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  • 1.
    Abedan Kondori, Farid
    et al.
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Yousefi, Shahrouz
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Li, Haibo
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Sonning, Samuel
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Sonning, Sabina
    3D Head Pose Estimation Using the Kinect2011Conference paper (Refereed)
    Abstract [en]

    Head pose estimation plays an essential role for bridging the information gap between humans and computers. Conventional head pose estimation methods are mostly done in images captured by cameras. However accurate and robust pose estimation is often problematic. In this paper we present an algorithm for recovering the six degrees of freedom (DOF) of motion of a head from a sequence of range images taken by the Microsoft Kinectfor Xbox 360. The proposed algorithm utilizes a least-squares minimization of the difference between themeasured rate of change of depth at a point and the rate predicted by the depth rate constraint equation. We segment the human head from its surroundings and background, and then we estimate the head motion. Our system has the capability to recover the six DOF of the head motion of multiple people in one image. Theproposed system is evaluated in our lab and presents superior results.

  • 2.
    Abedan Kondori, Farid
    et al.
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Yousefi, Shahrouz
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Liu, Li
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Active human gesture capture for diagnosing and treating movement disorders2013Conference paper (Other academic)
    Abstract [en]

    Movement disorders prevent many people fromenjoying their daily lives. As with other diseases, diagnosisand analysis are key issues in treating such disorders.Computer vision-based motion capture systems are helpfultools for accomplishing this task. However Classical motiontracking systems suffer from several limitations. First theyare not cost effective. Second these systems cannot detectminute motions accurately. Finally they are spatially limitedto the lab environment where the system is installed. In thisproject, we propose an innovative solution to solve the abovementionedissues. Mounting the camera on human body, webuild a convenient, low cost motion capture system that canbe used by the patient in daily-life activities. We refer tothis system as active motion capture, which is not confinedto the lab environment. Real-time experiments in our labrevealed the robustness and accuracy of the system.

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    Active Human Gesture Capture for Diagnosing and Treating Movement Disorders
  • 3.
    Adjeiwaah, Mary
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Quality assurance for magnetic resonance imaging (MRI) in radiotherapy2017Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Magnetic resonance imaging (MRI) utilizes the magnetic properties of tissues to generate image-forming signals. MRI has exquisite soft-tissue contrast and since tumors are mainly soft-tissues, it offers improved delineation of the target volume and nearby organs at risk. The proposed Magnetic Resonance-only Radiotherapy (MR-only RT) work flow allows for the use of MRI as the sole imaging modality in the radiotherapy (RT) treatment planning of cancer. There are, however, issues with geometric distortions inherent with MR image acquisition processes. These distortions result from imperfections in the main magnetic field, nonlinear gradients, as well as field disturbances introduced by the imaged object. In this thesis, we quantified the effect of system related and patient-induced susceptibility geometric distortions on dose distributions for prostate as well as head and neck cancers. Methods to mitigate these distortions were also studied.

    In Study I, mean worst system related residual distortions of 3.19, 2.52 and 2.08 mm at bandwidths (BW) of 122, 244 and 488 Hz/pixel up to a radial distance of 25 cm from a 3T PET/MR scanner was measured with a large field of view (FoV) phantom. Subsequently, we estimated maximum shifts of 5.8, 2.9 and 1.5 mm due to patient-induced susceptibility distortions. VMAT-optimized treatment plans initially performed on distorted CT (dCT) images and recalculated on real CT datasets resulted in a dose difference of less than 0.5%.

     The magnetic susceptibility differences at tissue-metallic,-air and -bone interfaces result in local B0 magnetic field inhomogeneities. The distortion shifts caused by these field inhomogeneities can be reduced by shimming.  Study II aimed to investigate the use of shimming to improve the homogeneity of local  B0 magnetic field which will be beneficial for radiotherapy applications. A shimming simulation based on spherical harmonics modeling was developed. The spinal cord, an organ at risk is surrounded by bone and in close proximity to the lungs may have high susceptibility differences. In this region, mean pixel shifts caused by local B0 field inhomogeneities were reduced from 3.47±1.22 mm to 1.35±0.44 mm and 0.99±0.30 mm using first and second order shimming respectively. This was for a bandwidth of 122 Hz/pixel and an in-plane voxel size of 1×1 mm2.  Also examined in Study II as in Study I was the dosimetric effect of geometric distortions on 21 Head and Neck cancer treatment plans. The dose difference in D50 at the PTV between distorted CT and real CT plans was less than 1.0%.

    In conclusion, the effect of MR geometric distortions on dose plans was small. Generally, we found patient-induced susceptibility distortions were larger compared with residual system distortions at all delineated structures except the external contour. This information will be relevant when setting margins for treatment volumes and organs at risk.  

    The current practice of characterizing MR geometric distortions utilizing spatial accuracy phantoms alone may not be enough for an MR-only radiotherapy workflow. Therefore, measures to mitigate patient-induced susceptibility effects in clinical practice such as patient-specific correction algorithms are needed to complement existing distortion reduction methods such as high acquisition bandwidth and shimming.

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  • 4. Agogo, George O.
    et al.
    van der Voet, Hilko
    van 't Veer, Pieter
    Ferrari, Pietro
    Muller, David C.
    Sanchez-Cantalejo, Emilio
    Bamia, Christina
    Braaten, Tonje
    Knuppel, Sven
    Johansson, Ingegerd
    Umeå University, Faculty of Medicine, Department of Odontology.
    van Eeuwijk, Fred A.
    Boshuizen, Hendriek C.
    A method for sensitivity analysis to assess the effects of measurement error in multiple exposure variables using external validation data2016In: BMC Medical Research Methodology, E-ISSN 1471-2288, Vol. 16, article id 139Article in journal (Refereed)
    Abstract [en]

    Background: Measurement error in self-reported dietary intakes is known to bias the association between dietary intake and a health outcome of interest such as risk of a disease. The association can be distorted further by mismeasured confounders, leading to invalid results and conclusions. It is, however, difficult to adjust for the bias in the association when there is no internal validation data. Methods: We proposed a method to adjust for the bias in the diet-disease association (hereafter, association), due to measurement error in dietary intake and a mismeasured confounder, when there is no internal validation data. The method combines prior information on the validity of the self-report instrument with the observed data to adjust for the bias in the association. We compared the proposed method with the method that ignores the confounder effect, and with the method that ignores measurement errors completely. We assessed the sensitivity of the estimates to various magnitudes of measurement error, error correlations and uncertainty in the literature-reported validation data. We applied the methods to fruits and vegetables (FV) intakes, cigarette smoking (confounder) and all-cause mortality data from the European Prospective Investigation into Cancer and Nutrition study. Results: Using the proposed method resulted in about four times increase in the strength of association between FV intake and mortality. For weakly correlated errors, measurement error in the confounder minimally affected the hazard ratio estimate for FV intake. The effect was more pronounced for strong error correlations. Conclusions: The proposed method permits sensitivity analysis on measurement error structures and accounts for uncertainties in the reported validity coefficients. The method is useful in assessing the direction and quantifying the magnitude of bias in the association due to measurement errors in the confounders.

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  • 5.
    Ahlgren, Ulf
    et al.
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Kostromina, Elena
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Imaging the pancreatic beta cell: chapter 132011In: Type 1 diabetes: pathogenesis, genetics and immunotherapy / [ed] David Wagner, InTech, 2011Chapter in book (Refereed)
    Abstract [en]

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

  • 6.
    Ahmed, Masud Omar
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Teststation för industriella UV-celler2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    GE Healthcare Bio-Sciences AB in Umeå produce a variety of chromatography systems. One of the main components in chromatography is the UV module, which measure the light absorption of different wavelengths in the liquid being pumped through a cell. Currently at the Umeå site two types of UV-cells are produced; lab cells and industrial cells. The current test station for the industrial UV-cells is outdated, in disrepair and no longer supported.  GE has developed a test station for the lab cells that evaluates UV and flow properties, the data is stored in GE’s own production database, Prodas.

    The aim of this work is to design a test station for industrial UV-cells to improve the quality of the cells. The primary goal is a test station that can measure pressure, flow and absorption. The secondary goal is to discover and if possible, implement solutions that will streamline and automate the test station.

    A prototype of a test station for industrial UV-cells based on that for lab cells has been developed. The solution consists of an adapter that links the light path from the monitor through the UV-cell to the detector. The test station can measure pressure, flow and absorption but can only perform absorption and leakage tests.  Automation and efficiency have been accomplished in the form of scripts used to conduct absorption and leakage tests. The test station requires further development before it can be used in the production line.

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  • 7.
    Al Khodor, Rami
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Rörelseanalyssystem2014Independent thesis Basic level (professional degree), 180 HE creditsStudent thesis
    Abstract [sv]

    Idag ses ett ökat intresse för användandet av rörelseanalys inom olika sammanhang t.ex. övervakning, dataspel och diagnostisk undersökning av personers rörelsemönster med mera. Optisk rörelseanalys är den teknik som finns mest idag, men de systemen är dyra och saknar lämplig mjukvara för klinisk användning.

    En forskargrupp vid centrum för medicinsk teknik och strålningsfysik (CMTS) forskning och utvecklings avdelning (MT-FoU) vid Norrlands universitetssjukhus har sedan 2007 jobbat med en produktidé som bygger på att skapa ett nytt mobilt system för rörelseanalys som kan användas i medicinska undersökningar. Ett Arduino pro mini kort samt ett 9-axligt prototypkort som består av MPU-6000 och en magnetometer HMC5883L är anskaffat för att tillverka ett system i detta syfte.

    Syftet med projektet har varit att skapa ett verktyg som kan samla in rörelsemönster för att sedan presentera resultatet i ett diagram. Systemet skulle kunna samla in data från en sensor som inkluderar en 3D-accelerometer ett 3D-gyroskop och en 3D magnetometer för att därefter skicka det vidare till en dator där mätdata presenteras visuellt och sparas undan i en textfil.

