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  • 1. Abu-Rmileh, Amjad
    et al.
    Garcia-Gabin, Winston
    KTH, Skolan för elektro- och systemteknik (EES), Reglerteknik.
    Wiener sliding-mode control for artificial pancreas: A new nonlinear approach to glucose regulation2012Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, ISSN 0169-2607, Vol. 107, nr 2, s. 327-340Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Type 1 diabetic patients need insulin therapy to keep their blood glucose close to normal. In this paper an attempt is made to show how nonlinear control-oriented model may be used to improve the performance of closed-loop control of blood glucose in diabetic patients. The nonlinear Wiener model is used as a novel modeling approach to be applied to the glucose control problem. The identified Wiener model is used in the design of a robust nonlinear sliding mode control strategy. Two configurations of the nonlinear controller are tested and compared to a controller designed with a linear model. The controllers are designed in a Smith predictor structure to reduce the effect of system time delay. To improve the meal compensation features, the controllers are provided with a simple feedforward controller to inject an insulin bolus at meal time. Different simulation scenarios have been used to evaluate the proposed controllers. The obtained results show that the new approach out-performs the linear control scheme, and regulates the glucose level within safe limits in the presence of measurement and modeling errors, meal uncertainty and patient variations.

  • 2.
    Acharya, Chayan
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Hooker, Andrew C.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Turkyilmaz, Gulbeyaz Yildiz
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap. Ege Univ, Fac Pharm, Dept Biopharmaceut & Pharmacokinet, TR-35100 Izmir, Turkey..
    Jönsson, Siv
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Karlsson, Mats O.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    A diagnostic tool for population models using non-compartmental analysis: The ncappc package for R2016Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 127, s. 83-93Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background and objective: Non-compartmental analysis (NCA) calculates pharmacokinetic (PK) metrics related to the systemic exposure to a drug following administration, e.g. area under the concentration time curve and peak concentration. We developed a new package in R, called ncappc, to perform (i) a NCA and (ii) simulation-based posterior predictive checks (ppc) for a population PK (PopPK) model using NCA metrics. Methods: The nca feature of ncappc package estimates the NCA metrics by NCA. The ppc feature of ncappc estimates the NCA metrics from multiple sets of simulated concentration time data and compares them with those estimated from the observed data. The diagnostic analysis is performed at the population as well as the individual level. The distribution of the simulated population means of each NCA metric is compared with the corresponding observed population mean. The individual level comparison is performed based on the deviation of the mean of any NCA metric based on simulations for an individual from the corresponding NCA metric obtained from the observed data. The ncappc package also reports the normalized prediction distribution error (NPDE) of the simulated NCA metrics for each individual and their distribution within a population. Results: The ncappc produces two default outputs depending on the type of analysis performed, i.e., NCA and PopPK diagnosis. The PopPK diagnosis feature of ncappc produces 8 sets of graphical outputs to assess the ability of a population model to simulate the concentration time profile of a drug and thereby evaluate model adequacy. In addition, tabular outputs are generated showing the values of the NCA metrics estimated from the observed and the simulated data, along with the deviation, NPDE, regression parameters used to estimate the elimination rate constant and the related population statistics. Conclusions: The ncappc package is a versatile and flexible tool-set written in R that successfully estimates NCA metrics from concentration time data and produces a comprehensive set of graphical and tabular output to summarize the diagnostic results including the model specific outliers. The output is easy to interpret and to use in evaluation of a population PK model. ncappc is freely available on CRAN (http://crantoprojectorg/web/packages/ncappc/index.html/) and GitHub (https://github.comicacha0227/ncappc/). 

  • 3.
    Ahnesjö, Anders
    et al.
    Uppsala University, Sweden.
    van Veelen, Bob
    Elekta Brachytherapy, Netherlands.
    Carlsson Tedgren, Åsa
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för radiologiska vetenskaper. Linköpings universitet, Medicinska fakulteten. Region Östergötland, Centrum för kirurgi, ortopedi och cancervård, Radiofysikavdelningen US. Karolinska University Hospital, Sweden.
    Collapsed cone dose calculations for heterogeneous tissues in brachytherapy using primary and scatter separation source data2017Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 139, s. 17-29Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background and Objective: Brachytherapy is a form of radiation therapy using sealed radiation sources inserted within or in the vicinity of the tumor of, e.g., gynecological, prostate or head and neck cancers. Accurate dose calculation is a crucial part of the treatment planning. Several reviews have called for clinical software with model-based algorithms that better take into account the effects of patient individual distribution of tissues, source-channel and shielding attenuation than the commonly employed TG-43 formalism which simply map homogeneous water dose distributions onto the patient. In this paper we give a comprehensive and thorough derivation of such an algorithm based on collapsed cone point-kernel superposition, and describe details of its implementation into a commercial treatment planning system for clinical use. Methods: A brachytherapy version of the collapsed-cone algorithm using analytical raytraces of the primary photon radiation followed by successive scattering dose calculation for once and multiply scattered photons is described in detail, including derivation of the corresponding set of recursive equations for energy transport along cone axes/transport lines and the coupling to clinical source modeling. Specific implementation issues for setting up of the calculation grid, handling of intravoxel gradients and voxels partly containing non patient applicator material are given. Results: Sample runs for two clinical cases are shown, one being a gynecological application with a tungsten-shielded applicator and one a breast implant. These two cases demonstrate the impact of improved dose calculation versus TG-43 formalism. Conclusions: Use of model-based dose calculation algorithms for brachytherapy taking the three-dimensional treatment geometry into account increases the dosimetric accuracy in planning and follow up of treatments. The comprehensive description and derivations provided gives a rigid background for further clinical, educational and research applications. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

  • 4.
    Ahnesjö, Anders
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Medicinsk strålningsvetenskap.
    van Veelen, Bob
    Elekta Brachytherapy, NL-3905 TH Veenendaal, Netherlands..
    Tedgren, Asa Carlsson
    Linkoping Univ, Fac Hlth Sci, Dept Med & Hlth Sci IMH, Radiat Phys, SE-58185 Linkoping, Sweden.;Karolinska Univ Hosp, Dept Med Phys, Sect Radiotherapy Phys & Engn, SE-17176 Stockholm, Sweden..
    Collapsed cone dose calculations for heterogeneous tissues in brachytherapy using primary and scatter separation source data2017Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 139, s. 17-29Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background and Objective: Brachytherapy is a form of radiation therapy using sealed radiation sources inserted within or in the vicinity of the tumor of, e.g., gynecological, prostate or head and neck cancers. Accurate dose calculation is a crucial part of the treatment planning. Several reviews have called for clinical software with model-based algorithms that better take into account the effects of patient individual distribution of tissues, source-channel and shielding attenuation than the commonly employed TG-43 formalism which simply map homogeneous water dose distributions onto the patient. In this paper we give a comprehensive and thorough derivation of such an algorithm based on collapsed cone point-kernel superposition, and describe details of its implementation into a commercial treatment planning system for clinical use. Methods: A brachytherapy version of the collapsed-cone algorithm using analytical raytraces of the primary photon radiation followed by successive scattering dose calculation for once and multiply scattered photons is described in detail, including derivation of the corresponding set of recursive equations for energy transport along cone axes/transport lines and the coupling to clinical source modeling. Specific implementation issues for setting up of the calculation grid, handling of intravoxel gradients and voxels partly containing non patient applicator material are given. Results: Sample runs for two clinical cases are shown, one being a gynecological application with a tungsten-shielded applicator and one a breast implant. These two cases demonstrate the impact of improved dose calculation versus TG-43 formalism. Conclusions: Use of model-based dose calculation algorithms for brachytherapy taking the three-dimensional treatment geometry into account increases the dosimetric accuracy in planning and follow up of treatments. The comprehensive description and derivations provided gives a rigid background for further clinical, educational and research applications.

