Multiscale vision model for event detection and reconstruction in two-photon imaging data

Reliable detection of calcium waves in multiphoton imaging data is challenging because of the low signal-to-noise ratio and because of the unpredictability of the time and location of these spontaneous events. This paper describes our approach to calcium wave detection and reconstruction based on a modified multiscale vision model, an object detection framework based on the thresholding of wavelet coefficients and hierarchical trees of significant coefficients followed by nonlinear iterative partial object reconstruction, for the analysis of two-photon calcium imaging data. The framework is discussed in the context of detection and reconstruction of intercellular glial calcium waves. We extend the framework by a different decomposition algorithm and iterative reconstruction of the detected objects. Comparison with several popular state-of-the-art image denoising methods shows that performance of the multiscale vision model is similar in the denoising, but provides a better segmenation of the image into meaningful objects, whereas other methods need to be combined with dedicated thresholding and segmentation utilities

Inhibitory Control Over Ca2+ Sparks via Mechanosensitive Channels Is Disrupted in Dystrophin Deficient Muscle but Restored by Mini-Dystrophin Expression

Background: In dystrophic skeletal muscle, osmotic stimuli somehow relieve inhibitory control of dihydropyridine receptors (DHPR) on spontaneous sarcoplasmic reticulum elementary Ca release events (ECRE) in high Ca external environments. Such 'uncontrolled' Ca sparks were suggested to act as dystrophic signals. They may be related to mechanosensitive pathways but the mechanisms are elusive. Also, it is not known whether truncated dystrophins can correct the dystrophic disinhibition. Methodology/Principal Findings: We recorded ECRE activity in single intact fibers from adult wt, mdx and mini-dystrophin expressing mice (MinD) under resting isotonic conditions and following hyper-/ hypo-osmolar external shock using confocal microscopy and imaging techniques. Isotonic ECRE frequencies were small in wt and MinD fibers, but were markedly increased in mdx fibers. Osmotic challenge dramatically increased ECRE activity in mdx fibers. Sustained osmotic challenge induced marked exponential ECRE activity adaptation that was three times faster in mdx compared to wt and MinD fibers. Rising external Ca concentrations amplified osmotic ECRE responses. The eliminated ECRE suppression in intact osmotically stressed mdx fibers was completely and reversibly resuscitated by streptomycine (200 μM), spider peptide GsMTx-4 (5 μM) and Gd (20 μM) that block unspecific, specific cationic and Ca selective mechanosensitive channels (MsC), respectively. ECRE morphology was not substantially altered by membrane stress. During hyperosmotic challenge, membrane potentials were polarised and a putative depolarisation through aberrant MsC negligible excluding direct activation of ECRE through tubular depolarisation. Conclusions/Significance: Dystrophin suppresses spontaneous ECRE activity by control of mechanosensitive pathways which are suggested to interact with the inhibitory DHPR loop to the ryanodine receptor. MsC-related disinhibition prevails in dystrophic muscle and can be resuscitated by transgenic mini-dystrophin expression. Our results have important implications for the pathophysiology of DMD where abnormal MsC in dystrophic muscle confer disruption of microdomain Ca homeostasis. MsC blockers should have considerable therapeutic potential if more muscle specific compounds can be found

Counting of RBCs and WBCs in noisy normal blood smear microscopic images

This work focuses on the segmentation and counting of peripheral blood smear particles which plays a vital role in medical diagnosis. Our approach profits from some powerful processing techniques. Firstly, the method used for denoising a blood smear image is based on the Bivariate wavelet. Secondly, image edge preservation uses the Kuwahara filter. Thirdly, a new binarization technique is introduced by merging the Otsu and Niblack methods. We have also proposed an efficient step-by-step procedure to determine solid binary objects by merging modified binary, edged images and modified Chan-Vese active contours. The separation of White Blood Cells (WBCs) from Red Blood Cells (RBCs) into two sub-images based on the RBC (blood’s dominant particle) size estimation is a critical step. Using Granulometry, we get an approximation of the RBC size. The proposed separation algorithm is an iterative mechanism which is based on morphological theory, saturation amount and RBC size. A primary aim of this work is to introduce an accurate mechanism for counting blood smear particles. This is accomplished by using the Immersion Watershed algorithm which counts red and white blood cells separately. To evaluate the capability of the proposed framework,experiments were conducted on normal blood smear images. This framework was compared to other published approaches and found to have lower complexity and better performance in its constituent steps; hence, it has a better overall performance