    En viktig detalj att ta hänsyn till vid konstruktionen av det nya systemet var att konstruktionen gjordes med hjälp av billiga standardkomponenter och kretskort. Projektet har genomförts och några testmätningar har gjorts. Ett resultat sparades undan i en textfil och ett diagram har tagits fram som beskriver ett lårs rörelsemönster vid normal gång.

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    Rörelseanalyssystem
  • 8.
    Albano, Amanda
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Exploratory statistical study of long-term variability in echocardiographic indices (echocardiovariability) in healthy and diseased1987Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Heart rate variability, HRV, has been well researched for some decades. The oscillations of the heart rate is studied over a time period of some minutes up to 24 hours, it is measured with electrocardiography, ECG. From this one has concluded that the heart rate signal oscillates in accordance with the respiration, the resistance in the vessels etc.

    The most frequently used examination method of the heart is done with ultrasound, called echocardiography. One interesting variable at a time is measured and it is measured for a single heartbeat. With inspiration ofthe HRV studies this project focuses on some of the variables measured with ultrasound but over time andsimultaneously. The variables of interest are the myocardial motion and the blood flow in the left part ofthe heart, they are measured over two minutes. To complement these variables the well known variables HRand Resp are measured with ECG and added to the analysis.

    The methods used for analysing the variables are first of all descriptive statistics like mean and standard deviation. Secondly spectral analysis is performed to investigate in which frequencies the variables oscillates. Through coherence this is compared with the spectrum for HR where the three peaks have known origin. Finally principal component analysis, PCA, is performed as a method to compare all variables at the same time.

    The analyses are performed on seven measurements from five (5) healthy persons and five measurementsfrom four (4) patients with the disease FAP (“Skelleftesjukan”). The variables are investigated and described for the healthy persons first, then the healthy persons and patients are compared.

    The result from the study shows that most of the echo-variables oscillate in accordance with the respirationand the heart rate. For a healthy person the oscillations are within normal values and the relative deviation isaround 10%. The patients with FAP are most affected in the variables connected to the myocardium apartfrom HR, which is known since before.

    The coherence between the echo-variables and HR is low in one of VLF, very low frequency, or LF, lowfrequency, region and high in the other. In HF, high frequency, region the coherence is high for all variables.

    Finally the PCA was conducted on measurements from all healthy persons as one data set, from one ofthe healthy persons and from one of the patients with FAP. The analysis showed that for healthy personsrespiration is the process causing most variation and all of the echo-variables have a correlation to therespiration. For a patient with FAP the respiration is not as salient. A PCA over blocks of data at different time points however show that the signals are not oscillating in the same way multivariately over the wholetime series.

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    AmandaAlbano_MScthesis
  • 9.
    Ali, Hazrat
    et al.
    Hamad Bin Khalifa University, Qatar Foundation, College of Science and Engineering, Doha, Qatar.
    Grönlund, Christer
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Shah, Zubair
    Hamad Bin Khalifa University, Qatar Foundation, College of Science and Engineering, Doha, Qatar.
    Leveraging GANs for data scarcity of COVID-19: Beyond the hype2023In: 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW), IEEE Computer Society, 2023, p. 659-667Conference paper (Refereed)
    Abstract [en]

    Artificial Intelligence (AI)-based models can help in diagnosing COVID-19 from lung CT scans and X-ray images; however, these models require large amounts of data for training and validation. Many researchers studied Generative Adversarial Networks (GANs) for producing synthetic lung CT scans and X-Ray images to improve the performance of AI-based models. It is not well explored how good GAN-based methods performed to generate reliable synthetic data. This work analyzes 43 published studies that reported GANs for synthetic data generation. Many of these studies suffered data bias, lack of reproducibility, and lack of feedback from the radiologists or other domain experts. A common issue in these studies is the unavailability of the source code, hindering reproducibility. The included studies reported rescaling of the input images to train the existing GANs architecture without providing clinical insights on how the rescaling was motivated. Finally, even though GAN-based methods have the potential for data augmentation and improving the training of AI-based models, these methods fall short in terms of their use in clinical practice. This paper highlights research hotspots in countering the data scarcity problem, identifies various issues as well as potentials, and provides recommendations to guide future research. These recommendations might be useful to improve acceptability for the GAN-based approaches for data augmentation as GANs for data augmentation are increasingly becoming popular in the AI and medical imaging research community.

  • 10.
    Ali, Hazrat
    et al.
    College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
    Nyman, Emma
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine.
    Näslund, Ulf
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine.
    Grönlund, Christer
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Translation of atherosclerotic disease features onto healthy carotid ultrasound images using domain-to-domain translation2023In: Biomedical Signal Processing and Control, ISSN 1746-8094, E-ISSN 1746-8108, Vol. 85, article id 104886Article in journal (Refereed)
    Abstract [en]

    Objective: In this work, we evaluated a model for the translation of atherosclerotic disease features onto healthy carotid ultrasound images.

    Methods: An un-paired domain-to-domain translation model – the cycle Generative Adversarial Network (cycleGAN) – was trained to translate between carotid ultrasound images of healthy arteries and images of pronounced disease. Translation performance was evaluated using the measurement of wall thickness in original and generated images. In addition, we explored disease translation in different tissue segments (subcutaneous tissue, muscle, lumen, far wall, and deep tissues), using structural similarity index measure (SSIM) maps.

    Results: Features of pronounced disease were successfully translated to the healthy images (1.2 (0.33) mm vs 0.43 (0.07) mm, p < 0.001), while overall anatomy was retained as SSIM value was equal to 0.78 (0.02). Exploration of translated features showed that both arterial wall and subcutaneous tissues were modified in the translation, but that the subcutaneous tissue was subject to distortion of the anatomy in some cases. The image quality influenced the disease translation performance.

    Conclusion: The results show that the model can learn a mapping between healthy and diseased images while retaining the overall anatomical contents. This is the first study on atherosclerosis disease translation in medical images.

    Significance: The concept of translating disease onto existing healthy images may serve purposes such as education, cardiovascular risk communication in health conversations, or personalized modelling in precision medicine.

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    fulltext
  • 11.
    Ali, Hazrat
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Umander, Johannes
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Rohlén, Robin
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Grönlund, Christer
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    A Deep Learning Pipeline for Identification of Motor Units in Musculoskeletal Ultrasound2020In: IEEE Access, E-ISSN 2169-3536, Vol. 8, p. 170595-170608Article in journal (Refereed)
    Abstract [en]

    Skeletal muscles are functionally regulated by populations of so-called motor units (MUs). An MU comprises a bundle of muscle fibers controlled by a neuron from the spinal cord. Current methods to diagnose neuromuscular diseases and monitor rehabilitation, and study sports sciences rely on recording and analyzing the bio-electric activity of the MUs. However, these methods provide information from a limited part of a muscle. Ultrasound imaging provides information from a large part of the muscle. It has recently been shown that ultrafast ultrasound imaging can be used to record and analyze the mechanical response of individual MUs using blind source separation. In this work, we present an alternative method - a deep learning pipeline - to identify active MUs in ultrasound image sequences, including segmentation of their territories and signal estimation of their mechanical responses (twitch train). We train and evaluate the model using simulated data mimicking the complex activation pattern of tens of activated MUs with overlapping territories and partially synchronized activation patterns. Using a slow fusion approach (based on 3D CNNs), we transform the spatiotemporal image sequence data to 2D representations and apply a deep neural network architecture for segmentation. Next, we employ a second deep neural network architecture for signal estimation. The results show that the proposed pipeline can effectively identify individual MUs, estimate their territories, and estimate their twitch train signal at low contraction forces. The framework can retain spatio-temporal consistencies and information of the mechanical response of MU activity even when the ultrasound image sequences are transformed into a 2D representation for compatibility with more traditional computer vision and image processing techniques. The proposed pipeline is potentially useful to identify simultaneously active MUs in whole muscles in ultrasound image sequences of voluntary skeletal muscle contractions at low force levels.

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  • 12.
    Ali, Hazrat
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics. Department of Electrical and Computer Engineering, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan.
    Umander, Johannes
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Rohlén, Robin
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Röhrle, Oliver
    Stuttgart Center for Simulation Technology (SC SimTech), University of Stuttgart, Stuttgart, Germany; Institute for Modelling and Simulation of Biomechanical Systems, Chair for Computational Biophysics and Biorobotics, University of Stuttgart, Stuttgart, Germany.
    Grönlund, Christer
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Modelling intra-muscular contraction dynamics using in silico to in vivo domain translation2022In: Biomedical engineering online, E-ISSN 1475-925X, Vol. 21, no 1, article id 46Article in journal (Refereed)
    Abstract [en]

    Background: Advances in sports medicine, rehabilitation applications and diagnostics of neuromuscular disorders are based on the analysis of skeletal muscle contractions. Recently, medical imaging techniques have transformed the study of muscle contractions, by allowing identifcation of individual motor units’ activity, within the whole studied muscle. However, appropriate image-based simulation models, which would assist the continued development of these new imaging methods are missing. This is mainly due to a lack of models that describe the complex interaction between tissues within a muscle and its surroundings, e.g., muscle fbres, fascia, vasculature, bone, skin, and subcutaneous fat. Herein, we propose a new approach to overcome this limitation.

    Methods: In this work, we propose to use deep learning to model the authentic intramuscular skeletal muscle contraction pattern using domain-to-domain translation between in silico (simulated) and in vivo (experimental) image sequences of skeletal muscle contraction dynamics. For this purpose, the 3D cycle generative adversarial network (cycleGAN) models were evaluated on several hyperparameter settings and modifcations. The results show that there were large diferences between the spatial features of in silico and in vivo data, and that a model could be trained to generate authentic spatio-temporal features similar to those obtained from in vivo experimental data. In addition, we used diference maps between input and output of the trained model generator to study the translated characteristics of in vivo data.

    Results: This work provides a model to generate authentic intra-muscular skeletal muscle contraction dynamics that could be used to gain further and much needed physiological and pathological insights and assess and overcome limitations within the newly developed research feld of neuromuscular imaging.

