in establishing optimal visualization of the aortic root, to reduce the amount of contrast medium used in each patient.

    BACKGROUND: During transcatheter aortic valve implantation, it is necessary to obtain an optimal fluoroscopic projection for deployment of the valve showing the aortic ostium with the three cusps aligned in the beam direction. This may require repeat aortic root angiograms at this stage of the procedure with a high amount of contrast medium with a risk of detrimental influence on renal function.

    METHODS: We studied the conventional way and an echo guided way to optimize visualisation of the aortic root. Echocardiography was used initially allowing easier alignment of the image intensifier with the transducer's direction.

    RESULTS: Contrast volumes, radiation/fluoroscopy exposure times, and postoperative creatinine levels were significantly less in patients having the echo-guided orientation of the optimal fluoroscopic angles compared with patients treated with the conventional approach.

    CONCLUSION: We present a user-friendly echo-guided method to facilitate fluoroscopy adjustment during transcatheter aortic valve implantation. In our series, the amounts of contrast medium and radiation have been significantly reduced, with a concomitant reduction in detrimental effects on renal function in the early postoperative phase.

  • 37. Bassan, Gioia
    et al.
    Larsson, David
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Nordenfur, Tim
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Bjällmark, Anna
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Larsson, Matilda
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Acquisition of multiple mode shear wave propagation in transversely isotropic medium using dualprobe setup2015Konferansepaper (Fagfellevurdert)
  • 38. Bassan, Gioia
    et al.
    Larsson, David
    KTH, Medicinsk bildteknik.
    Nordenfur, Tim
    KTH, Medicinsk bildteknik.
    Bjällmark, Anna
    KTH, Medicinsk bildteknik.
    Larsson, Matilda
    KTH, Medicinsk bildteknik.
    Acquisition of multiple mode shear wave propagation in transversely isotropic medium using dualprobe setup2015Konferansepaper (Fagfellevurdert)
  • 39.
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Quantitative and automated microscopy: Where do we stand after 80 years of research?2014Inngår i: Proc. 11th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE Press, 2014, 274-277 s.Konferansepaper (Fagfellevurdert)
  • 40.
    Bengtsson, Ewert
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Dahlqvist, Bengt
    Eriksson, Olle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Jarkrans, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Nordin, Bo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Stenkvist, Björn
    Cervical Pre-screening Using Computerized Image Analysis1983Inngår i: Proceedings of the 3rd Scandinavian Conference on Image Analysis, Köpenhamn, 1983, 404-411 s.Konferansepaper (Fagfellevurdert)
  • 41.
    Bengtsson, Ewert
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Dahlqvist, Bengt
    Eriksson, Olle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Jarkrans, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Nordin, Bo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Stenkvist, Björn
    Studie av reproducerbarheten av mikroskopiska cellbilder med TV-kamera1982Rapport (Annet vitenskapelig)
  • 42.
    Bengtsson, Ewert
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Malm, Patrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Screening for Cervical Cancer Using Automated Analysis of PAP-Smears2014Inngår i: Computational & Mathematical Methods in Medicine, ISSN 1748-670X, E-ISSN 1748-6718, Vol. 2014, 842037:1-12 s.Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Cervical cancer is one of the most deadly and common forms of cancer among women if no action is taken to prevent it, yet it is preventable through a simple screening test, the so-called PAP-smear. This is the most effective cancer prevention measure developed so far. But the visual examination of the smears is time consuming and expensive and there have been numerous attempts at automating the analysis ever since the test was introduced more than 60 years ago. The first commercial systems for automated analysis of the cell samples appeared around the turn of the millennium but they have had limited impact on the screening costs. In this paper we examine the key issues that need to be addressed when an automated analysis system is developed and discuss how these challenges have been met over the years. The lessons learned may be useful in the efforts to create a cost-effective screening system that could make affordable screening for cervical cancer available for all women globally, thus preventing most of the quarter million annual unnecessary deaths still caused by this disease.