  • 5.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datoriserad bildanalys.
    BlobFinder, a tool for fluorescence microscopy image cytometry2009Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 94, nr 1, s. 58-65Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Images can be acquired at high rates with modern fluorescence microscopy hardware, giving rise to a demand for high-speed analysis of image data. Digital image cytometry, i.e., automated measurements and extraction of quantitative data from images of cells, provides valuable information for many types of biomedical analysis. There exists a number of different image analysis software packages that can be programmed to perform a wide array of useful measurements. However, the multi-application capability often compromises the simplicity of the tool. Also, the gain in speed of analysis is often compromised by time spent learning complicated software. We provide a free software called BlobFinder that is intended for a limited type of application, making it easy to use, easy to learn and optimized for its particular task. BlobFinder can perform batch processing of image data and quantify as well as localize cells and point like source signals in fluorescence microscopy images, e.g., from FISH, in situ PLA and padlock probing, in a fast and easy way.

  • 6.
    Amiri, Saeid
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen, Matematisk statistik.
    von Rosen, Dietrich
    On the efficiency of bootstrap method into the analysis contingency table2011Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 104, nr 2, s. 182-187Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The bootstrap method is a computer intensive statistical method that is widely used in performing nonparametric inference. Categorica ldata analysis,inparticular the analysis of contingency tables, is commonly used in applied field. This work considers nonparametric bootstrap tests for the analysis of contingency tables. There are only a few research papers which exploit this field. The p-values of tests in contingency tables are discrete and should be uniformly distributed under the null hypothesis. The results of this article show that corresponding bootstrap versions work better than the standard tests. Properties of the proposed tests are illustrated and discussed using Monte Carlo simulations. This article concludes with an analytical example that examines the performance of the proposed tests and the confidence interval of the association coefficient.

  • 7.
    Aoki, Yasunori
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Monika, Sundqvist
    AstraZeneca, Cardiovasc & Metab Dis, Innovat Med & Early Dev Biotech Unit, Pepparedsleden 1, S-43183 Molndal, Sweden.
    Hooker, Andrew C.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Gennemark, Peter
    AstraZeneca, Cardiovasc & Metab Dis, Innovat Med & Early Dev Biotech Unit, Pepparedsleden 1, S-43183 Molndal, Sweden.
    PopED lite: an optimal design software for preclinical pharmacokinetic and pharmacodynamic studies2016Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 127, s. 126-143Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background and Objective

    Optimal experimental design approaches are seldom used in preclinical drug discovery. The objective is to develop an optimal design software tool specifically designed for preclinical applications in order to increase the efficiency of drug discovery in vivo studies.

    Methods

    Several realistic experimental design case studies were collected and many preclinical experimental teams were consulted to determine the design goal of the software tool. The tool obtains an optimized experimental design by solving a constrained optimization problem, where each experimental design is evaluated using some function of the Fisher Information Matrix. The software was implemented in C++ using the Qt framework to assure a responsive user-software interaction through a rich graphical user interface, and at the same time, achieving the desired computational speed. In addition, a discrete global optimization algorithm was developed and implemented.

    Results

    The software design goals were simplicity, speed and intuition. Based on these design goals, we have developed the publicly available software PopED lite (http://www.bluetree.me/PopED_lite). Optimization computation was on average, over 14 test problems, 30 times faster in PopED lite compared to an already existing optimal design software tool. PopED lite is now used in real drug discovery projects and a few of these case studies are presented in this paper.

    Conclusions

    PopED lite is designed to be simple, fast and intuitive. Simple, to give many users access to basic optimal design calculations. Fast, to fit a short design-execution cycle and allow interactive experimental design (test one design, discuss proposed design, test another design, etc). Intuitive, so that the input to and output from the software tool can easily be understood by users without knowledge of the theory of optimal design. In this way, PopED lite is highly useful in practice and complements existing tools.

  • 8.
    Bauwens, Maite
    et al.
    Vrije Universiteit Brussel, Belgium.
    Ohlsson, Henrik
    Linköpings universitet, Institutionen för systemteknik, Reglerteknik. Linköpings universitet, Tekniska högskolan.
    Barbé, Kurt
    Vrije Universiteit Brussel, Belgium.
    Beelaerts, Veerle
    Vrije Universiteit Brussel, Belgium.
    Dehairs, Frank
    Vrije Universiteit Brussel, Belgium.
    Schoukens, Johan
    Vrije Universiteit Brussel, Belgium.
    On Climate Reconstruction Using Bivalve Shells: Three Methods To Interpret the Chemical Signature of a Shell2011Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 104, nr 2, s. 104-111Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To improve our understanding of the climate process and to assess the human impact on current global warming, past climate reconstruction is essential. The chemical composition of a bivalve shell is strongly coupled to environmental variations and therefore ancient shells are potential climate archives. The nonlinear nature of the relation between environmental condition (e.g. the seawater temperature) and proxy composition makes it hard to predict the former from the latter, however. In this paper we compare the ability of three nonlinear system identification methods to reconstruct the ambient temperature from the chemical composition of a shell. The comparison shows that nonlinear multi-proxy approaches are potentially useful tools for climate reconstructions and that manifold based methods result in smoother and more precise temperature reconstruction.

  • 9. Bora, Kangkana
    et al.
    Chowdhury, Manish
    KTH, Skolan för teknik och hälsa (STH).
    Mahanta, Lipi B.
    Kundu, Malay Kumar
    Das, Anup Kumar
    Automated classification of Pap smear images to detect cervical dysplasia2017Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 138, s. 31-47Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background and objectives: The present study proposes an intelligent system for automatic categorization of Pap smear images to detect cervical dysplasia, which has been an open problem ongoing for last five decades. Methods: The classification technique is based on shape, texture and color features. It classifies the cervical dysplasia into two-level (normal and abnormal) and three-level (Negative for Intraepithelial Lesion or Malignancy, Low-grade Squamous Intraepithelial Lesion and High-grade Squamous Intraepithelial Lesion) classes reflecting the established Bethesda system of classification used for diagnosis of cancerous or precancerous lesion of cervix. The system is evaluated on two generated databases obtained from two diagnostic centers, one containing 1610 single cervical cells and the other 1320 complete smear level images. The main objective of this database generation is to categorize the images according to the Bethesda system of classification both of which require lots of training and expertise. The system is also trained and tested on the benchmark Herlev University database which is publicly available. In this contribution a new segmentation technique has also been proposed for extracting shape features. Ripplet Type I transform, Histogram first order statistics and Gray Level Co-occurrence Matrix have been used for color and texture features respectively. To improve classification results, ensemble method is used, which integrates the decision of three classifiers. Assessments are performed using 5 fold cross validation. Results: Extended experiments reveal that the proposed system can successfully classify Pap smear images performing significantly better when compared with other existing methods. Conclusion: This type of automated cancer classifier will be of particular help in early detection of cancer.

  • 10. Edvardsson, Hannes
    et al.
    Smedby, Örjan
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för medicin och vård, Radiologi. Östergötlands Läns Landsting, Bildmedicinskt centrum, Avdelningen för radiologi US. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Compact and efficient 3D shape description through radial function approximation2003Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 72, nr 2, s. 89-97Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A fast and simple method for three-dimensional shape description is described. The method views a 3D object as a radial distance function on the unit sphere, and thus reduces the dimensionality of the description problem by one. The radial distance function is approximated by Fourier methods in the basis of the spherical harmonic polynomials. The necessary integration is carried out on the object boundary, rather than on the unit sphere. Consequently, there is no need of a parameterisation of the object surface. The description makes it possible to compare shapes in a computationally very simple way. Solutions on how to cope with translated and rotated objects are discussed. The method is developed for star-shaped objects, but is stable even if the input image is non-star-shaped. The method is tested in a data set from magnetic resonance imaging (MRI) of the brain. Potential medical applications are discussed. ⌐ 2002 Elsevier Science Ireland Ltd. All rights reserved.