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  • 13.
    Ambarki, Khalid
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Lindqvist, Tomas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Wåhlin, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Petterson, E
    Warntjes, JBM
    Birgander, Richard
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology.
    Malm, Jan
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Neuroscience.
    Eklund, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Evaluation of automatic measurement of the intracranial volume based on quantitative MR imaging2012In: American Journal of Neuroradiology, ISSN 0195-6108, E-ISSN 1936-959X, Vol. 33, no 10, p. 1951-1956Article in journal (Refereed)
    Abstract [en]

    BACKGROUND AND PURPOSE: Brain size is commonly described in relation to ICV, whereby accurate assessment of this quantity is fundamental. Recently, an optimized MR sequence (QRAPMASTER) was developed for simultaneous quantification of T1, T2, and proton density. ICV can be measured automatically within minutes from QRAPMASTER outputs and a dedicated software, SyMRI. Automatic estimations of ICV were evaluated against the manual segmentation.

    MATERIALS AND METHODS: In 19 healthy subjects, manual segmentation of ICV was performed by 2 neuroradiologists (Obs1, Obs2) by using QBrain software and conventional T2-weighted images. The automatic segmentation from the QRAPMASTER output was performed by using SyMRI. Manual corrections of the automatic segmentation were performed (corrected-automatic) by Obs1 and Obs2, who were blinded from each other. Finally, the repeatability of the automatic method was evaluated in 6 additional healthy subjects, each having 6 repeated QRAPMASTER scans. The time required to measure ICV was recorded.

    RESULTS: No significant difference was found between reference and automatic (and corrected-automatic) ICV (P > .25). The mean difference between the reference and automatic measurement was -4.84 ± 19.57 mL (or 0.31 ± 1.35%). Mean differences between the reference and the corrected-automatic measurements were -0.47 ± 17.95 mL (-0.01 ± 1.24%) and -1.26 ± 17.68 mL (-0.06 ± 1.22%) for Obs1 and Obs2, respectively. The repeatability errors of the automatic and the corrected-automatic method were <1%. The automatic method required 1 minute 11 seconds (SD = 12 seconds) of processing. Adding manual corrections required another 1 minute 32 seconds (SD = 38 seconds).

    CONCLUSIONS: Automatic and corrected-automatic quantification of ICV showed good agreement with the reference method. SyMRI software provided a fast and reproducible measure of ICV.

  • 14.
    Andersson, Britt
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Svängande sensorer hittar prostatacancer2010In: medtechinfo.comArticle in journal (Other (popular science, discussion, etc.))
  • 15. Andersson, Martin
    et al.
    Mattsson, Soren
    Johansson, Lennart
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Leide-Svegborn, Sigrid
    A biokinetic and dosimetric model for ionic indium in humans2017In: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560, Vol. 62, no 16, p. 6397-6407Article in journal (Refereed)
    Abstract [en]

    This paper reviews biokinetic data for ionic indium, and proposes a biokinetic model for systemic indium in adult humans. The development of parameter values focuses on human data and indium in the form of ionic indium(III), as indium chloride and indium arsenide. The model presented for systemic indium is defined by five different pools: plasma, bone marrow, liver, kidneys and other soft tissues. The model is based on two subsystems: one corresponding to indium bound to transferrin and one where indium is transported back to the plasma, binds to red blood cell transferrin and is then excreted through the kidneys to the urinary bladder. Absorbed doses to several organs and the effective dose are calculated for In-111- and In-113m-ions. The proposed biokinetic model is compared with previously published biokinetic indium models published by the ICRP. The absorbed doses are calculated using the ICRP/ICRU adult reference phantoms and the effective dose is estimated according to ICRP Publication 103. The effective doses for In-111 and In-113m are 0.25 mSv MBq(-1) and 0.013 mSv MBq(-1) respectively. The updated biokinetic and dosimetric models presented in this paper take into account human data and new animal data, which represent more detailed and presumably more accurate dosimetric data than that underlying previous models for indium.

  • 16.
    Andersson, Nina
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Cerebrospinal fluid infusion methods: development and validation on patients with idiopathic normal pressure hydrocephalus2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cerebrospinal fluid (CSF) infusion tests can be used to estimate the dynamic properties of the CSF system. Idiopathic normal pressure hydrocephalus (INPH) is a syndrome signified by a disturbance to the CSF system, where the cause is unknown and the diagnosis is difficult to determine. As an aid in identifying patients with INPH who will improve after shunt surgery, infusion tests are commonly used to determine the outflow conductance (Cout), or outflow resistance (Rout=1/Cout), of the CSF system. The tests are also used to determine shunt function in vivo. The general aim of this thesis was to develop and validate CSF infusion methods, to investigate the dynamics of the CSF system. The methods should be applicable to patients with INPH, to aid in the quest to further improve the diagnosis and management of this syndrome.

    An existing mathematical model describing the dynamics of the CSF system was further developed. The characteristics of the model were verified and the effect of expanding intracranial air on the intracranial pressure (ICP) was simulated. The simulations supported the recommendation to maintain sea-level pressure during air ambulance transportation of patients with suspected intracranial air.

    A recently developed infusion apparatus was evaluated, on an experimental model as well as on a patient material. The repetitiveness in estimating Cout was found to be good. A statistically significant difference was found between the repeated Cout estimations in the patient group, indicating that there might have been a small physiological change introduced during the infusion test. A parameter, ∆Cout, was proposed and evaluated. It proved to reflect the reliability of individual Cout investigations in a clinically useful way, as well as to provide easily interpreted information.

    An adaptive algorithm for assessment of Cout was developed and evaluated on a patient group. The new algorithm was shown to reduce the investigation time, from 60 minutes, by 14.3 ± 5.9 minutes (mean ± SD), p<0.01, without reducing the reliability of the estimated Cout below clinically relevant levels.

    The relationship between ICP and CSF outflow was studied in a group of patients investigated for INPH. It was found that in the range of moderate increase from baseline pressure, the assumption of a pressure independent Rout was confirmed (p=0.5). However, at larger pressure increments, the relationship had a non-linear tendency (p<0.05). This indicates that the traditional view of a pressure independent Rout might have to be questioned in the region where ICP exceeds baseline pressure too much.

    Infusion tests can be performed in different ways, where three main categories may be distinguished. The bolus infusion method was compared to the constant pressure and constant flow infusion methods, on an experimental model as well as on a patient material. When physiological pressure fluctuations were added to the model, significant differences were found in the determination of Cout in the range of clinical importance, i.e. low Cout (p<0.05). The finding was supported by the patient investigations, the difference was however not significant.

    With the application of the new methods developed in this thesis, and the increased knowledge concerning relationships between CSF dynamic parameters, the CSF infusion test was further improved with the ability to increase measurement reliability in a reduced time. This constitutes a good basis to perform a large multi-centre study with the main goal to determine the predictive value of the parameter Cout.

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  • 17.
    Anerillas, Luis Oliveros
    et al.
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Kingham, Paul J.
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Lammi, Mikko
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Wiberg, Mikael
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB). Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Hand Surgery.
    Kelk, Peyman
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Three-dimensional osteogenic differentiation of bone marrow mesenchymal stem cells promotes matrix metallopeptidase 13 (Mmp13) expression in type i collagen hydrogels2021In: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 22, no 24, article id 13594Article in journal (Refereed)
    Abstract [en]

    Autologous bone transplantation is the principal method for reconstruction of large bone defects. This technique has limitations, such as donor site availability, amount of bone needed and morbidity. An alternative to this technique is tissue engineering with bone marrow-derived mesenchymal stem cells (BMSCs). In this study, our aim was to elucidate the benefits of culturing BMSCs in 3D compared with the traditional 2D culture. In an initial screening, we combined BMSCs with four different biogels: unmodified type I collagen (Col I), type I collagen methacrylate (ColMa), an alginate and cellulose-based bioink (CELLINK) and a gelatin-based bioink containing xanthan gum (GelXA-bone). Col I was the best for structural integrity and maintenance of cell morphology. Osteogenic, adipogenic, and chondrogenic differentiations of the BMSCs in 2D versus 3D type I collagen gels were investigated. While the traditional pellet culture for chondrogenesis was superior to our tested 3D culture, Col I hydrogels (i.e., 3D) favored adipogenic and osteogenic differentiation. Further focus of this study on osteogenesis were conducted by comparing 2D and 3D differentiated BMSCs with Osteoimage® (stains hydroxyapatite), von Kossa (stains anionic portion of phosphates, carbonates, and other salts) and Alizarin Red (stains Ca2+ deposits). Multivariate gene analysis with various covariates showed low variability among donors, successful osteogenic differentiation, and the identification of one gene (matrix metallopeptidase 13, MMP13) significantly differentially expressed in 2D vs. 3D cultures. MMP13 protein expression was confirmed with immunohistochemistry. In conclusion, this study shows evidence for the suitability of type I collagen gels for 3D osteogenic differentiation of BMSCs, which might improve the production of tissue-engineered constructs for treatment of bone defects.

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  • 18.
    Arnlund, Caroline
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Utveckling av sensor för mätning av hjärtaktivitet2014Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Motion analysis is a necessary tool when it comes to evaluation, monitoring and diagnosis of all the diseases that affect the human musculoskeletal system. There are only a few clinical walking laboratories in Sweden, where the patients can receive a more detailed and objective evaluation of their walking patterns. The problem with these laboratories is that they are relatively expensive and resource-demanding.

    The department of research and development at NUS has initiated a research project where AnyMo, a mobile system for measuring of moving patterns, was produced. The aim of this thesis was to further develop the existing system to simultaneously measure the electrical activity of the heart (ECG).

    The parts that were constructed during this project was an ECG sensor and a Master Unit, coupled to an existing motion sensor (part of the AnyMo system). The information that was collected from these sensors was stored locally in a memory on the system’s Master Unit.

    The finished product was tested and evaluated on a stationary bike at different pace and heart rate.

