| 1. |
- Allalou, Amin, 1981-, et al.
(författare)
-
BlobFinder, a tool for fluorescence microscopy image cytometry
- 2009
-
Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 94:1, s. 58-65
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 2. |
|
|
| 3. |
- Fu, Qiang, et al.
(författare)
-
Anaesthesia record system on handheld computers : pilot experience and uses for quality control and clinical guidelines
- 2005
-
Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier. - 0169-2607 .- 1872-7565. ; 77:2, s. 155-63
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 4. |
- Gelzinis, A., et al.
(författare)
-
Automated speech analysis applied to laryngeal disease categorization
- 2008
-
Ingår i: Computer Methods and Programs in Biomedicine. - Amsterdam : Elsevier. - 0169-2607 .- 1872-7565. ; 91:1, s. 36-47
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 5. |
- Holmberg, Björn, et al.
(författare)
-
Possibilities of texture based motion analysis
- 2006
-
Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 84:1, s. 1-10
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 6. |
- Kindlund, E, et al.
(författare)
-
GRAT--genome-scale rapid alignment tool
- 2007
-
Ingår i: Computer methods and programs in biomedicine. - : Elsevier BV. - 0169-2607. ; 86:1, s. 87-92
-
Tidskriftsartikel (refereegranskat)
|
|
| 7. |
|
|
| 8. |
|
|
| 9. |
- Malusek, Alexandr, et al.
(författare)
-
CTmod : a toolkit for Monte Carlo simulation of projections including scatter in computed tomography
- 2008
-
Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier. - 0169-2607 .- 1872-7565. ; 90:2, s. 167-178
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 10. |
- Sepehri, Amir A., et al.
(författare)
-
Computerized screening of children congenital heart diseases
- 2008
-
Ingår i: Computerized screening of children congenital heart diseases CMPB. - United Kingdom : Elsevier BV. - 0169-2607. ; 92:2, s. 186-192
-
Tidskriftsartikel (refereegranskat)abstract
- In this paper, we propose a method for automated screening of congenital heart diseases in children through heart sound analysis techniques. Our method relies on categorizing the pathological murmurs based on the heart sections initiating them. We show that these pathelogical murmur categories can be identified by examining the heart sound energy over specific frequency bands, which we call, Arash-Bands. To specify the Arash-Band for a category, we evaluate the energy of the heart sound over all possible frequency bands. The Arash-Band is the frequency band that provides the lowest error in clustering the instances of that category against the normal ones. The energy content of the Arash-Bands for different categories constitue a feature vector that is suitable for classification using a neural network. In order to train, and to evaluate the performance of the proposed method, we use a training data-bank, as well as a test data-bank, collectively consisting of ninety samples (normal and abnormal). Our results show that in more than 94% of cases, our method correctly identifies children with congenital heart diseases. This percentage improves to 100%, when we use the Jack-Knife validation method over all the 90 samples.
|
|
| 11. |
- Verikas, Antanas, et al.
(författare)
-
Multiple feature sets based categorization of laryngeal images
- 2007
-
Ingår i: Computer Methods and Programs in Biomedicine. - Amsterdam : Elsevier. - 0169-2607 .- 1872-7565. ; 85:3, s. 257-266
-
Tidskriftsartikel (refereegranskat)abstract
- This paper is concerned with an automated analysis of laryngeal images aiming to categorize the images into three decision classes, namely healthy, nodular, and diffuse. The problem is treated as an image analysis and classification task. Aiming to obtain a comprehensive description of laryngeal images, multiple feature sets exploiting information on image colour, texture, geometry, image intensity gradient direction, and frequency content are extracted. A separate support vector machine (SVM) is used to categorize features of each type into the decision classes. The final image categorization is then obtained based on the decisions provided by a committee of support vector machines. Bearing in mind a high similarity of the decision classes, the correct classification rate of over 94% obtained when testing the system on 785 laryngeal images recorded at the Department of Otolaryngology, Kaunas University of Medicine is rather promising.
|
|
| 12. |
- Von Rosen, Dietrich
(författare)
-
Does noise reduction matter for curve fitting in growth curve models?
- 2009
-
Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 96, s. 173-181
-
Tidskriftsartikel (refereegranskat)abstract
- In this paper, we discuss the efficiency of noise reduction for curve fitting in nonlinear growth curve models We use singular spectrum analysis as a nonlinear-nonparametric denoising method A set of longitudinal measurements is used in considering the performance of the method we also use artificially generated data sets with and without noise for the purpose of validation of the results obtained in this study The results show that noise reduction is important for curve fitting in growth curve models and also, that the singular spectrum analysis technique can be used as a powerful tool for noise reduction in longitudinal measurements (C) 2009 Elsevier Ireland Ltd All rights reserved
|
|
| 13. |
- Wallin, Johan E., et al.
(författare)
-
A tool for neutrophil guided dose adaptation in chemotherapy
- 2009
-
Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 93:3, s. 283-291
-
Tidskriftsartikel (refereegranskat)abstract
- Chemotherapy dosing in anticancer treatment is a balancing act between achieving concentrations that are effective towards the malignancy and that result in acceptable side-effects. Neutropenia is one major side-effect of many antitumor agents, and is related to an increased risk of infection. A model capable of describing the time-course of myelosuppression from administered drug could be used in individual dose selection. In this paper we describe the transfer of a previously developed semi-mechanistic model for myelosuppression from NONMEM to a dosing tool in MS Excel, with etoposide as an example. The tool proved capable to solve a differential equation system describing the pharmacokinetics and pharmacodynamics, with estimation performance comparable to NONMEM. In the dosing tool the user provides neutrophil measures from a previous treatment course and request for the dose that results in a desired nadir in the upcoming course through a Bayesian estimation procedure.
|
|