  • 11.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    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.
    fMRI Analysis on the GPU - Possibilities and Challenges2012Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 105, nr 2, s. 145-161Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Functional magnetic resonance imaging (fMRI) makes it possible to non-invasively measure brain activity with high spatial resolution.There are however a number of issues that have to be addressed. One is the large amount of spatio-temporal data that needsto be processed. In addition to the statistical analysis itself, several preprocessing steps, such as slice timing correction and motioncompensation, are normally applied. The high computational power of modern graphic cards has already successfully been used forMRI and fMRI. Going beyond the first published demonstration of GPU-based analysis of fMRI data, all the preprocessing stepsand two statistical approaches, the general linear model (GLM) and canonical correlation analysis (CCA), have been implementedon a GPU. For an fMRI dataset of typical size (80 volumes with 64 x 64 x 22 voxels), all the preprocessing takes about 0.5 s on theGPU, compared to 5 s with an optimized CPU implementation and 120 s with the commonly used statistical parametric mapping(SPM) software. A random permutation test with 10 000 permutations, with smoothing in each permutation, takes about 50 s ifthree GPUs are used, compared to 0.5 - 2.5 h with an optimized CPU implementation. The presented work will save time forresearchers and clinicians in their daily work and enables the use of more advanced analysis, such as non-parametric statistics, bothfor conventional fMRI and for real-time fMRI.

  • 12. Foracchia, Marco
    et al.
    Hooker, Andrew C.
    Vicini, Paolo
    Ruggeri, Alfredo
    POPED, a software for optimal experiment design in population kinetics.2004Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 74, nr 1, s. 29-46Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Population kinetic analysis is the methodology used to quantify inter-subject variability in kinetic studies. It entails the collection of (possibly sparse) data from dynamic experiments in a group of subjects and their quantitative interpretation by means of a mathematical model. This methodology is widely used in the pharmaceutical industry (where it is termed "pharmacokinetic population analysis") and recently it is becoming increasingly used in other areas of biomedical research. Unlike traditional kinetic studies, where the number of subjects can be quite small, population kinetic studies require large numbers of subjects. It is, therefore, of great interest to design these studies in the most efficient manner possible, to maximize the information content provided by the data. In this paper we propose an algorithm and a computer program, POPED, for the optimal design of a population kinetic experiment. In particular, the number of samples for each subject and the design of the individual sampling strategies, i.e. the number and location of the time points at which the output variable is sampled, will be considered. Among the various criteria proposed in the literature, D and ED optimality are the ones implemented in our software program, since they are the most widely used. A brief description of the techniques employed to perform design optimization is given, together with some details on their actual implementation. Some examples are then presented to show the program usage and the results provided.

  • 13.
    Fu, Qiang
    et al.
    Karolinska Institutet, Stockholm, Sweden.
    Xue, Zhanggang
    Zhongshan Hospital affiliated to Fudan University, Shanghai, China.
    Zhu, Jie
    Computer Informatics College of Fudan University, Shanghai, China.
    Fors, Uno
    Karolinska Institutet, Stockholm, Sweden.
    Klein, Gunnar
    Karolinska Institutet, Stockholm, Sweden.
    Anaesthesia record system on handheld computers: pilot experience and uses for quality control and clinical guidelines2005Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 77, nr 2, s. 155-63Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper describes a mobile information system to collect patient information for anesthesia quality control. In this system, a mobile database program was designed for use on handheld computers (Pocket PC). This program is used to collect patient data at the bedside on the handhelds, with a daily synchronization of the data between the anaesthesiologists' handhelds with the anaesthesia database. All collected data are later used for quality control analysis. Furthermore, clinical guidelines will be included on these same handhelds. During the pilot phase, data from a sample set of about 300 patients were incorporated. The processes and interfaces of the system are presented in the paper. The current mobile database system has been designed to replace the original paper-based data collection system. The individual anaesthesiologist's handheld synchronizes patient data daily with anaesthesia database center. This information database is analyzed and used not only to give feedback to the individual doctor or center, but also to review the use of the guidelines provided and the results of their utilization.

  • 14. García-Olalla, Oscar
    et al.
    Alegre, Enrique
    Fernández-Robles, Laura
    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.
    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.
    Acrosome integrity assessment of boar spermatozoa images using an early fusion of texture and contour descriptors2015Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 120, nr 1, s. 49-64Artikkel i tidsskrift (Fagfellevurdert)
  • 15.
    Gelzinis, A.
    et al.
    Department of Applied Electronics, Kaunas University of Technology, Lithuania.
    Verikas, Antanas
    Högskolan i Halmstad, Sektionen för Informationsvetenskap, Data– och Elektroteknik (IDE), Halmstad Embedded and Intelligent Systems Research (EIS).
    Bacauskiene, M.
    Department of Applied Electronics, Kaunas University of Technology, Lithuania.
    Automated speech analysis applied to laryngeal disease categorization2008Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 91, nr 1, s. 36-47Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The long-term goal of the work is a decision support system for diagnostics of laryngeal diseases. Colour images of vocal folds, a voice signal, and questionnaire data are the information sources to be used in the analysis. This paper is concerned with automated analysis of a voice signal applied to screening of laryngeal diseases. The effectiveness of 11 different feature sets in classification of voice recordings of the sustained phonation of the vowel sound /a/ into a healthy and two pathological classes, diffuse and nodular, is investigated. A k-NN classifier, SVM, and a committee build using various aggregation options are used for the classification. The study was made using the mixed gender database containing 312 voice recordings. The correct classification rate of 84.6% was achieved when using an SVM committee consisting of four members. The pitch and amplitude perturbation measures, cepstral energy features, autocorrelation features as well as linear prediction cosine transform coefficients were amongst the feature sets providing the best performance. In the case of two class classification, using recordings from 79 subjects representing the pathological and 69 the healthy class, the correct classification rate of 95.5% was obtained from a five member committee. Again the pitch and amplitude perturbation measures provided the best performance.

  • 16.
    Gustafsson, Mikael
    et al.
    Linköpings universitet, Institutionen för molekylär och klinisk medicin, Medicinsk mikrobiologi. Linköpings universitet, Hälsouniversitetet.
    Magnusson, Karl-Eric
    Linköpings universitet, Institutionen för molekylär och klinisk medicin, Medicinsk mikrobiologi. Linköpings universitet, Hälsouniversitetet.
    A distributed image-processing system for measurements of intracellular calcium in living cells1991Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 36, nr 4, s. 199-221Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    During the last decade, image-processing techniques have been introduced as a valuable tool in biologically oriented research. In combination with novel fluorescent probes, these techniques permit assessment of subcellular distributions of several intracellularly important cations, such as free calcium ions and protons. Typically, systems used for image processing are located centrally around the experimental setup. This configuration has drawbacks, mainly because the laborious extraction and processing of data that generally follow an experimental session limits the access to the system for other investigators. We describe here the principles of a distributed image processing system, based on IBM-compatible personal computers (PCs), that without extra hardware can cope with all the necessary image processing involved in imaging of intracellular cations. The potential of the PC as an image processor, however, reaches beyond this specific application and many image processing tasks can be carried out successfully on a standard PC. Thus, the centrally located dedicated image processor is used only for image acquisition in the experimental situation. This in turn optimizes the utilization of expensive resources and increases efficiency. The mouse-operated software is described in detail, so that interested investigators can extract useful parts for integration into their own applications and experimental environment.