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    Utveckling av sensor för mätning av hjärtaktivitet
  • 19. Asan, Noor Badariah
    et al.
    Noreland, Daniel
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Hassan, Emadeldeen
    Umeå University, Faculty of Science and Technology, Department of Computing Science. Department of Electronics and Electrical Communications, Menoufia University, Menouf, Egypt.
    Shah, Syaiful Redzwan Mohd
    Rydberg, Anders
    Blokhuis, Taco J.
    Carlsson, Per-Ola
    Voigt, Thiemo
    Augustine, Robin
    Intra-body microwave communication through adipose tissue2017In: Healthcare technology letters, E-ISSN 2053-3713, Vol. 4, no 4, p. 115-121Article in journal (Refereed)
    Abstract [en]

    The human body can act as a medium for the transmission of electromagnetic waves in the wireless body sensor networks context. However, there are transmission losses in biological tissues due to the presence of water and salts. This Letter focuses on lateral intra-body microwave communication through different biological tissue layers and demonstrates the effect of the tissue thicknesses by comparing signal coupling in the channel. For this work, the authors utilise the R-band frequencies since it overlaps the industrial, scientific and medical radio (ISM) band. The channel model in human tissues is proposed based on electromagnetic simulations, validated using equivalent phantom and ex-vivo measurements. The phantom and ex-vivo measurements are compared with simulation modelling. The results show that electromagnetic communication is feasible in the adipose tissue layer with a low attenuation of approximate to 2 dB per 20 mm for phantom measurements and 4 dB per 20 mm for ex-vivo measurements at 2 GHz. Since the dielectric losses of human adipose tissues are almost half of ex-vivo tissue, an attenuation of around 3 dB per 20 mm is expected. The results show that human adipose tissue can be used as an intra-body communication channel.

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  • 20. Asan, Noor Badariah
    et al.
    Redzwan, Syaiful
    Rydberg, Anders
    Augustine, Robin
    Noreland, Daniel
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Hassan, Emadeldeen
    Umeå University, Faculty of Science and Technology, Department of Computing Science. Department of Electronics and Electrical Communications, Menoufia University, Menouf, Egypt.
    Voigt, Thiemo
    Human Fat Tissue: A Microwave Communication Channel2017In: 2017 First IEEE MTT-S International Microwave Bio Conference (IMBIOC), IEEE, 2017Conference paper (Refereed)
    Abstract [en]

    In this paper, we present an approach for communication through human body tissue in the R-band frequency range. This study examines the ranges of microwave frequencies suitable for intra-body communication. The human body tissues are characterized with respect to their transmission properties using simulation modeling and phantom measurements. The variations in signal coupling with respect to different tissue thicknesses are studied. The simulation and phantom measurement results show that electromagnetic communication in the fat layer is viable with attenuation of approximately 2 dB per 20 mm.

  • 21. Asan, Noor Badariah
    et al.
    Velander, Jacob
    Redzwan, Syaiful
    Perez, Mauricio D.
    Hassan, Emadeldeen
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Blokhuis, Taco J.
    Voigt, Thiemo
    Augustine, Robin
    Effect of Thickness Inhomogeneity in Fat Tissue on In-Body Microwave Propagation2018In: Proceedings of the 2018 IEEE/MTT-S International Microwave Biomedical Conference (IMBIOC), IEEE, 2018, p. 136-138Conference paper (Refereed)
    Abstract [en]

    In recent studies, it has been found that fat tissue can be used as a microwave communication channel. In this article, the effect of thickness inhomogeneities in fat tissues on the performance of in-body microwave communication at 2.45 GHz is investigated using phantom models. We considered two models namely concave and convex geometrical fat distribution to account for the thickness inhomogeneities. The thickness of the fat tissue is varied from 5 mm to 45 mm and the Gap between the transmitter/receiver and the starting and ending of concavity/convexity is varied from 0 mm to 25 mm for a length of 100 mm to study the behavior in the microwave propagation. The phantoms of different geometries, concave and convex, are used in this work to validate the numerical studies. It was noticed that the convex model exhibited higher signal coupling by an amount of 1 dB (simulation) and 2 dB (measurement) compared to the concave model. From the study, it was observed that the signal transmission improves up to 30 mm thick fat and reaches a plateau when the thickness is increased further.

  • 22.
    Asplund, Raquel
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Evaluation of a cloud-based image analysis and image display system for medical images2015Independent thesis Basic level (university diploma), 180 HE creditsStudent thesis
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  • 23.
    Axelsson, Jan
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Imlook4d: introducing an extendable research 4d analysis software2014In: XII Turku PET Symposium, 24-27 May 2014, Turku, Finland: the symposium of Nordic Association for Clinical Physics (NACP), 2014, p. 63-63Conference paper (Other academic)
    Abstract [en]

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

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

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

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

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

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

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

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

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

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  • 24.
    Axelsson, Jan
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Sörensen, Jens
    PET-center, Department of Radiology, Oncology and Radiation Sciences, Uppsala University, Uppsala, Sweden.
    The 2D Hotelling filter: a quantitativenoise-reducing principal-component filter fordynamic PET data, with applications in patientdose reduction2013In: BMC Medical Physics, E-ISSN 1756-6649, Vol. 13, no 1Article in journal (Refereed)
    Abstract [en]

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

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  • 25. Badariah Asan, Noor
    et al.
    Hassan, Emadeldeen
    Umeå University, Faculty of Science and Technology, Department of Computing Science. Department of Electronics and Electrical Communications, Menoufia University, Menouf, Egypt.
    Velander, Jacob
    Redzwan Mohd Shah, Syaiful
    Noreland, Daniel
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Blokhuis, Taco J.
    Wadbro, Eddie
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Berggren, Martin
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Voigt, Thiemo
    Augustine, Robin
    Characterization of the Fat Channel for Intra-Body Communication at R-Band Frequencies2018In: Sensors, E-ISSN 1424-8220, Vol. 18, no 9, article id 2752Article in journal (Refereed)
    Abstract [en]

    In this paper, we investigate the use of fat tissue as a communication channel between in-body, implanted devices at R-band frequencies (1.7–2.6 GHz). The proposed fat channel is based on an anatomical model of the human body. We propose a novel probe that is optimized to efficiently radiate the R-band frequencies into the fat tissue. We use our probe to evaluate the path loss of the fat channel by studying the channel transmission coefficient over the R-band frequencies. We conduct extensive simulation studies and validate our results by experimentation on phantom and ex-vivo porcine tissue, with good agreement between simulations and experiments. We demonstrate a performance comparison between the fat channel and similar waveguide structures. Our characterization of the fat channel reveals propagation path loss of ∼0.7 dB and ∼1.9 dB per cm for phantom and ex-vivo porcine tissue, respectively. These results demonstrate that fat tissue can be used as a communication channel for high data rate intra-body networks.

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  • 26.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Kuljus, Kristi
    Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia.
    Johansson, Adam
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Bolin, David
    Department of Mathematical Sciences, Chalmers and University of Gothenburg, Gothenburg, Sweden.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Prediction of CT images from MR images with hidden Markov and random field models2016In: Proceedings of the 8th International Workshop on Spatio-Temporal Modelling / [ed] A. Iftimi, J. Mateu and F. Montes, 2016, p. 163-163Conference paper (Other academic)
  • 27.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Liu, Xijia
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Garpebring, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Statistical learning in computed tomography image estimation2018In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 45, no 12, p. 5450-5460Article in journal (Refereed)
    Abstract [en]

    Purpose: There is increasing interest in computed tomography (CT) image estimations from magneticresonance (MR) images. The estimated CT images can be utilized for attenuation correction, patientpositioning, and dose planning in diagnostic and radiotherapy workflows. This study aims to introducea novel statistical learning approach for improving CT estimation from MR images and to compare theperformance of our method with the existing model-based CT image estimation methods.

    Methods: The statistical learning approach proposed here consists of two stages. At the trainingstage, prior knowledge about tissue types from CT images was used together with a Gaussian mixturemodel (GMM) to explore CT image estimations from MR images. Since the prior knowledge is notavailable at the prediction stage, a classifier based on RUSBoost algorithm was trained to estimatethe tissue types from MR images. For a new patient, the trained classifier and GMMs were used topredict CT image from MR images. The classifier and GMMs were validated by using voxel-leveltenfold cross-validation and patient-level leave-one-out cross-validation, respectively.

    Results: The proposed approach has outperformance in CT estimation quality in comparison withthe existing model-based methods, especially on bone tissues. Our method improved CT image estimationby 5% and 23% on the whole brain and bone tissues, respectively.

    Conclusions: Evaluation of our method shows that it is a promising method to generate CTimage substitutes for the implementation of fully MR-based radiotherapy and PET/MRI applications

  • 28.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Model-based Estimation of Computed Tomography Images2017Manuscript (preprint) (Other academic)
    Abstract [en]

    There is a growing interest to get a fully MR based radiotherapy. The most important development needed is to obtain improved bone tissue estimation. Existing model-based methods have performed poorly on bone tissues. This paper aims to obtainimproved estimation of bone tissues. Skew-Gaussian mixture model (SGMM) isproposed to further investigate CT image estimation from MR images. The estimation quality of the proposed model is evaluated using leave-one-out cross-validation method on real data. In comparison with the existing model-based approaches, the approach utilized in this paper outperforms in estimation of bone tissues, especiallyon dense bone tissues.