  • 43.
    Berggren, Karl
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Medicinsk bildfysik. Philips Healthcare, Sweden.
    Danielsson, Mats
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Medicinsk bildfysik.
    Fredenberg, Erik
    Philips Healthcare, Sweden.
    Rayleigh imaging in spectral mammography2016Inngår i: MEDICAL IMAGING 2016: PHYSICS OF MEDICAL IMAGING, 2016, 97830AKonferansepaper (Fagfellevurdert)
    Abstract [en]

    Spectral imaging is the acquisition of multiple images of an object at different energy spectra. In mammography, dual-energy imaging (spectral imaging with two energy levels) has been investigated for several applications, in particular material decomposition, which allows for quantitative analysis of breast composition and quantitative contrast-enhanced imaging. Material decomposition with dual-energy imaging is based on the assumption that there are two dominant photon interaction effects that determine linear attenuation: the photoelectric effect and Compton scattering. This assumption limits the number of basis materials, i.e. the number of materials that are possible to differentiate between, to two. However, Rayleigh scattering may account for more than 10% of the linear attenuation in the mammography energy range. In this work, we show that a modified version of a scanning multi-slit spectral photon-counting mammography system is able to acquire three images at different spectra and can be used for triple-energy imaging. We further show that triple-energy imaging in combination with the efficient scatter rejection of the system enables measurement of Rayleigh scattering, which adds an additional energy dependency to the linear attenuation and enables material decomposition with three basis materials. Three available basis materials have the potential to improve virtually all applications of spectral imaging.

  • 44.
    Bergholm, Fredrik
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik.
    Hamid Muhammed, Hamed
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik.
    Larsolle, A.
    Acquiring instantaneous multispectral imagery using a single image sensor with multiple filter mosaic2007Konferansepaper (Annet vitenskapelig)
  • 45.
    Bergström, Per
    et al.
    Luleå University of Technology.
    Khodadad, Davood
    Luleå University of Technology.
    Hällstig, Emil
    Optronic Partner dp AB.
    Sjödahl, Mikael
    Luleå University of Technology.
    Single Shot Shape Evaluation Using Dual-Wavelength Holographic Reconstructions and Regularization2013Inngår i: Fringe 2013: 7th International Workshop on Advanced Optical Imaging and Metrology / [ed] Wolfgang Osten, Springer, 2013, 103-108 s.Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The aim of this work is to evaluate the shape of a free form object using single shot digital holography. The digital holography results in a gradient field and wrapped phase maps representing the shape of the object. The task is then to find a surface representation from this data which is an inverse problem. To solve this inverse problem we are using regularization with additional shape information from the CAD-model of the measured object.

  • 46. Bernard, Olivier
    et al.
    Bosch, J G
    Heyde, Brecht
    Alessandrini, Martino
    Barbosa, Daniel
    Camarasu-Pop, S
    Cervenansky, F
    Valette, S
    Mirea, O
    Bernier, M
    Jodoin, P M
    Domingos, J S
    Stebbing, R V
    Keraudren, K
    Oktay, O
    Caballero, J
    Shi, W
    Rueckert, D
    Milletari, F
    Ahmadi, S A
    Smistad, E
    Lindseth, F
    van Stralen, M
    Wang, Chunliang
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Smedby, Örjan
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildbehandling och visualisering.
    Donal, E
    Monaghan, M
    Papachristidis, A
    Geleijnse, M L
    Galli, E
    Dhooge, Jan
    Standardized evaluation system for left ventricular segmentation algorithms in 3D echocardiography.2015Inngår i: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254XArtikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Real-time 3D Echocardiography (RT3DE) has been proven to be an accurate tool for left ventricular (LV) volume assessment. However, identification of the LV endocardium remains a challenging task, mainly because of the low tissue/blood contrast of the images combined with typical artifacts. Several semi and fully automatic algorithms have been proposed for segmenting the endocardium in RT3DE data in order to extract relevant clinical indices, but a systematic and fair comparison between such methods has so far been impossible due to the lack of a publicly available common database. Here, we introduce a standardized evaluation framework to reliably evaluate and compare the performance of the algorithms developed to segment the LV border in RT3DE. A database consisting of 45 multivendor cardiac ultrasound recordings acquired at different centers with corresponding reference measurements from 3 experts are made available. The algorithms from nine research groups were quantitatively evaluated and compared using the proposed online platform. The results showed that the best methods produce promising results with respect to the experts' measurements for the extraction of clinical indices, and that they offer good segmentation precision in terms of mean distance error in the context of the experts' variability range. The platform remains open for new submissions.