Multiscale image analysis of calcium dynamics in cardiac myocytes

Cardiac myocytes constitute a unique physiological system. They are the muscle cells that build up heart tissue and provide the force to pump blood by synchronously contracting at every beat. This contraction is regulated by calcium concentration, among other ions, which exhibits a very complex behaviour, rich in dynamical states at the molecular, cellular and tissue levels. Details of such dynamical patterns are closely related to the mechanisms responsible for cardiac function and also cardiac disease, which is the first cause of death in the modern world. The emerging field of translational cardiology focuses on the study of how such mechanisms connect and influence each other across spatial and temporal scales finally yielding to a certain clinical condition. In order to study such patterns, we benefit from the recent and very important advances in the field of experimental cell physiology. In particular, fluorescence microscopy allows us to observe the distribution of calcium in the cell with a spatial resolution below the micron and a frame rate around the millisecond, thus providing a very accurate monitoring of calcium fluxes in the cell. This thesis is the result of over five years' work on biological signal and digital image processing of cardiac cells. During this period of time the aim has been to develop computational techniques for extracting quantitative data of physiological relevance from microscopy images at different scales. The two main subjects covered in the thesis are image segmentation and classification methods applied to fluorescence microscopy imaging of cardiac myocytes. These methods are applied to a variety of problems involving different space and time scales such as the localisation of molecular receptors, the detection and characterisation of spontaneous calcium-release events and the propagation of calcium waves across a culture of cardiac cells. The experimental images and data have been provided by four internationally renowned collaborators in the field. It is thanks to them and their teams that this thesis has been possible. They are Dr. Leif Hove-Madsen from the Institut de Ciències Cardiovasculars de Catalunya in Barcelona, Prof. S. R. Wayne Chen from the Department of Physiology and Pharmacology in the Libin Cardiovascular Institute of Alberta, University of Calgary, Dr. Peter P. Jones from the Department of Physiology in the University of Otago, and Prof. Glen Tibbits from the Department of Biomedical Physiology & Kinesiology at the Simon Fraser University in Vancouver. The work belongs to the biomedical engineering discipline, focusing on the engineering perspective by applying physics and mathematics to solve biomedical problems. Specifically, we frame our contributions in the field of computational translational cardiology, attempting to connect molecular mechanisms in cardiac cells up to cardiac disease by developing signal and image-processing methods and machine-learning methods that are scalable through the different scales. This computational approach allows for a quantitative, robust and reproducible analysis of the experimental data and allows us to obtain results that otherwise would not be possible by means of traditional manual methods. The results of the thesis provide specific insight into different cell mechanisms that have a non-negligible impact at the clinical level. In particular, we gain a deeper knowledge of cell mechanisms related to cardiac arrhythmia, fibrillation phenomena, the emergence of alternans and anomalies in calcium handling due to cell ageing.Els cardiomiòcits constitueixen un sistema fisiològic únic. Són les cèl·lules muscular que formen el cor i proporcionen la força per bombar la sang fent una contracció a cada batec. La regulació d'aquesta contracció es fa mitjançant concentració de calci (entre d'altres ions) i presenta una dinàmica molt complexa tant a l'escala molecular, cel·lular i de teixit. Detalls d'aquesta dinàmica estan fortament relacionats amb la funció cardíaca i per sobre de tot amb patologies cardíaques. La disciplina emergent de la cardiologia translacional es centra en l'estudi de com aquests