  • 29.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Model-based Estimation of Computed Tomography Images2017In: 3rd International Researchers, Statisticians and Young Statisticians Congress: Abstract Book, Selcuk University , 2017, p. 84-Conference paper (Other academic)
    Abstract [en]

    Statistical methods are required to estimate computed tomography (CT) images from magnetic resonance (MR) images. The main purpose of estimating CT images was to get a fully MR based radiotherapy. Specifically, bone tissues and air are indistinguishable on MR images. But, there is a good contrast between soft tissue and other tissues on MR images. On CT images, there is eyecatching contrast between bone and non-bone tissues. Therefore, the main reason for CT estimation is to get improved bone tissues estimation and to use the estimated CT in fully MR based radiotherapy. The estimated CT images (also called substitute CT or Pseudo-CT images) are used for attenuation correction and dose planning in MR based radiotherapy. Gaussian mixture model (GMM) is used to investigate CT image estimation from MR images without taking spatial information into account. Markov random field (MRF) and hidden Markov model (HMM) are used to extend the approach by taking spatial dependence into account. Leave-one-dataset-out cross-validation method on five datasets (obtained from head of five patients) is used to evaluate the performance of the models. In terms of MAE, the use of spatial information improves the overall quality of CT image estimation. In this application, HMM is computationally faster and has superior performance on MRF. However, it has poor performance on bone tissues. On the other hand, MRF is computationally expensive and intractable for log-likelihood based model diagnostic. These two behaviour of HMM and MRF motivated this work to further probe the estimation of CT images from MR images by partitioning the data into bone and non-bone tissues. The partitioning of the data was based on CT value threshold. Skew-Gaussian mixture model (SGMM) and GMM applied on each partition. In terms of MAE, SGMM and GMM* (GMM applied to each partition) performed better than HMM and MRF on the bone tissues.

  • 30.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Zhou, Zhiyong
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Cronie, Ottmar
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Adaptive algorithm for sparse signal recovery2019In: Digital signal processing (Print), ISSN 1051-2004, E-ISSN 1095-4333, Vol. 87, p. 16p. 10-18Article in journal (Refereed)
    Abstract [en]

    The development of compressive sensing in recent years has given much attention to sparse signal recovery. In sparse signal recovery, spike and slab priors are playing a key role in inducing sparsity. The use of such priors, however, results in non-convex and mixed integer programming problems. Most of the existing algorithms to solve non-convex and mixed integer programming problems involve either simplifying assumptions, relaxations or high computational expenses. In this paper, we propose a new adaptive alternating direction method of multipliers (AADMM) algorithm to directly solve the suggested non-convex and mixed integer programming problem. The algorithm is based on the one-to-one mapping property of the support and non-zero element of the signal. At each step of the algorithm, we update the support by either adding an index to it or removing an index from it and use the alternating direction method of multipliers to recover the signal corresponding to the updated support. Moreover, as opposed to the competing “adaptive sparsity matching pursuit” and “alternating direction method of multipliers” methods our algorithm can solve non-convex problems directly. Experiments on synthetic data and real-world images demonstrated that the proposed AADMM algorithm provides superior performance and is computationally cheaper than the recently developed iterative convex refinement (ICR) and adaptive matching pursuit (AMP) algorithms.

  • 31. Becher, Tobias H
    et al.
    Miedema, Martijn
    Kallio, Merja
    Papadouri, Thalia
    Karaoli, Christina
    Sophocleous, Louiza
    Rahtu, Marika
    van Leuteren, Ruud W
    Waldmann, Andreas D
    Strodthoff, Claas
    Yerworth, Rebecca
    Dupré, Antoine
    Benissa, Mohamed-Rida
    Nordebo, Sven
    Khodadad, Davood
    Department of Physics and Electrical Engineering, Linnaeus University, Vaxjö, Sweden.
    Bayford, Richard
    Vliegenthart, Roseanne
    Rimensberger, Peter C
    van Kaam, Anton H
    Frerichs, Inéz
    Prolonged Continuous Monitoring of Regional Lung Function in Infants with Respiratory Failure2022In: Annals of the American Thoracic Society, ISSN 2329-6933, E-ISSN 2325-6621, Vol. 19, no 6, p. 991-999Article in journal (Refereed)
    Abstract [en]

    Rationale: Electrical impedance tomography (EIT) allows instantaneous and continuous visualization of regional ventilation and changes in end-expiratory lung volume at the bedside. There is particular interest in using EIT for monitoring in critically ill neonates and young children with respiratory failure. Previous studies have focused only on short-term monitoring in small populations. The feasibility and safety of prolonged monitoring with EIT in neonates and young children have not been demonstrated yet. Objectives: To evaluate the feasibility and safety of long-term EIT monitoring in a routine clinical setting and to describe changes in ventilation distribution and homogeneity over time and with positioning in a multicenter cohort of neonates and young children with respiratory failure. Methods: At four European University hospitals, we conducted an observational study (NCT02962505) on 200 patients with postmenstrual ages (PMA) between 25 weeks and 36 months, at risk for or suffering from respiratory failure. Continuous EIT data were obtained using a novel textile 32-electrode interface and recorded at 48 images/s for up to 72 hours. Clinicians were blinded to EIT images during the recording. EIT parameters and the effects of body position on ventilation distribution were analyzed offline. Results: The average duration of EIT measurements was 53 ± 20 hours. Skin contact impedance was sufficient to allow image reconstruction for valid ventilation analysis during a median of 92% (interquartile range, 77-98%) of examination time. EIT examinations were well tolerated, with minor skin irritations (temporary redness or imprint) occurring in 10% of patients and no moderate or severe adverse events. Higher ventilation amplitude was found in the dorsal and right lung areas when compared with the ventral and left regions, respectively. Prone positioning resulted in an increase in the ventilation-related EIT signal in the dorsal hemithorax, indicating increased ventilation of the dorsal lung areas. Lateral positioning led to a redistribution of ventilation toward the dependent lung in preterm infants and to the nondependent lung in patients with PMA > 37 weeks. Conclusions: EIT allows continuous long-term monitoring of regional lung function in neonates and young children for up to 72 hours with minimal adverse effects. Our study confirmed the presence of posture-dependent changes in ventilation distribution and their dependency on PMA in a large patient cohort. Clinical trial registered with www.clinicaltrials.gov (NCT02962505).

  • 32.
    Behndig, Oscar
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Tissue ultrasound localization microscopy - Superresolution imaging of skeletal muscle fascial structures at micrometer resolution2022Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Skeletal muscle fascia is a connective tissue which provides structure and aids with force transfer in a muscle. Currently there are no good ways of detecting and analyzing micrometer thick structures of this tissue in-vivo. In this thesis, we created a model to detect skeletal muscle fascia, and tested its performance using simulated data. Utilizing the ultrasound simulation software Vantage, which operates through MATLAB, we created a simulation model which replicates the properties and behaviour of skeletal muscle fascia. To detect the tissue, we changed and adapted a previously implemented model of ultrasound localization microscopy (ULM), previously only used to create super resolutionimages of blood vessels. Finally we evaluated the models ability to locate and determine the thickness of the simulated fascia. Additionally we tested the models ability to separate adjacent objects.

    We found that our model was successful at detecting and localizing the simulated fascia, with a sub wavelength accuracy. The precision of the located fascia appears more accurate for horizontally aligned objects compared to the vertically aligned ones. The results from determining the thickness of the fascia proved relatively successful as well. However the results showed a high variance. This could be improved through an inclusion of stocasticity in the simulation model we developed. Finally the ability to distinguish two objects close to eachother showed successful results as well. The method was able to clearly detect a fascia circle with a 0.5mm diameter. It was unable to detect the sides a fascia circle with a 0.25mm diameter.

    The main limitation with the model we have developed lies in the simulations performed. The simulation model we used was very basic, meaning that it did not perfectly represent the skeletal muscle fascia we sought to examine. Further development of the simulation model is required to provide a result which is more representative of real skeletal muscle fascia.

    The analysis of this first model shows promise in detecting the simplified fascia provided by our simulation model. At this stage, the method will require more extensive testing, together with a more thorough statistical analysis, before we can state the usefulness of the method.

  • 33.
    Berglund, Anders
    et al.
    Umeå University, Faculty of Medicine, Department of Odontology.
    Branting-Ekenbäck, C
    Ohlson, M
    En översikt över chairside CAD/CAM-system i Sverige. Garanteras patientsäkerheten genom CE-märkningen av utrustning och material?2013Report (Other academic)
    Abstract [sv]

    Inom odontologin har Computer-Aided Design/Computer-Aided Manufacturing (CAD/CAM) blivit allt vanligare, främst på tandtekniska laboratorier, men tekniken blir också vanligare på tandläkarklinikerna, s.k. chairside CAD/CAM. Chairside CAD/CAM innebär att tandläkaren efter preparationen av en tand framställer tandersättningen i tre steg. I första steget används en intraoral scanner istället för den traditionella avtryckstagningen (Mörmann et al., 2002; Beuer et al., 2008; Hehn, 2001). Man kan även scanna modeller och avtryck, vilket kan vara bra om patienten har svårt att gapa eller har hög salivproduktion, då scannrarna är känsliga för fuktiga miljöer (Kachalia et al., 2010). Det digitala avtrycket överförs till datorn, där uppgifterna bearbetas och en modell av tänderna skapas i 3D. I det andra steget designar tandläkaren tandersättningen på 3D-modellen. Här bestämmer tandläkaren kusphöjd, kontakter approximalt, utsträckning mot preparationsgränsen och utseende på tandersättningen. I det tredje steget fräses tandersättningen fram ur ett keramblock i en fräsmaskin. Ofta målas kronan här för att karaktärisera den och ge den ett mer tandlikt utseende innan den bränns i ugn. Med större möjligheter att själv kunna sköta hela processen fram till färdig tandkonstruktion måste tandläkaren fundera över hur kvaliteten och säkerheten hos de färdiga produkterna kan säkerställas. Färdiga tandtekniska arbeten räknas som specialanpassade medicintekniska produkter och ska inte CE-märkas men de material som ingår i arbetet är oftast CE-märkta. Lag (1993:584) om medicintekniska produkter och Läkemedelsverkets föreskrifter (LVFS 2003:11) om medicintekniska produkter innehåller krav på att medicintekniska produkter som släpps ut på marknaden ska vara lämpliga och säkra för sina användningsområden genom att krav ställs som ska leda till att allvarliga avvikelser, olyckor och tillbud på grund av produkterna så långt som möjligt ska kunna undvikas. Avvikelser inkluderar här både funktionsfel och misstänkta biverkningar. Innan ett tandtekniskt laboratorium får börja leverera tandtekniska arbeten till tandläkare måste ett antal krav vara uppfyllda för att bl.a. säkerställa säkerheten hos dessa produkter för patienterna. Laboratoriet ska vara registrerat hos Läkemedelsverket och vid registreringen måste man intyga att man har en tillverkningsverksamhet som uppfyller de krav för specialanpassade medicintekniska produkter som ställs i LVFS 2003:11. Medicintekniska produkter ska konstrueras och tillverkas på ett sådant sätt att de inte äventyrar patienternas kliniska tillstånd eller säkerhet, användarnas eller i förekommande fall andra personers hälsa och säkerhet, när de används under avsedda förhållanden och för sitt avsedda ändamål. Riskerna med att använda produkterna ska vara acceptabla med tanke på fördelarna för patienten och förenliga med en hög hälso-och säkerhetsnivå. Detta innefattar omfattande krav både på produkt och tillverkningsprocess. Det finns en del oklarheter rörande hur det regelverk som styr framställningen av tandtekniska arbeten tillämpas för arbeten tillverkade med chairside CAD/CAM.