  • 47. Bhatt, Manish
    et al.
    Ayyalasomayajula, Kalyan R.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Yalavarthy, Phaneendra K.
    Generalized Beer–Lambert model for near-infrared light propagation in thick biological tissues2016Inngår i: Journal of Biomedical Optics, ISSN 1083-3668, E-ISSN 1560-2281, Vol. 21, nr 7, 076012Artikkel i tidsskrift (Fagfellevurdert)
  • 48.
    Bianchi, Kevin
    et al.
    ISIT UMR6284 CNRS, Univ. d’Auvergne BP10448, F-63000 Clermont-Ferrand.
    Vacavant, Antoine
    ISIT UMR6284 CNRS, Univ. d’Auvergne BP10448, F-63000 Clermont-Ferrand.
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Terve, Pierre
    KEOSYS Company 1, impasse Auguste Fresnel, F 44815 Saint Herblain.
    Sarry, Laurent
    ISIT UMR6284 CNRS, Univ. d’Auvergne BP10448, F-63000 Clermont-Ferrand.
    Dual B-spline Snake for Interactive Myocardial Segmentation2013Konferansepaper (Fagfellevurdert)
    Abstract [en]

    This paper presents a novel interactive segmentation formalism based on two coupledB-Spline snake models to efficiently and simultaneously extract myocardial walls fromshort-axis magnetic resonance images. The main added value of this model is interactionas it is possible to quickly and intuitively correct the result in complex cases withoutrestarting the whole segmentation working flow. During this process, energies computedfrom the images guide the user to the best position of the model.

  • 49.
    Björklund, Tomas
    KTH, Skolan för teknik och hälsa (STH).
    Automatic evaluation of breast density in mammographic images2012Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The goal of this master thesis is to develop a computerized method for automatic estimation of the mammographic density of mammographic images from 5 different types of mammography units.

     

    Mammographic density is a measurement of the amount of fibroglandular tissue in a breast. This is the single most attributable risk factor for breast cancer; an accurate measurement of the mammographic density can increase the accuracy of cancer prediction in mammography. Today it is commonly estimated through visual inspection by a radiologist, which is subjective and results in inter-reader variation.

     

    The developed method estimates the density as a ratio of #pixels-containing-dense-tissue over #pixels-containing-any-breast-tissue and also according to the BI-RADS density categories. To achieve this, each mammographic image is:

    • corrected for breast thickness and normalized such that some global threshold can separate dense and non-dense tissue.
    • iteratively thresholded until a good threshold is found.  This process is monitored and automatically stopped by a classifier which is trained on sample segmentations using features based on different image intensity characteristics in specified image regions.
    • filtered to remove noise such as blood vessels from the segmentation.
    • Finally, the ratio of dense tissue is calculated and a BI-RADS density class is assigned based on a calibrated scale (after averaging the ratings of both craniocaudal images for each patient). The calibration is based on resulting density ratio estimations of over 1300 training samples against ratings by radiologists of the same images.

     

    The method was tested on craniocaudal images (not included in the training process) acquired with different mammography units of 703 patients which had also been rated by radiologists according to the BI-RADS density classes. The agreement with the radiologist rating in terms of Cohen’s weighted kappa is substantial (0.73). In 68% of the cases the agreement is exact, only in 1.2% of the cases the disagreement is more than 1 class.

  • 50.
    Björnfot, Magnus
    Linköpings universitet, Institutionen för systemteknik, Datorseende.
    Extension of DIRA (Dual-Energy Iterative Algorithm) to 3D Helical CT2017Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    There is a need for quantitative CT data in radiation therapy. Currently there are only few algorithms that address this issue, for instance the commercial DirectDensity algorithm. In scientific literature, an example of such an algorithm is DIRA. DIRA is an iterative model-based reconstruction method for dual-energy CT whose goal is to determine the material composition of the patient from accurate linear attenuation coefficients. It has been implemented in a two dimensional geometry, i.e., it could process axial scans only.  There was a need to extend DIRA so that it could process projection data generated in helical scanning geometries. The newly developed algorithm (DIRA-3D) implemented (i) polyenergetic semi-parallel projection generation, (ii) mono-energetic parallel projection generation and (iii) the PI-method for image reconstruction. The computation experiments showed that the accuracies of the resulting LAC and mass fractions were comparable to the ones of the original DIRA. The results converged after 10 iterations.

1234567 1 - 50 of 605
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