mecanismes es connecten i s'influencien entre sí a través de diferents escales temporals i espacials finalment donant lloc a condicions clíniques. Per estudiar aquests patrons ens beneficiem dels recents avenços en fisiologia i biologia cel·lular. En particular, la microscòpia de fluorescència ens permet observar la distribució de calci dins una cèl·lula amb una resolució espacial per sota de la micra i temporal per sota del mil·lisegon, permetent un monitoratge acurat dels fluxos de calci en la cèl·lula cardíaca. Aquesta tesi és el resultat de més de cinc anys de feina en processament de senyal i imatge de cardiomiòcits humans. Durant aquest període de temps l'objectiu principal ha estat desenvolupar tècniques computacionals per extraure dades d'imatges de microscòpia amb rellevància fisiològica. Els dos temes principals coberts a la tesi són segmentació d'imatges i classificadors, aplicats a imatges de microscòpia de fluorescència de cardiomiòcits. Els mètodes s'apliquen a diferents problemes involucrant diverses escales espacials i temporals, des de determinar la posició de receptors a l’escala molecular passant detectar i caracteritzar alliberament espontani de calci intracel·lular fins a la propagació d'ones de calci en un cultiu de cèl·lules cardíaques. Les dades experimentals han estat proporcionades per quatre col·laboradors de renom internacional. És gràcies a ells i els seus equips que aquesta tesi ha estat possible. Són el Dr. Leif Hove-Madsen de l'Institut de Ciències Cardiovasculars de Catalunya a Barcelona, el Dr. S.R. Wayne Chen del Department of Physiology and Pharmacology al Libin Cardiovascular Institute of Alberta, University of Calgary, el Dr. Peter P. Jones del Department of Physiology a la University of Otago, i el Dr. Glen Tibbits del Department of Biomedical Physiology & Kinesiology de la Simon Fraser University a Vancouver. El treball pertany a la disciplina de la enginyeria biomèdica, fent èmfasi a la perspectiva de l'enginyeria, aplicant física i matemàtiques per solucionar problemes de la biomedicina. Específicament, s'emmarca en la cardiologia translacional computacional, mirant de connectar mecanismes a l’escala molecular amb patologies cardíaques mitjançant tècniques de processament de dades i aprenentatge automàtic que són escalables a les diferents escales d’aplicació. Aquest enfocament computacional permet una anàlisi quantitatiu, robust i reproduïble de les dades experimentals i ens permet d'obtenir resultats que serien impossibles d'assolir mitjançant els tradicionals mètodes manuals. Els resultats que proporciona la tesi han permès aprofundir en l'enteniment de diferents mecanismes fisiològics amb impacte en l'àmbit clínic. Particularment hem permès d’assolir coneixements relacionats amb l'arítmia cardíaca, la fibril·lació, processos d'alternança i anomalies relacionades amb l’envelliment

Plasma Biology

Irving Langmuir coined the name “plasma” to describe an ionized gas back in 1927. Just over 90 years later, plasma technology is becoming increasingly important in our daily life. For example, in the medical field and dentistry, plasma is used as a method of disinfection and sterilization. Moreover, additional potential novel applications of this technology in different forms of therapy have been proposed. In the agricultural sector, plasma technology could contribute to higher crop yields by enhancing seed germination and the growth of plants, as well as the preservation of foods by disinfection. Plasma technology could also be utilized in environmental applications, including water treatment and remediation, as well as treatment of exhaust gases. Although recent extensive studies have uncovered the broad potential of plasma technology, its mechanisms of action remain unclear. Therefore, further studies aimed at elucidating the molecular mechanisms of plasma technology are required. This book is composed of original articles and reviews investigating the molecular mechanisms of plasma biology. Relevant areas of study include applications in plasma medicine, plasma agriculture, as well as plasma chemistry. Studies on potential therapeutic approaches using plasma itself and plasma-treated solutions are also included