  • 34.
    Björnfot, Cecilia
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Multiband functional magnetic resonance imaging (fMRI) for functional connectivity assessments2018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    During resting state the brain exhibits synchronized activity within all major brain networks. Using blood oxygen level dependent (BOLD) resting state functional magnetic resonance imaging (fMRI) based detection it is possible to quantify the degree of correlation, connectivity, between regions of interest and assess information regarding the integrity of the inter-regional functional integration. A newly available multiband echo planar imaging (EPI) fMRI sequence allows for faster scan times which possibly allows us to better examine large-scale networks and increase the understanding of brain function/dysfunction. This thesis will assess how the newly developed sequence compares to a conventional EPI sequence for detecting resting state connectivity of canonical brain networks. The data acquisitions were made on a 3 Tesla scanner using a 32 channel head coil. The hypothesis was that the multiband sequence would produce a better result since it has faster sampling rate, thus more data points in its time-series to support the statistical analyses.

    Using Pearson’s linear correlation between the average time-series (approximately 12 minutes long) within a seed-region and all voxels contained in the image volume, correlation maps where created for each of the eight participants using data normalized to Montreal Neurological Institute (MNI) space. The resting state networks (RSN) were then found by performing a one sample T-test on group level. Six seed-coordinates, based on literature, where used revealing the the homotopic connections in anterior Hippocampus, Motor cortex, Dorsal attention, Visual and the Default mode network (DMN) as well for an anterior-posterior connection in the DMN.

    By comparing the maximum T-values within the regions for the RSN no systematic difference could be found between the multiband and conventional fMRI data. Further tests were conducted to evaluate if the sequences would differentiate in their results if the acquisition time was shortened, i.e shortening the time-series in the voxels. However no such difference could be established.Importantly, the results are specific to the 32 channel head coil used in the current study. Presumably recently available and improved coil designs could better exploit the multiband technique.

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  • 35.
    Blusi, Madeleine
    et al.
    Umeå University, Faculty of Medicine, Department of Community Medicine and Rehabilitation. Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Nieves, Juan Carlos
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Feasibility and Acceptability of Smart Augmented Reality Assisting Patients with Medication Pillbox Self-Management2019In: Studies in Health Technology and Informatics, ISSN 0926-9630, E-ISSN 1879-8365, Vol. 264, p. 521-525Article in journal (Refereed)
    Abstract [en]

    Complex prescribed medicine regimens require extensive self-management. Handling multiple pills can be confusing; using a pillbox organiser is a common strategy. A smart Medication Coach Intelligent Agent (MCIA) can support patients in handling medicine. The aim of this research was to evaluate the feasibility and acceptability of the MCIA. A prototype was tested with 15 participants, age 17-76, filled a pillbox according to prescription assisted by the MCIA implemented in a Microsoft HoloLens. A quantitative method using questionnaires was applied. Results showed that using the MCIA implemented in an AR-headset, to assist people with prescribed polypharmacy regimen in filling a pillbox, was feasible and acceptable. There was a difference related to age regarding people's willingness to use an AR-headset for medication self-management. People older than 65 felt less comfortable using the technology and were also more hesitant to use the technology than those under 65.

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  • 36.
    Bodén, Ida
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Surgery.
    Nilsson, David
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Naredi, Peter
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Surgery.
    Lindholm-Sethson, Britta
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Characterization of healthy skin using near infrared spectroscopy and skin impedance2008In: Medical and Biological Engineering and Computing, ISSN 0140-0118, E-ISSN 1741-0444, Vol. 46, no 10, p. 985-995Article in journal (Refereed)
    Abstract [en]

    Near infrared spectroscopy (NIR) and skin impedance (IMP) spectroscopy are two methods suggested for diagnoses of diseases inducing adverse effects in skin. The reproducibility of these methods and their potential value in non-invasive diagnostics were investigated. Measurements were performed in vivo on healthy skin at five anatomic body sites on eight young women. partial least squares discriminant analysis showed that both methods were useful for classification of the skin characteristics at the sites. Inter-individually the NIR model gave 100% correct classification while the IMP model provided 92%. Intra-individually the NIR model gave 88% correct classification whereas the IMP model did not provide any useful classification. The correct classification was increased to 93% when both datasets were combined, which demonstrates the value of adding information. Partial least squares discriminant analysis gave 72% correct predictions of skin sites while the combined model slightly improved to 73%.

  • 37.
    Bodén, Ida
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Surgery.
    Nyström, Josefina
    Swedish University of Agricultural Sciences, Unit of Biomass Technology and Chemistry.
    Lundskog, Bertil
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Zazo, Virginia
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Dermatology and Venerology.
    Geladi, Paul
    Swedish University of Agricultural Sciences, Unit of Biomass Technology and Chemistry.
    Lindholm-Sethson, Britta
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Naredi, Peter
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Surgery.
    Non-invasive identification of melanoma with near-infrared and skin impedance spectroscopy2013In: Skin research and technology, ISSN 0909-752X, E-ISSN 1600-0846, Vol. 19, no 1, p. e473-e478Article in journal (Refereed)
    Abstract [en]

    Background/purpose: An early diagnosis of cutaneous malignant melanoma is of high importance for good prognosis. An objective, non-invasive instrument could improve the diagnostic accuracy of melanoma and decrease unnecessary biopsies. The aim of this study was to investigate the use of Near infrared and skin impedance spectroscopy in combination as a tool to distinguish between malignant and benign skin tumours.

    Methods: Near infrared and skin impedance spectra were collected in vivo on 50 naevi or suspect melanomas prior to excision. Received data was analysed with multivariate techniques and the results were compared to histopathology analyses of the tumours. A total of 12 cutaneous malignant melanomas, 19 dysplastic naevi and 19 benign naevi were included in the study.

    Results: The observed sensitivity and specificity of the proposed method were 83% and 95%, respectively, for malignant melanoma.

    Conclusions: The results indicate that the combination of near infrared and skin impedance spectroscopy is a promising tool for non-invasive diagnosis of suspect cutaneous malignant melanomas. 

  • 38.
    Brantefors, Per
    Umeå University, Faculty of Medicine, Department of Radiation Sciences. Umeå University, Faculty of Science and Technology, Department of Physics. Karolinska Institutet, Department of Clinical Neuroscience.
    Dynamic fMRI brain connectivity: A study of the brain’s large-scale network dynamics2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Approximately 20% of the body’s energy consumption is ongoingly consumed by the brain, where the main part is due to the neural activity, which is only increased slightly when doing a demanding task. This ongoingly neural activity are studied with the so called resting-state fMRI, which mean that the neural activity in the brain is measured for participants with no specific task. These studies have been useful to understand the neural function and how the neural networks are constructed and cooperate. This have also been helpful in several clinical research, for example have differences been identified between bipolar disorder and major depressive disorder. Recent research has focused on temporal properties of the ongoing activity and it is well known that neural activity occurs in bursts. In this study, resting-state fMRI data and temporal graph theory is used to develop a point based method (PBM) to quantify these bursts at a nodal level. By doing this, the bursty pattern can be further investigated and the nodes showing the most bursty pattern (i.e hubs) can be identified. The method developed shows a robustness regarding several different aspects. In the method is two different variance threshold algorithms suggested. One local variance threshold (LVT) based on the individual variance of the edge time-series and one global variance threshold (GVT) based on the variance of all edges time-series, where the GVT shows the highest robustness. However, the choice of threshold needs to be adapted for the aims of the current study. Finally, this method ends up in a new measure to quantify this bursty pattern named bursty centrality. The derived temporal graph theoretical measure was correlated with traditional static graph properties used in resting state and showed a low but significant correlation. By applying this method on resting-state fMRI data for 32 young adults was it possible to identify regions of the brain that showed the most dynamic properties, these regions differed between the two thresholding algorithms

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  • 39.
    Bredberg, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    VATTENKVALITET I HEMODIALYS: UTVECKLING OCH UTVÄRDERING AV ETT ÖVERVAKNINGSPROGRAM2024Independent thesis Basic level (university diploma), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Dialysis is a crucial aspect of healthcare, involving the replacement of kidney functions with a hemodialysis machine. A critical component of this process is ensuring the water used is free from bacteria and other byproducts. To ensure water quality, two key measurements need to be considered: disinfection efficiency (𝐴0) and water conductivity.

    To simplify the process of checking water quality, a program has been developed in an earlier thesis, to monitor and display 𝐴0 and conductivity in a graphical format, and to send warnings if these measurements exceed specified thresholds, the data is acquired directly from the sensors on the machine. Additionally, the program generates reports detailing these warnings. A new type of water purification system has been installed, requiring an update to the software to handle the new data format, which is available on a web page provided by the creator.

    This thesis focused on further developing the program to support an additional water purification system. A script in C# was written to automatically download log files daily at a predetermined time. The log files were then processed to remove unnecessary data, thereby reducing their size, 𝐴0 and conductivity values were plotted over a time series. Warnings for values exceeding or falling below thresholds were documented in a text file, and these warnings were emailed to relevant personnel.