  • 17.
    Hallberg, Niklas
    et al.
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, MDALAB - Human Computer Interfaces.
    Johansson, M
    Timpka, Toomas
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för hälsa och samhälle, Socialmedicin och folkhälsovetenskap. Östergötlands Läns Landsting, Folkhälsovetenskapligt centrum, Folkhälsovetenskapligt centrum.
    A prototype computer network service for occupational therapists. 1999Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 59, s. 45-54Artikkel i tidsskrift (Fagfellevurdert)
  • 18.
    Holmberg, Björn
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    Lanshammar, Håkan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    Possibilities of texture based motion analysis2006Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 84, nr 1, s. 1-10Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Analysis of motion patterns in the human locomotion apparatus is important in many clinical areas like orthopaedics, physiotherapy, neurology, and sports medicine. Today marker based human motion analysis (HMA) is completely dominant in the clinical context. Technically, these systems are stable and dependable, and about a dozen variants are commercially available. One drawback of such systems is the time consuming and error prone marker placement.

    The purpose of the present contribution is to show that it is possible, with existing simple technology and methods, to build systems that do not depend on anatomically placed markers and yet produce an accuracy in knee joint center estimation comparable to marker based systems.

    It is shown that texture based methods can give estimates of knee joint center of rotation that can be compared to knee joint center estimates from marker based systems. Due to different definitions of the knee joint center position some bias is seen between the two estimates.

  • 19.
    Knutsson, Hans
    et al.
    Linköpings universitet, Institutionen för systemteknik, Bildbehandling. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats T.
    Linköpings universitet, Institutionen för systemteknik, Bildbehandling. Linköpings universitet, Tekniska högskolan.
    Kronander, Torbjörn
    SECTRA AB, Linköping, Sweden.
    Hemmendorff, Magnus
    Linköpings universitet, Institutionen för systemteknik, Bildbehandling. Linköpings universitet, Tekniska högskolan.
    Spatio-temporal filtering of digital angiography image data1998Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 57, nr 1-2, s. 115-123Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    As welfare diseases become more common all over the world the demand for angiography examinations is increasing rapidly. The development of advanced medical signal processing methods has with few exceptions been concentrated towards CT and MR while traditional contrast based radiology depend on methods developed for ancient photography techniques despite the fact that angiography sequences are generally recorded in digital form. This article presents a new approach for processing of angiography sequences based on advanced image processing methods. The developed algorithm automatically processes angiography sequences containing motion artifacts that cannot be processed by conventional methods like digital subtraction angiography (DSA) and pixel shift due to non uniform motions. The algorithm can in simple terms be described as an ideal pixelshift filter carrying out shifts of different directions and magnitude according to the local motions in the image. In difference to conventional methods it is fully automatic, no mask image needs to be defined and the manual pixelshift operations, which are extremely time consuming, are eliminated. The algorithm is efficient and robust and is designed to run on standard hardware of a powerful workstation which excludes the need for expensive dedicated angiography platforms. Since there is no need to make additional recordings if the patient moves, the patient is exposed to less amount of radiation and contrast fluid. The most exciting benefits by this method are, however, that it opens up new areas for contrast based angiography that are not possible to process with conventional methods e.g. nonuniform motions and multiple layers of moving tissue. Advanced image processing methods provide significantly better image quality and noise suppression but do also provide the means to compute flow velocity and visualize the flow dynamics in the arterial trees by e.g. using color. Initial tests have proven that it is possible to discriminate capillary blood flow from angiography data which opens up interesting possibilities for estimating the blood flow in the heart muscle without use of nuclear methods.

  • 20.
    Koch, Sabine
    et al.
    CMD Center for Human - Computer Studies , Uppsala University, Uppsala, Sweden.
    Wagner, Ina-Veronika
    CMD Center for Human - Computer Studies , Uppsala University, Uppsala, Sweden.
    Seipel, Stefan
    CMD Center for Human - Computer Studies , Uppsala University, Uppsala, Sweden.
    Schneider, Werner
    CMD Center for Human - Computer Studies , Uppsala University, Uppsala, Sweden.
    Controlled Diagnosis-Oriented Enhancement of Automatically Segmented Radiographs in Dentistry1998Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 57, nr 1-2, s. 125-131Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A method for controlled diagnosis-oriented enhancement of selected regions of interest in intraoral radiographs is presented. Image enhancement is accomplished by adaptive non-linear grey scale transformation depending on the result of objective quality measurement. In order to assure reliable image duality measurement as well as controlled image enhancement, automatic image segmentation is applied to avoid the influence of disturbing factors (e.g. metallic restorations) on quality measurement and image enhancement. Based on existing a-priori knowledge about object structure and composition of the selected regions of interest in intraoral radiographs, different image segmentation algorithms and image enhancement procedures were developed for different types of diagnosis. (C) 1998 Elsevier Science Ireland Ltd. All rights reserved.

  • 21.
    Kohli, Sunil
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Sahlén, K.
    Linköpings universitet, Hälsouniversitetet.
    Löfman, Owe
    Linköpings universitet, Hälsouniversitetet.
    Sivertun, Åke
    Linköpings universitet, Hälsouniversitetet.
    Foldevi, Mats
    Linköpings universitet, Institutionen för hälsa och samhälle, Allmänmedicin. Linköpings universitet, Hälsouniversitetet.
    Trell, Erik
    Linköpings universitet, Institutionen för hälsa och samhälle, Allmänmedicin. Linköpings universitet, Hälsouniversitetet.
    Wigertz, Ove
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Individuals living in areas with high background radon: a GIS method to identify populations at risk1997Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 53, nr 2, s. 105-112Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Objective: to identify and link populations and individuals that live within high risk areas. Design: census registers and disease registers which contain data on individuals can only give aggregate statistics relating to postal code districts, town, county or state boundaries. However environmental risk factors rarely, if ever, respect these man-made boundaries. What is needed is a method to rapidly identify individuals who may live within a described area or region and to further identify the disease(s) occurring among these individuals and/or in these areas. Method: this paper describes a method for linking the standard registers available in Sweden, notably the residence-property addresses they contain and the geographical coordinate setting of these, to map the population as a point coverage. Using standard GIS methods this coverage could be linked, merged or intersected with any other map to create new subsets of population. Representation of populations down to the individual level by automatised spatialisation of available census data is in its simplicity a new informatics method which in the designated GIS medium adds a new power of resolution. Results: we demonstrate this using the radon maps provided by the local communes. The Swedish annual population registration records of 1991 for the county ofÖstergötland and the property register available at the Central Statistical Bureau of Sweden formed the main data sources. By coupling the address in the population register to the property register each individual was mapped to the centroid of a property. By intersecting the population coverage with the radon maps, the population living in high, normal or low risk areas was identified and then analysed and stratified by commune, sex and age. The resulting tables can be linked to other databases, e.g. disease registers, to visualise and analyse geographical and related patterns. The methodology can be adapted for use with any other environmental map or small area. It can also be expanded to the fourth dimension by linking likewise available migration information to generate immediately coordinate-set, accumulated exposition and similar data.

  • 22. Kundu, M. K.
    et al.
    Chowdhury, Manish
    KTH, Skolan för teknik och hälsa (STH).
    Das, S.
    Interactive radiographic image retrieval system2017Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 139, s. 209-220Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background and Objective Content based medical image retrieval (CBMIR) systems enable fast diagnosis through quantitative assessment of the visual information and is an active research topic over the past few decades. Most of the state-of-the-art CBMIR systems suffer from various problems: computationally expensive due to the usage of high dimensional feature vectors and complex classifier/clustering schemes. Inability to properly handle the “semantic gap” and the high intra-class versus inter-class variability problem of the medical image database (like radiographic image database). This yields an exigent demand for developing highly effective and computationally efficient retrieval system. Methods We propose a novel interactive two-stage CBMIR system for diverse collection of medical radiographic images. Initially, Pulse Coupled Neural Network based shape features are used to find out the most probable (similar) image classes using a novel “similarity positional score” mechanism. This is followed by retrieval using Non-subsampled Contourlet Transform based texture features considering only the images of the pre-identified classes. Maximal information compression index is used for unsupervised feature selection to achieve better results. To reduce the semantic gap problem, the proposed system uses a novel fuzzy index based relevance feedback mechanism by incorporating subjectivity of human perception in an analytic manner. Results Extensive experiments were carried out to evaluate the effectiveness of the proposed CBMIR system on a subset of Image Retrieval in Medical Applications (IRMA)-2009 database consisting of 10,902 labeled radiographic images of 57 different modalities. We obtained overall average precision of around 98% after only 2–3 iterations of relevance feedback mechanism. We assessed the results by comparisons with some of the state-of-the-art CBMIR systems for radiographic images. Conclusions Unlike most of the existing CBMIR systems, in the proposed two-stage hierarchical framework, main importance is given on constructing efficient and compact feature vector representation, search-space reduction and handling the “semantic gap” problem effectively, without compromising the retrieval performance. Experimental results and comparisons show that the proposed system performs efficiently in the radiographic medical image retrieval field.

  • 23.
    Lindbom, Lars
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap, Avdelningen för farmakokinetik och läkemedelsterapi.
    Ribbing, Jakob
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap, Avdelningen för farmakokinetik och läkemedelsterapi.
    Jonsson, E Niclas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap, Avdelningen för farmakokinetik och läkemedelsterapi.
    Perl-speaks-NONMEM (PsN) – a Perl module for NONMEM related programming2004Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 75, nr 2, s. 85-94Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The NONMEM program is the most widely used nonlinear regression software in population pharmacokinetic/pharmacodynamic (PK/PD) analyses. In this article we describe a programming library, Perl-speaks-NONMEM (PsN), intended for programmers that aim at using the computational capability of NONMEM in external applications. The library is object oriented and written in the programming language Perl. The classes of the library are built around NONMEM's data, model and output files. The specification of the NONMEM model is easily set or changed through the model and data file classes while the output from a model fit is accessed through the output file class. The classes have methods that help the programmer perform common repetitive tasks, e.g. summarising the output from a NONMEM run, setting the initial estimates of a model based on a previous run or truncating values over a certain threshold in the data file. PsN creates a basis for the development of high-level software using NONMEM as the regression tool.

  • 24. Liuhanen, Sasu
    et al.
    Sallisalmi, Marko
    Pettilä, Ville
    Oksala, Niku
    Tenhunen, Jyrki
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Anestesiologi och intensivvård.
    Indirect measurement of the vascular endothelial glycocalyx layer thickness in human submucosal capillaries with a plug-in for ImageJ2013Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 110, nr 1, s. 38-47Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BACKGROUND:

    The thickness of vascular endothelial glycocalyx layer can be measured indirectly during a spontaneous leukocyte passage from oral submucosal capillaries in humans. The subsequent differences in red blood cell (RBC) column widths, before a spontaneous white blood cell passage (pre-WBC) and after a spontaneous WBC passage (post-WBC) can be used in off-line analysis to measure glycocalyx thickness: [pre-WBC width-post-WBC width]/2. We created and validated a semi-automatic plug-in for ImageJ to measure the endothelial glycocalyx layer thickness.

    METHODS:

    Video clips presenting human sublingual microvasculature were created with a side-stream dark field imaging device. Spontaneous leukocyte passages in capillaries were analyzed from video clips with ImageJ. The capillary glycocalyx layer thickness was measured by the indirect approach with two manual and two semi-automatic methods.

    RESULTS:

    There were no statistically significant differences between glycocalyx layer thicknesses measured with different methods, even though small inter-method differences in RBC column thicknesses could be detected. Inter-rater differences were systematically smaller with both semi-automatic methods. Intra-rater coefficient of variation [CV] (95% CI) was largest when measurements were made completely manually [9.2% (8.4-10.0)], but improved significantly with automatic image enhancement prior to manual measurement [7.2% (6.4-8.0)]. CV could be improved further when using semi-automatic analysis with an in-frame median filter radius of 1 pixel [5.8% (5.0-6.6)], or a median filter radius of 2 pixels [4.3% (3.5-5.1)].

    CONCLUSIONS:

    Semi-automatic analysis of glycocalyx decreased the intra-rater CV and the inter-rater differences compared to the manual method. On average, each of the four methods yielded equal results for the glycocalyx thickness. Being the only feasible bed side method in most clinical scenarios, indirect measurement of glycocalyx thickness with orthogonal polarization spectral imaging or side-stream dark field imaging device and our plug-in can advance the study of glycocalyx layer pathology in man.

  • 25.
    Malm, Patrik
    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.
    Balakrishnan, Byju N.
    Sujathan, Vilayil K.
    Kumar, Rajesh
    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.
    Debris removal in Pap-smear images2013Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 111, nr 1, s. 128-138Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Since its introduction in the 1940s the Pap-smear test has helped reduce the incidence of cervical cancer dramatically in countries where regular screening is standard. The automation of this procedure is an open problem that has been ongoing for over fifty years without reaching satisfactory results. Existing systems are discouragingly expensive and yet they are only able to make a correct distinction between normal and abnormal samples in a fraction of cases. Therefore, they are limited to acting as support for the cytotechnicians as they perform their manual screening. The main reason for the current limitations is that the automated systems struggle to overcome the complexity of the cell structures. Samples are covered in artefacts such as blood cells, overlapping and folded cells, and bacteria, that hamper the segmentation processes and generate large number of suspicious objects. The classifiers designed to differentiate between normal cells and pre-cancerous cells produce unpredictable results when classifying artefacts. In this paper, we propose a sequential classification scheme focused on removing unwanted objects, debris, from an initial segmentation result, intended to be run before the actual normal/abnormal classifier. The method has been evaluated using three separate datasets obtained from cervical samples prepared using both the standard Pap-smear approach as well as the more recent liquid based cytology sample preparation technique. We show success in removing more than 99% of the debris without loosing more than around one percent of the epithelial cells detected by the segmentation process.

  • 26.
    Malusek, Alexandr
    et al.
    Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiofysik. Linköpings universitet, Hälsouniversitetet.
    Sandborg, Michael
    Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiofysik. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Centrum för kirurgi, ortopedi och cancervård, Radiofysikavdelningen US.
    Alm Carlsson, Gudrun
    Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiofysik. Linköpings universitet, Hälsouniversitetet.
    CTmod: a toolkit for Monte Carlo simulation of projections including scatter in computed tomography2008Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 90, nr 2, s. 167-178Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The CTmod toolkit is a set of C++ class libraries based on the CERN’s application development framework ROOT. It uses the Monte Carlo method to simulate energy imparted to a CT-scanner detector array. Photons with a given angle–energy distribution are emitted from the X-ray tube approximated by a point source, transported through a phantom, and their contribution to the energy imparted per unit surface area of each detector element is scored. Alternatively, the scored quantity may be the fluence, energy fluence, plane fluence, plane energy fluence, or kerma to air in the center of each detector element. Phantoms are constructed from homogenous solids or voxel arrays via overlapping. Implemented photon interactions (photoelectric effect, coherent scattering, and incoherent scattering) are restricted to the energy range from 10 to 200 keV. Variance reduction techniques include the collision density estimator and survival biasing combined with the Russian roulette. The toolkit has been used to estimate the amount of scatter in cone beam computed tomography and planar radiography.