    The updated program successfully displays 𝐴0 and conductivity in a graph, providing a quick overview of water quality. Additionally, the system sends both weekly and daily warning emails when a significant number of warnings accumulate throughout the week. While the program has been successfully developed and demonstrates the intended functionality, further improvements are needed for larger-scale deployment within Region Västerbotten. Enhancements such as more efficient plotting tools capable of handling large data volumes and a more user-friendly interface are necessary for broader usability.

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  • 40. Brolin, Gustav
    et al.
    Edenbrandt, Lars
    Granerus, Goeran
    Olsson, Anna
    Afzelius, David
    Gustafsson, Agneta
    Jonsson, Cathrine
    Hagerman, Jessica
    Johansson, Lena
    Riklund, Katrine
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology. EQUALIS AB, Uppsala, Sweden.
    Ljungberg, Michael
    The accuracy of quantitative parameters in Tc-99m-MAG3 dynamic renography: a national audit based on virtual image data2016In: Clinical Physiology and Functional Imaging, ISSN 1475-0961, E-ISSN 1475-097X, Vol. 36, no 2, p. 146-154Article in journal (Refereed)
    Abstract [en]

    Assessment of image analysis methods and computer software used in Tc-99m-MAG3 dynamic renography is important to ensure reliable study results and ultimately the best possible care for patients. In this work, we present a national multicentre study of the quantification accuracy in Tc-99m-MAG3 renography, utilizing virtual dynamic scintigraphic data obtained by Monte Carlo-simulated scintillation camera imaging of digital phantoms with time-varying activity distributions. Three digital phantom studies were distributed to the participating departments, and quantitative evaluation was performed with standard clinical software according to local routines. The differential renal function (DRF) and time to maximum renal activity (T-max) were reported by 21 of the 28 Swedish departments performing Tc-99m-MAG3 studies as of 2012. The reported DRF estimates showed a significantly lower precision for the phantom with impaired renal uptake than for the phantom with normal uptake. The T-max estimates showed a similar trend, but the difference was only significant for the right kidney. There was a significant bias in the measured DRF for all phantoms caused by different positions of the left and right kidney in the anterior-posterior direction. In conclusion, this study shows that virtual scintigraphic studies are applicable for quality assurance and that there is a considerable uncertainty associated with standard quantitative parameters in dynamic Tc-99m-MAG3 renography, especially for patients with impaired renal function.

  • 41.
    Brynolfsson, Patrik
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Using radial k-space sampling and temporal filters in MRI to improve temporal resolution2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In this master thesis methods for increasing temporal resolution when reconstructing radially sampled MRI data have been developed and evaluated. This has been done in two steps; first the order in which data is sampled in k-space has been optimized, and second; temporal filters have been developed in order to utilize the high sampling density in central regions of k-space as a result of the polar sampling geometry to increase temporal resolution while maintaining image quality.By properly designing the temporal filters the temporal resolution is increased by a factor 3–20 depending on other variables such as imageresolution and the size of the time varying areas in the image. The results are obtained from simulated raw data and subsequent reconstruction. The next step should be to acquire and reconstruct raw data to confirm the results.

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  • 42.
    Brynolfsson, Patrik
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Wirestam, Ronnie
    Lund University.
    Karlsson, Mikael
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Garpebring, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences. CJ Gorter Center for High Field MRI, Leiden University Medical Center, Leiden, Netherlands.
    Combining phase and magnitude information for contrast agent quantification in dynamic contrast-enhanced MRI using statistical modeling2015In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 74, no 4, p. 1156-1164Article in journal (Refereed)
    Abstract [en]

    Purpose: The purpose of this study was to investigate, using simulations, a method for improved contrast agent (CA) quantification in DCE-MRI.

    Methods: We developed a maximum likelihood estimator that combines the phase signal in the DCE-MRI image series with an additional CA estimate, e.g. the estimate obtained from magnitude data. A number of simulations were performed to investigate the ability of the estimator to reduce bias and noise in CA estimates. Noise levels ranging from that of a body coil to that of a dedicated head coil were investigated at both 1.5T and 3T.

    Results: Using the proposed method, the root mean squared error in the bolus peak was reduced from 2.24 to 0.11 mM in the vessels and 0.16 to 0.08 mM in the tumor rim for a noise level equivalent of a 12-channel head coil at 3T. No improvements were seen for tissues with small CA uptake, such as white matter.

    Conclusion: Phase information reduces errors in the estimated CA concentrations. A larger phase response from higher field strengths or higher CA concentrations yielded better results. Issues such as background phase drift need to be addressed before this method can be applied in vivo.

  • 43. Bujila, Robert
    et al.
    Kull, Love
    Danielsson, Mats
    Andersson, Jonas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Applying three different methods of measuring CTDIfree air to the extended CTDI formalism for wide-beam scanners (IEC 60601-2-44): a comparative study2018In: Journal of Applied Clinical Medical Physics, E-ISSN 1526-9914, Vol. 19, no 4, p. 281-289Article in journal (Refereed)
    Abstract [en]

    Purpose: The weighted CT dose index (CTDIw) has been extended for a nominal total collimation width (nT) greater than 40 mm and relies on measurements of CTDfree air. The purpose of this work was to compare three methods of measuring CTDIfree air and subsequent calculations of CTDIw to investigate their clinical appropriateness.

    Methods: The CTDIfree air, for multiple nTs up to 160 mm, was calculated from (1) high-resolution air kerma profiles from a step-and-shoot translation of a liquid ionization chamber (LIC) (considered to be a dosimetric reference), (2) pencil ionization chamber (PIC) measurements at multiple contiguous positions, and (3) air kerma profiles obtained through the continuous translation of a solid-state detector. The resulting CTDIfree air was used to calculate the CTDIw, per the extended formalism, and compared.

    Results: The LIC indicated that a 40 mm nT should not be excluded from the extension of the CTDIw formalism. The solid-state detector differed by as much as 8% compared to the LIC. The PIC was the most straightforward method and gave equivalent results to the LIC.

    Conclusions: The CTDIw calculated with the latest CTDI formalism will differ most for 160 mm nTs (e.g., whole-organ perfusion or coronary CT angiography) compared to the previous CTDI formalism. Inaccuracies in the measurement of CTDIfree air will subsequently manifest themselves as erroneous calculations of the CTDIw, for nTs greater than 40 mm, with the latest CTDI formalism. The PIC was found to be the most clinically feasible method and was validated against the LIC.

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  • 44.
    Bäcklund, Tomas
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Development and validation of a system for clinical assessment of gait cycle parameter in patients with idiopathic normal pressure hydocephalus2013Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A number of parameters have been identified as characteristic of the walking pattern in patients with INPH. Most of these have been identified through qualitative surveys and manually conducted test batteries. In order to obtain quantitative, standardized and objective measures, which enable studies based on larger patient populations and comparable results, there is a need for a user-friendly system that can measure specific key parameters over time in a reliable manner in everyday clinical work. Step height, width and the variability in the gait cycle are such parameters which are interesting research areas for this group of patient.

    Problems with balance and gait are very common in other patient groups as well, particularly in neurological diseases such as Parkinson's disease, multiple sclerosis and stroke.

    This is the reason that the development of this gait analyzer is performed. Giving access to a simple and objective method for estimating gait and balance ability in clinical routine investigations would increase the ability to provide the right kind of treatment, confirm treatment results, and conducting larger research studies. Therefore, this equipment can contribute to the assessment of diseases which contain impaired gait. As a first test of the usability and for the validation of accuracy and repeatability of the equipment a group of healthy volunteers was used. Results from tests on healthy subjects show god repeatability between measurements, for step width at normal gait the difference was -0,2 ±0,34 cm (mean, ±SD) and step height 0,69 ±3,34 cm. The stride time variability in the healthy group where very small 0,00048 ±0,00028 s2 with a difference between test of 0,000019 ±0,00038 s2. Three pilot patients have been tested where we have clearly seen indications of increased stride time variability and reduced step height.

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    Utveckling och validering av ett system för klinisk bedömning av gångcykelns parametrar hos patienter med idiopatisk normaltrycks hydrocephalus
  • 45.
    Bäcklund, Tomas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics. Umeå University, Faculty of Medicine, Department of Clinical Sciences.
    Wearable systems and sensors for the assessment of motor control: Development and validation of methods for clinical assessment of idiopathic normal pressure hydrocephalus2021Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Human gait and balance are controlled by automatic processes in the central nervous system, and in sensory and proprioceptive systems. If a disturbance occurs in any of these complex structures, it may lead to balance and gait problems. Equally important are the systems controlling the upper extremity functions where reach, grasp and manipulation skills may be affected. For the neurodegenerative disease idiopathic normal pressure hydrocephalus (iNPH), balance and gait disturbances are cardinal symptoms. Motor control of the upper extremities is also affected. In clinic today, physical impairment of persons with iNPH is commonly visually assessed using subjective, course tests with ordinal scales with the risk of missing minor changes. There is a lack of objective and quantitative ways to measure motor control in daily patient care. The aim of this thesis was to develop and validate tools for objective assessment of parameters that affect motor control in persons with iNPH.

    Postural stability in stance and walking was assessed using gyroscopes in patients with iNPH, healthy elderly (HE) and patients with ventriculomegaly (VM). Compared to HE, patients with iNPH had reduced postural stability and relied less on vision. iNPH patients also had a lower trunk sway velocity than VM during walking. The gyroscopic system could quantitatively assess postural deficits in iNPH, making it a potentially useful tool for diagnosis and for clinical follow-up. The differences found during gait also suggests that walking, rather than quiet stance, should be further investigated for facilitating differential diagnosis compared to other patient groups with ventriculomegaly.