  • 27.
    Martins da Silva, Margarida
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    Lemos, João M.
    Coito, Ana
    Costa, Bertinho A.
    Wigren, Torbjörn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    Mendonça, Teresa
    Local identifiability and sensitivity analysis of neuromuscular blockade and depth of hypnosis models2014Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 113, nr 1, s. 23-36Artikkel i tidsskrift (Fagfellevurdert)
  • 28.
    Medvedev, Alexander
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    Zhusubaliyev, Zhanybai T.
    Southwest State Univ, Dept Comp Sci, 50 Years October Str 94, RU-305040 Kursk, Russia.
    Rosén, Olov
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    Martins da Silva, Margarida
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    Oscillations-free PID control of anesthetic drug delivery in neuromuscular blockade2019Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 171, s. 119-131Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background and Objectives: The PID-control of drug delivery or the neuromuscular blockade (NMB) in closed-loop anesthesia is considered. The NMB system dynamics portrayed by a Wiener model can exhibit sustained nonlinear oscillations under realistic PID gains and for physiologically feasible values of the model parameters. Such oscillations, also repeatedly observed in clinical trials, lead to under- and overdosing of the administered drug and undermine patient safety. This paper proposes a tuning policy for the proportional PID gain that via bifurcation analysis ensures oscillations-free performance of the control loop. Online estimates of the Wiener model parameters are needed for the controller implementation and monitoring of the closed-loop proximity to oscillation.

    Methods: The nonlinear dynamics of the PID-controlled NMB system are studied by bifurcation analysis. A database of patient models estimated under PID-controlled neuromuscular blockade during general anesthesia is utilized, along with the corresponding clinical measurements. The performance of three recursive algorithms is compared in the application at hand: an extended Kalman filter, a conventional particle filter (PF), and a PF making use of an orthonormal basis to estimate the probability density function from the particle set.

    Results: It is shown that with a time-varying proportional PID gain, the type of equilibria of the closed-loop system remains the same as in the case of constant controller gains. The recovery time and frequency of oscillations are also evaluated in simulation over the database of patient models. Nonlinear identification techniques based on model linearization yield biased parameter estimates and thus introduce superfluous uncertainty. The bias and variance of the estimated models are related to the computational complexity of the identification algorithms, highlighting the superiority of the PFs in this safety-critical application.

    Conclusions: The study demonstrates feasibility of the proposed oscillation-free control strategy combining bifurcation theory based design and online parameter estimation by PF.

  • 29.
    Memedi, Mevludin
    et al.
    Högskolan Dalarna, Akademin Industri och samhälle, Datateknik.
    Westin, Jerker
    Högskolan Dalarna, Akademin Industri och samhälle, Datateknik.
    Nyholm, Dag
    Dougherty, Mark
    Högskolan Dalarna, Akademin Industri och samhälle, Datateknik.
    Groth, Torgny
    A web application for follow-up of results from a mobile device test battery for Parkinson's disease patients2011Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 104, nr 2, s. 219-226Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper describes a web-based system for enabling remote monitoring of patients with Parkinson's disease (PD) and supporting clinicians in treating their patients. The system consists of a patient node for subjective and objective data collection based on a handheld computer, a service node for data storage and processing, and a web application for data presentation. Using statistical and machine learning methods, time series of raw data are summarized into scores for conceptual symptom dimensions and an "overall test score" providing a comprehensive profile of patient's health during a test period of about one week. The handheld unit was used quarterly or biannually by 65 patients with advanced PD for up to four years at nine clinics in Sweden. The IBM Computer System Usability Questionnaire was administered to assess nurses' satisfaction with the web application. Results showed that a majority of the nurses were quite satisfied with the usability although a sizeable minority were not. Our findings support that this system can become an efficient tool to easily access relevant symptom information from the home environment of PD patients. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

  • 30.
    Memedi, Mevludin
    et al.
    Dalarna University.
    Westin, Jerker
    Dalarna University.
    Nyholm, Dag
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Neurologi.
    Dougherty, Mark
    Dalarna University.
    Groth, Torgny
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Biomedicinsk informatik och teknik.
    A web application for follow-up of results from a mobile device test battery for Parkinson’s disease patients2011Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 104, nr 2, s. 219-226Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A test battery consisting of self-assessments and motor tests for patients with Parkinson’s disease (PD) was constructed and implemented on a hand computer with touch screen in a telemedicine setting. In this work, a Web-based system was developed to deliver decision support information to treating clinical staff for assessing PD symptoms in their patients. Test results from the hand unit are transferred to a central server and processed into scores for different symptom dimensions and an “overall test score” reflecting the overall condition of the patient during a test period. The IBM Computer System Usability Questionnaire was administered to assess the users’ satisfaction with the system. Results showed that a majority of users who completed the evaluation were quite satisfied with the usability although a sizeable minority were not.  Response times were tested by simulating up to 100 users accessing the web application at the same time. The average page completion times were in the range of 0.5 seconds indicating fast response. The system was able to summarize the test-battery data and present them in a useful manner. Its main contribution is a novel way to easily access symptom information from the home environment of patients.

  • 31.
    Memedi, Mevludin
    et al.
    Örebro universitet, Akademin för naturvetenskap och teknik. Department of Economy and Society, Computer Engineering, Dalarna University, Borlänge, Sweden.
    Westin, Jerker
    Department of Economy and Society, Computer Engineering, Dalarna University, Borlänge, Sweden.
    Nyholm, Dag
    Department of Neuroscience, Neurology, Uppsala University, Uppsala, Sweden.
    Dougherty, Mark
    Department of Economy and Society, Computer Engineering, Dalarna University, Borlänge, Sweden.
    Groth, Torgny
    Department of Medical Sciences, Biomedical Informatics and Engineering, Uppsala University, Uppsala, Sweden.
    A web application for follow-up of results from a mobile device test battery for Parkinson's disease patients2011Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 104, nr 2, s. 219-226Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper describes a web-based system for enabling remote monitoring of patients with Parkinson's disease (PD) and supporting clinicians in treating their patients. The system consists of a patient node for subjective and objective data collection based on a handheld computer, a service node for data storage and processing, and a web application for data presentation. Using statistical and machine learning methods, time series of raw data are summarized into scores for conceptual symptom dimensions and an “overall test score” providing a comprehensive profile of patient's health during a test period of about one week. The handheld unit was used quarterly or biannually by 65 patients with advanced PD for up to four years at nine clinics in Sweden. The IBM Computer System Usability Questionnaire was administered to assess nurses’ satisfaction with the web application. Results showed that a majority of the nurses were quite satisfied with the usability although a sizeable minority were not. Our findings support that this system can become an efficient tool to easily access relevant symptom information from the home environment of PD patients.

  • 32.
    Noz, Marilyn E.
    et al.
    New York University.
    Maguire Jr., Gerald Q.
    Columbia University, Department of Computer Science.
    QSH: a minimal but highly portable image display and handling toolkit1988Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 27, nr 3, s. 229-240Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We describe a software system developed to handle images obtained from different sources, namely, computer-assisted tomography, positron emission tomography, single photon emission tomography and magnetic resonance imaging. In developing the system, it was necessary to address the following points. (1) The types of values that were encountered in both the header information and the pixel elements, namely, integers, floating point numbers, complex numbers and strings. (2) The use of domain-dependent sets of keys, that is, how to choose keys and how to stabilize the use of keys among the user population. This is, for example, how information such as the patient name, or the activity in becquerel is kept. It is necessary to keep both the key values and the units. (3) The development of a method for providing a database using flat files, i.e. linear text. (4) The maintenance of a history of values and operations. This is necessary in order to address the problem of determining from an image was produced. The connection between an image and how it was derived is analogous to describing how a secondary standard is derived from a primary one.

  • 33.
    Nyberg, Joakim
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Ueckert, Sebastian
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Strömberg, Eric
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Hennig, Stefanie
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Karlsson, Mats O.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Hooker, Andrew C.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    PopED: An extended, parallelized, nonlinear mixed effects models optimal design tool2012Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 108, nr 2, s. 789-805Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Several developments have facilitated the practical application and increased the general use of optimal design for nonlinear mixed effects models. These developments include new methodology for utilizing advanced pharmacometric models, faster optimization algorithms and user friendly software tools. In this paper we present the extension of theoptimal design software PopED, which incorporates many of these recent advances into aneasily useable enhanced GUI. Furthermore, we present new solutions to problems related to the design of experiments such as: faster and more robust FIM calculations and optimizations, optimizing over cost/utility functions and diagnostic tools and plots to evaluate designperformance. Examples for; (i) Group size optimization and efficiency translation, (ii) Cost/constraint optimization, (iii) Optimizations with different FIM approximations and (iv) optimization with parallel computing demonstrate the new features in PopED and underline the potential use of this tool when designing experiments. 

  • 34.
    Nyänen, P
    et al.
    Technical Research Centre of Finland Tampere.
    Chowdhury, Shamsul
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Wigertz, Ove
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Evaluation of decision support systems in medicine1991Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 34, s. 229-238Artikkel i tidsskrift (Fagfellevurdert)
  • 35.
    Persson, Mats
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för folkhälsa och klinisk medicin, Allmänmedicin.
    Bohlin, Jens
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    Eklund, Patrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    Development and maintenance of guideline-based decision support for pharmacological treatment of hypertension2000Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 61, nr 3, s. 209-219Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The objective was to build a computer-based decision support system (DSS), which could apply the formal rules embedded in guidelines regarding pharmacological treatment of hypertension. The aim was also to test VISUAL BASIC as a development tool for DSS's in health care. From the Swedish guidelines for treatment of hypertension, the most widely accepted and scientifically best proved treatment strategies were chosen and implemented as rules. A DSS that is capable of applying the evidence-based rules extracted from guidelines regarding drug treatment of hypertension, to any patient's medical profile, was constructed. The output consists of a recommendation regarding preferred generic drug class and also a written report, reflecting decision steps provided by the rule-base and inference engine. We also provide methods for formalising an implementable language of guidelines. A mainstream programming language like VISUAL BASIC can be an alternative when building complicated decision support systems. A logic formal notation can facilitate communication between the expert and the programmer. The program is a stand-alone product independent of computerized medical records and thereby easy to install and maintain.

  • 36.
    Pham, Tuan D
    School of Engineering and Information Technology, University of New South Wales, Canberra, Australia.
    Supervised restoration of degraded medical images using multiple-point geostatistics2012Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 106, nr 3, s. 201-209Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Reducing noise in medical images has been an important issue of research and development for medical diagnosis, patient treatment, and validation of biomedical hypotheses. Noise inherently exists in medical and biological images due to the acquisition and transmission in any imaging devices. Being different from image enhancement, the purpose of image restoration is the process of removing noise from a degraded image in order to recover as much as possible its original version. This paper presents a statistically supervised approach for medical image restoration using the concept of multiple-point geostatistics. Experimental results have shown the effectiveness of the proposed technique which has potential as a new methodology for medical and biological image processing.

  • 37.
    Rudowski, Robert
    et al.
    Inst Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Waraw.
    Frostell, Clas
    Danderyds sjukhus .
    Gill, Hans
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    A knowledge-based support system for mechanical ventilation of hte lungs. The KUSIVAR concept and prototype1989Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 30, s. 59-70Artikkel i tidsskrift (Fagfellevurdert)
  • 38.
    Rudowski, Robert
    et al.
    Polish Acadmy of Science Worsaw, Poland.
    Ludwigs, Ulf
    Södersjukhuset Stockholm.
    Gill, Hans
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Matuszewski, A
    Polish Academy of Science Warsaw, Poland.
    Baehrendz, S
    Karolinska Institutet Stockholm.
    Matell, George
    Karolinska Institutet Stockholm.
    Statistical models for prediction of arterial oxygen and carbon dioxide tensions during mechanical ventilation1991Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 34, s. 191-199Artikkel i tidsskrift (Fagfellevurdert)
  • 39.
    Sandborg, Michael
    et al.
    Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiofysik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Östergötlands Läns Landsting, Kirurgi- och onkologicentrum, Radiofysikavdelningen. Linköpings universitet, Hälsouniversitetet.
    Dance, David
    The Royal Marsden Hospital.
    Persliden, Jan
    Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiofysik. Linköpings universitet, Hälsouniversitetet.
    Alm Carlsson, Gudrun
    Linköpings universitet, Institutionen för medicin och hälsa, Medicinsk radiofysik. Linköpings universitet, Hälsouniversitetet.
    A Monte Carlo program for the calculation of contrast, noise and absorbed dose in diagnostic radiology1994Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 42, nr 3, s. 167-180Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A Monte Carlo computer program has been developed for the simulation of X-ray photon transport in diagnostic X-ray examinations. The simulation takes account of the incident photon energy spectrum and includes a phantom (representing the patient), an anti-scatter grid and an image receptor. The primary objective for developing the program was to study and optimise the design of anti-scatter grids. The program estimates image quality in terms of contrast and signal-to-noise ratio, and radiation risk in terms of mean absorbed dose in the patient. It therefore serves as a tool for the optimisation of the radiographic procedure. A description is given of the program and the variance-reduction techniques used. The computational method was validated by comparison with measurements and other Monte Carlo simulations.

  • 40.
    Saranummi, Niilo
    et al.
    Medical Engineering Lab Tampere.
    Groth, Torgny
    Uppsala universitet .
    Rosenfalck, Annelise
    Aalborg University .
    Wigertz, Ove
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Knowledge-based systems in medicine - a Nordic research and development programme1991Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 34, s. 81-89Artikkel i tidsskrift (Fagfellevurdert)
  • 41. Sarve, Hamid
    et al.
    Lindblad, Joakim
    Borgefors, Gunilla
    Johansson, Carina B.
    Örebro universitet, Hälsoakademin.
    Extracting 3D information on bone remodeling in the proximity of titanium implants in SR mu CT image volumes2011Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 102, nr 1, s. 25-34Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bone-implant integration is measured in several ways. Traditionally and routinely, 2D histological sections of samples, containing bone and the biomaterial, are stained and analyzed using a light microscope. Such histological section provides detailed cellular information about the bone regeneration in the proximity of the implant. However, this information reflects the integration in only a very small fraction, a 10 mu m thick slice, of the sample. In this study, we show that feature values quantified on 2D sections are highly dependent on the orientation and the placement of the section, suggesting that a 3D analysis of the whole sample is of importance for a more complete judgment of the bone structure in the proximity of the implant. We propose features describing the 3D data by extending the features traditionally used for 20-analysis. We present a method for extracting these features from 3D image data and we measure them on five 3D SR mu CT image volumes. We also simulate cuts through the image volume positioned at all possible section positions. These simulations show that the measurement variations due to the orientation of the section around the center line of the implant are about 30%.

  • 42.
    Sarve, Hamid
    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.
    Lindblad, Joakim
    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.
    Borgefors, Gunilla
    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.
    Johansson, Carina B.
    Extracting 3D information on bone remodeling in the proximity of titanium implants in SRμCT image volumes2011Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 102, nr 1, s. 25-34Artikkel i tidsskrift (Fagfellevurdert)
  • 43.
    Seipel, Stefan
    et al.
    Högskolan i Gävle, Institutionen för matematik, natur- och datavetenskap, Ämnesavdelningen för datavetenskap.
    Wagner, I V
    Koch, S
    Schneider, W
    Oral Implant Treatment Planning in a Virtual Reality Environment1998Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 57, nr 1-2, s. 95-103Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A system for three-dimensional oral implant treatment planning is presented. Virtual reality technologies are used in order to improve the human image interpretation and planning performance. The methods described are based on computer tomography (CT) data of the mandible and of the maxilla. A novel approach to volume rendering and voxel based modelling of implants is introduced which allows interactive three-dimensional manipulation of the anatomic model and real-time manipulation of virtual implants. A spline-based reconstruction method is described to assess the implant site in a clinically oriented view with regard to bone structures and angulation. Two parameters are deduced which represent the bone properties at the surface of implants. While an implant is navigated with six degrees of freedom, these parameters are acoustically rendered which is a novel approach to exploration of spatial bone properties in a CT data set.