    The gait in patients with iNPH is according to guidelines defined as slow, shuffling with a low foot-lift, and wide based. To objectively quantify the latter two features, a system (Striton) was developed in-house to assess the increased distance between the feet and the peak heel-height at the push-off phase of the gait cycle. It was validated in experimental setups, compared to gold standard motion capture systems (MCS), on healthy elderly (HE), through test-retest and day-to-day evaluations, and in four patients with iNPH. Striton demonstrated high correlations, in step-width and in heel-height, compared with the MCS. The mean step-width in the HE was 5.2 ± 0.9 cm (mean±Standard Deviation) and the heel-height 16.7±0.6 cm. Test-retest and day-to-day variations were small, ±0.5 cm in step-width and ±1.2 cm in heel-height, and differences in the parameters were seen between HE and iNPH both before and after surgery. Thus, Striton has the potential of quantitatively assessing gait parameters in HE and iNPH in a valuable manner.

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  • 46.
    Bäcklund, Tomas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Grip, Helena
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Öhberg, Fredrik
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Sundström, Nina
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Single sensor measurement of heel-height during the push-off phase of gait2021In: Physiological Measurement, ISSN 0967-3334, E-ISSN 1361-6579, Vol. 42, no 10, article id 105016Article in journal (Refereed)
    Abstract [en]

    Objective: In healthy gait a forceful push-off is needed to get an efficient leg swing and propulsion, and a high heel lift makes a forceful push-off possible. The power of the push-off is decreased with increased age and in persons with impaired balance and gait. The aim of this study was to evaluate whether a wearable equipment (Striton) and algorithms to estimate vertical heel-height during gait from a single optical distance sensor is reliable and feasible for clinical applications.

    Approach: To assess heel-height with the Striton system an optical distance sensor was used to measure the distance to the floor along the shank. An algorithm was created to transform this measure to a vertical distance. The heel-height was validated in an experimental setup, against a 3D motion capture system (MCS), and test-retest and day-to-day tests were performed on 10 elderly persons. As a reference material 83 elderly persons were included, and heel-height was measured before and after surgery in four patients with the neurological disorder idiopathic normal pressure hydrocephalus (iNPH).

    Main results: In the experimental setup the accuracy was high with a maximum error of 2% at all distances, target colours and inclination angles, and the correlation to the MCS was R = 0.94. Test-retest and day-to-day tests were equal within ±1.2 cm. Mean heel-height of the elderly persons was 16.5 ± 0.6 cm and in the patients with iNPH heel-height was increased from 11.2 cm at baseline to 15.3 cm after surgery.

    Significance: Striton can reliably measure heel-height during gait, with low test-retest and day-to-day variability. The system was easy to attach, and simple to use, which makes it suitable for clinical applications.

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  • 47.
    Bölenius, Karin
    et al.
    Umeå University, Faculty of Medicine, Department of Nursing.
    Brulin, Christine
    Umeå University, Faculty of Medicine, Department of Nursing.
    Grankvist, Kjell
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Clinical chemistry.
    Lindkvist, Marie
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Epidemiology and Global Health.
    Söderberg, Johan
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Clinical chemistry.
    A content validated questionnaire for assessment of self reported venous blood sampling practices2012In: BMC Research Notes, E-ISSN 1756-0500, Vol. 5, p. 39-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Venous blood sampling is a common procedure in health care. It is strictly regulated by national and international guidelines. Deviations from guidelines due to human mistakes can cause patient harm. Validated questionnaires for health care personnel can be used to assess preventable "near misses"--i.e. potential errors and nonconformities during venous blood sampling practices that could transform into adverse events. However, no validated questionnaire that assesses nonconformities in venous blood sampling has previously been presented. The aim was to test a recently developed questionnaire in self reported venous blood sampling practices for validity and reliability.

    FINDINGS: We developed a questionnaire to assess deviations from best practices during venous blood sampling. The questionnaire contained questions about patient identification, test request management, test tube labeling, test tube handling, information search procedures and frequencies of error reporting. For content validity, the questionnaire was confirmed by experts on questionnaires and venous blood sampling. For reliability, test-retest statistics were used on the questionnaire answered twice. The final venous blood sampling questionnaire included 19 questions out of which 9 had in total 34 underlying items. It was found to have content validity. The test-retest analysis demonstrated that the items were generally stable. In total, 82% of the items fulfilled the reliability acceptance criteria.

    CONCLUSIONS: The questionnaire could be used for assessment of "near miss" practices that could jeopardize patient safety and gives several benefits instead of assessing rare adverse events only. The higher frequencies of "near miss" practices allows for quantitative analysis of the effect of corrective interventions and to benchmark preanalytical quality not only at the laboratory/hospital level but also at the health care unit/hospital ward.

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  • 48.
    Börlin, Niclas
    et al.
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Thien, Truike
    Katholieke Universiteit Nijmegen, Nijmegen, Holland.
    Kärrholm, Johan
    Sahlgrenska University Hospital, Göteborg, Sweden.
    The precision of radiostereometric measurements: manual vs. digital measurements2002In: Journal of Biomechanics, ISSN 0021-9290, E-ISSN 1873-2380, Vol. 35, no 1, p. 69-79Article in journal (Refereed)
    Abstract [en]

    The precision of digital vs. manual radiostereometric measurements in total hip arthroplasty was evaluated using repeated stereoradiographic exposures with an interval of 10–15 min. Ten Lubinus SP2 stems cemented into bone specimens and 12 patients with the same stem design were used to evaluate the precision of stem translations and rotations. The precision of translations and rotations of the cup and femoral head penetration was studied in 12 patients with whole polyethylene cups.

    The use of a measurement method based on digitised radiographs improved the precision for some of the motion parameters, whereas many of them did not change. A corresponding pattern was observed for both the intra- and interobserver error. Of the wear parameters, the most pronounced improvements were the 3D wear and in the proximal-distal direction, although the anterior-posterior precision was also improved. The mean errors of rigid body and elliptic fitting decreased in all evaluations but one, consistent with a more reproducible identification of the markers centres and the edge of the femoral head.

    Increased precision of radiostereometric measurements may be used to increase the statistical power of future randomised studies and to study new fields in orthopaedics requiring higher precision than has been available with RSA based on manual measurements.

  • 49.
    Candefjord, Stefan
    et al.
    Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF). Department of Computer Science Electrical and Space Engineering, Luleå University of Technology, Luleå, Sweden; Signals and Systems, Chalmers University of Technology, Gothenburg, Sweden; MedTech West, Sahlgrenska University Hospital, Gothenburg, Sweden.
    Murayama, Yoshinobu
    Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF). Department of Electrical and Electronics Engineering, College of Engineering, Nihon University, Fukushima, Japan.
    Nyberg, Morgan
    Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF). Department of Computer Science, Electrical and Space Engineering, Luleå University of Technology, Luleå, Sweden.
    Hallberg, Josef
    Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF). Department of Computer Science Electrical and Space Engineering, Luleå University of Technology, Luleå, Sweden.
    Ramser, Kerstin
    Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF). Department of Computer Science Electrical and Space Engineering, Luleå University of Technology, Luleå, Sweden.
    Ljungberg, Börje
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Urology and Andrology.
    Bergh, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Lindahl, Olof Anton
    Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF). Umeå University, Faculty of Medicine, Department of Radiation Sciences. Department of Computer Science Electrical and Space Engineering, Luleå University of Technology, Luleå, Sweden.
    Combining scanning haptic microscopy and fibre optic Raman spectroscopy for tissue characterization2012In: Journal of Medical Engineering & Technology, ISSN 0309-1902, E-ISSN 1464-522X, Vol. 36, no 6, p. 319-327Article in journal (Refereed)
    Abstract [en]

    The tactile resonance method (TRM) and Raman spectroscopy (RS) are promising for tissue characterization in vivo. Our goal is to combine these techniques into one instrument, to use TRM for swift scanning, and RS for increasing the diagnostic power. The aim of this study was to determine the classification accuracy, using support vector machines, for measurements on porcine tissue and also produce preliminary data on human prostate tissue. This was done by developing a new experimental set-up combining micro-scale TRMscanning haptic microscopy (SHM)for assessing stiffness on a micro-scale, with fibre optic RS measurements for assessing biochemical content. We compared the accuracy using SHM alone versus SHM combined with RS, for different degrees of tissue homogeneity. The cross-validation classification accuracy for healthy porcine tissue types using SHM alone was 6581%, and when RS was added it increased to 8187%. The accuracy for healthy and cancerous human tissue was 6770% when only SHM was used, and increased to 7277% for the combined measurements. This shows that the potential for swift and accurate classification of healthy and cancerous prostate tissue is high. This is promising for developing a tool for probing the surgical margins during prostate cancer surgery. 

  • 50.
    Candefjord, Stefan
    et al.
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Nyberg, Morgan
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Jalkanen, Ville
    Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF). Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Ramser, Kerstin
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Lindahl, Olof
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Combining fibre optic Raman spectroscopy and tactile resonance measurement for tissue characterization2010In: Measurement science and technology, ISSN 0957-0233, E-ISSN 1361-6501, Vol. 21, no 125801, p. 1-8Article in journal (Refereed)
    Abstract [en]

    Tissue characterization is fundamental for identification of pathological conditions. Raman spectroscopy (RS) and tactile resonance measurement (TRM) are two promising techniques that measure biochemical content and stiffness, respectively. They have potential to complement the golden standard-–histological analysis. By combining RS and TRM, complementary information about tissue content can be obtained and specific drawbacks can be avoided. The aim of this study was to develop a multivariate approach to compare RS and TRM information. The approach was evaluated on measurements at the same points on porcine abdominal tissue. The measurement points were divided into five groups by multivariate analysis of the RS data. A regression analysis was performed and receiver operating characteristic (ROC) curves were used to compare the RS and TRM data. TRM identified one group efficiently (area under ROC curve 0.99). The RS data showed that the proportion of saturated fat was high in this group. The regression analysis showed that stiffness was mainly determined by the amount of fat and its composition. We concluded that RS provided additional, important information for tissue identification that was not provided by TRM alone. The results are promising for development of a method combining RS and TRM for intraoperative tissue characterization.

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