  • 44.
    Sepehri, Amir A.
    et al.
    Amir Kabir University, Tehran, Iran.
    Ghareh Baghi, Arash
    Amir Kabir University, Tehran, Iran.
    Dutoit, Thierry
    TCTS Laboratory, Faculte Polytecnique de Mons, Belgium.
    Kocharian, Armen
    Medical University of Tehran, Iran.
    Kiani, A.
    Medical University of Tehran, Iran.
    A novel method for pediatric heart sound segmentation without using the ECG2010Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 99, nr 1, s. 43-48Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this paper, we propose a novel method for pediatric heart sounds segmentation by paying special attention to the physiological effects of respiration on pediatric heart sounds. The segmentation is accomplished in three steps. First, the envelope of a heart sounds signal is obtained with emphasis on the first heart sound (Si) and the second heart sound (S(2)) by using short time spectral energy and autoregressive (AR) parameters of the signal. Then, the basic heart sounds are extracted taking into account the repetitive and spectral characteristics of Si and S2 sounds by using a Multi-Layer Perceptron (MLP) neural network classifier. In the final step, by considering the diastolic and systolic intervals variations due to the effect of a child's respiration, a complete and precise heart sounds end-pointing and segmentation is achieved. 

  • 45.
    Shahsavar, Nosrat
    et al.
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Gill, Hans
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Wigertz, Ove
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Frostell, Claes
    Danderyds Hospital .
    Matell, George
    Södersjukhuset Stockholm.
    Ludwigs, Ulf
    Södersjukhuset Stockholm.
    KAVE: a tool for knowledge acquisition to support artificial ventilation1991Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 34, s. 115-123Artikkel i tidsskrift (Fagfellevurdert)
  • 46.
    Singh, A.K.
    et al.
    Rajasthan India.
    Moidu, Khalid
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Trell, Erik
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för hälsa och samhälle, Allmänmedicin.
    Wigertz, Ove
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Impact on the management and delivery of primary health care by a computer-based information system1992Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 37, s. 55-64Artikkel i tidsskrift (Fagfellevurdert)
  • 47.
    Sjöberg, Carl
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Avdelningen för sjukhusfysik.
    Ahnesjö, Anders
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Avdelningen för sjukhusfysik.
    Multi-atlas based segmentation using probabilistic label fusion with adaptive weighting of image similarity measures2013Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 110, nr 3, s. 308-319Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Label fusion multi-atlas approaches for image segmentation can give better segmentation results than single atlas methods. We present a multi-atlas label fusion strategy based on probabilistic weighting of distance maps. Relationships between image similarities and segmentation similarities are estimated in a learning phase and used to derive fusion weights that are proportional to the probability for each atlas to improve the segmentation result. The method was tested using a leave-one-out strategy on a database of 21 pre-segmented prostate patients for different image registrations combined with different image similarity scorings. The probabilistic weighting yields results that are equal or better compared to both fusion with equal weights and results using the STAPLE algorithm. Results from the experiments demonstrate that label fusion by weighted distance maps is feasible, and that probabilistic weighted fusion improves segmentation quality more the stronger the individual atlas segmentation quality depends on the corresponding registered image similarity. The regions used for evaluation of the image similarity measures were found to be more important than the choice of similarity measure.

  • 48.
    Smedby, Örjan
    Department of Diagnostic Radiology, Uppsala University.
    A scanning system for digital analysis of cineangiography films1992Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 39, nr 1-2, s. 103-111Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A system for scanning and digital analysis of cinefilms is presented and its performance is compared with entirely digital radiographic equipment. Apart from the difference between logarithmic and linear gray-scale representation, a higher noise level was found in the scanning system. When its spatial resolution was assessed visually, it was comparable to that of the digital system, although lower than when the cinefilming and scanning steps were evaluated separately. Algorithms for the correction of varying exposure and geometric ("pin-cushion") distortion are also presented. It is concluded that digital analysis after scanning of cinefilms can be a useful alternative to completely digital cineradiographic studies.

  • 49. Stathakis, Sotirios
    et al.
    Mavroidis, Panayiotis
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Karolinska Institute, Sweden.
    Shi, Chengyu
    Xu, Jun
    Kauweloa, Kevin I.
    Narayanasamy, Ganesh
    Papanikolaou, Niko
    gamma(+) index: A new evaluation parameter for quantitative quality assurance2014Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 114, nr 1Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Purpose: The accuracy dose delivery and the evaluation of differences between calculated and delivered dose distributions, has been studied by several groups. The aim of this investigation is to extend the gamma index by including radiobiological information and to propose a new index that we will here forth refer to as the gamma plus (gamma(+)). Further more, to validate the robustness of this new index in performing a quality control analysis of an IMRT treatment plan using pure radiobiological measures such as the biologically effective uniform dose ((D) over bar) and complication-free tumor control probability (P+). Material and methods: A new quality assurance index, the (gamma(+)), is proposed based on the theoretical concept of gamma index presented by Low et al. (1998). In this study, the dose difference, including the radiobiological dose information (biological effective dose, BED) is used instead of just the physical dose difference when performing the gamma(+) calculation. An in-house software was developed to compare different dose distributions based on the gamma(+) concept. A test pattern for a two-dimensional dose comparison was built using the in-house software platform. The gamma(+) index was tested using planar dose distributions (exported from the treatment planning system) and delivered (film) dose distributions acquired in a solid water phantom using a test pattern and a theoretical clinical case. Furthermore, a lung cancer case for a patient treated with IMRT was also selected for the analysis. The respective planar dose distributions from the treatment plan and the film were compared based on the gamma(+) index and were evaluated using the radiobiological measures of P+ and (D) over bar. Results: The results for the test pattern analysis indicate that the gamma(+) index distributions differ from those of the gamma index since the former considers radiobiological parameters that may affect treatment outcome. For the theoretical clinical case, it is observed that the gamma(+) index varies for different treatment parameters (e.g. dose per fraction). The dose area histogram (DAH) from the plan and film dose distributions are associated with P+ values of 50.8% and 49.0%, for a (D) over bar to the target of 54.0 Gy and 53.3 Gy, respectively. Conclusion: The gamma(+) index shows advantageous properties in the quantitative evaluation of dose delivery and quality control of IMRT treatments because it includes information about the expected responses and radiobiological doses of the individual tissues.

  • 50. Su, Fan-Chi
    et al.
    Mavroidis, Panayiotis
    Stockholms universitet, Naturvetenskapliga fakulteten, Medicinsk strålningsfysik (tills m KI).
    Shi, Chengyu
    Ferreira, Brigida Costa
    Papanikolaou, Niko
    A graphic user interface toolkit for specification, report and comparison of dose-response relations and treatment plans using the biologically effective uniform dose2010Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 100, nr 1, s. 69-78Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A toolkit (BEUDcal) has been developed for evaluating the effectiveness and for predicting the outcome of treatment plans by calculating the biologically effective uniform dose (BEUD) and complication-free tumor control probability. The input for the BEUDcal is the differential dose-volume histograms of organs exported from the treatment planning system. A clinical database is built for the dose-response parameters of different tumors and normal tissues. Dose-response probabilities of all the examined organs are illustrated together with the corresponding BEUDs and the P+ values. Furthermore, BEUDcal is able to generate a report that simultaneously presents the radiobiological evaluation together with the physical dose indices, showing the complementary relation between the physical and radiobiological treatment plan analysis performed by BEUDcal. Comparisons between treatment plans for helical tomotherapy and multileaf collimator-based intensity modulated radiotherapy of a lung patient were demonstrated to show the versatility of BEUDcal in the assessment and report of dose-response relations.

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