by Keyword: image
Martinez A, Hériché JK, Calvo M, Tischer C, Otxoa-de-Amezaga A, Pedragosa J, Bosch A, Planas AM, Petegnief V, (2023). Characterization of microglia behaviour in healthy and pathological conditions with image analysis tools Open Biology 13, 220200
Microglia are very sensitive to changes in the environment and respond through morphological, functional and metabolic adaptations. To depict the modifications microglia undergo under healthy and pathological conditions, we developed free access image analysis scripts to quantify microglia morphologies and phagocytosis. Neuron-glia cultures, in which microglia express the reporter tdTomato, were exposed to excitotoxicity or excitotoxicity + inflammation and analysed 8 h later. Neuronal death was assessed by SYTOX staining of nucleus debris and phagocytosis was measured through the engulfment of SYTOX+ particles in microglia. We identified seven morphologies: round, hypertrophic, fried egg, bipolar and three 'inflamed' morphologies. We generated a classifier able to separate them and assign one of the seven classes to each microglia in sample images. In control cultures, round and hypertrophic morphologies were predominant. Excitotoxicity had a limited effect on the composition of the populations. By contrast, excitotoxicity + inflammation promoted an enrichment in inflamed morphologies and increased the percentage of phagocytosing microglia. Our data suggest that inflammation is critical to promote phenotypical changes in microglia. We also validated our tools for the segmentation of microglia in brain slices and performed morphometry with the obtained mask. Our method is versatile and useful to correlate microglia sub-populations and behaviour with environmental changes.
JTD Keywords: classification, identification, image analysis, injury, morphometry, neuroinflammation, neurotoxicity, phagocytosis, Classification, Image analysis, Microglia, Morphometry, Neuroinflammation, Nitric-oxide, Phagocytosis
Barbacena P, Dominguez-Cejudo M, Fonseca CG, Gómez-González M, Faure LM, Zarkada G, Pena A, Pezzarossa A, Ramalho D, Giarratano Y, Ouarné M, Barata D, Fortunato IC, Misikova LH, Mauldin I, Carvalho Y, Trepat X, Roca-Cusachs P, Eichmann A, Bernabeu MO, Franco CA, (2022). Competition for endothelial cell polarity drives vascular morphogenesis in the mouse retina Developmental Cell 57, 2321-2333.e9
Blood-vessel formation generates unique vascular patterns in each individual. The principles governing the apparent stochasticity of this process remain to be elucidated. Using mathematical methods, we find that the transition between two fundamental vascular morphogenetic programs-sprouting angiogenesis and vascular remodeling-is established by a shift of collective front-to-rear polarity of endothelial cells in the mouse retina. We demonstrate that the competition between biochemical (VEGFA) and mechanical (blood-flow-induced shear stress) cues controls this collective polarity shift. Shear stress increases tension at focal adhesions overriding VEGFA-driven collective polarization, which relies on tension at adherens junctions. We propose that vascular morphogenetic cues compete to regulate individual cell polarity and migration through tension shifts that translates into tissue-level emergent behaviors, ultimately leading to uniquely organized vascular patterns.Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.
JTD Keywords: activation, angiogenesis, dynamics, flow, forces, image, mechanisms, vinculin, Angiogenesis, Cell polarity, Fluid shear, Mechanobiology, Morphogenesis, Shear stress
Fernández-Garibay, Xiomara, Gomez-Florit, Manuel, Domingues, Rui M A, Gomes, Manuela, Fernandez-Costa, Juan M., Ramon, Javier, (2022). Xeno-free bioengineered human skeletal muscle tissue using human platelet lysate-based hydrogels Biofabrication 14, 045015
Abstract Bioengineered human skeletal muscle tissues have emerged in the last years as new in vitro systems for disease modeling. These bioartificial muscles are classically fabricated by encapsulating human myogenic precursor cells in a hydrogel scaffold that resembles the extracellular matrix. However, most of these hydrogels are derived from xenogenic sources, and the culture media is supplemented with animal serum, which could interfere in drug testing assays. On the contrary, xeno-free biomaterials and culture conditions in tissue engineering offer increased relevance for developing human disease models. In this work, we used human platelet lysate-based nanocomposite hydrogels (HUgel) as scaffolds for human skeletal muscle tissue engineering. These hydrogels consist of human platelet lysate reinforced with cellulose nanocrystals (a-CNC) that allow tunable mechanical, structural, and biochemical properties for the 3D culture of stem cells. Here, we developed hydrogel casting platforms to encapsulate human muscle satellite stem cells in HUgel. The a-CNC content was modulated to enhance matrix remodeling, uniaxial tension, and self-organization of the cells, resulting in the formation of highly aligned, long myotubes expressing sarcomeric proteins. Moreover, the bioengineered human muscles were subjected to electrical stimulation, and the exerted contractile forces were measured in a non-invasive manner. Overall, our results demonstrated that the bioengineered human skeletal muscles could be built in xeno-free cell culture platforms to assess tissue functionality, which is promising for drug development applications.
JTD Keywords: 3d culture, generation, identification, image, manipulate, matrigel, mechanics, model, platelet lysate, scaffolds, tissue engineering, xeno-free, Platform, Skeletal muscle
Narciso M, Otero J, Navajas D, Farré R, Almendros I, Gavara N, (2021). Image-based method to quantify decellularization of tissue sections International Journal Of Molecular Sciences 22,
Tissue decellularization is typically assessed through absorbance-based DNA quantification after tissue digestion. This method has several disadvantages, namely its destructive nature and inadequacy in experimental situations where tissue is scarce. Here, we present an image processing algorithm for quantitative analysis of DNA content in (de)cellularized tissues as a faster, simpler and more comprehensive alternative. Our method uses local entropy measurements of a phase contrast image to create a mask, which is then applied to corresponding nuclei labelled (UV) images to extract average fluorescence intensities as an estimate of DNA content. The method can be used on native or decellularized tissue to quantify DNA content, thus allowing quantitative assessment of decellularization procedures. We confirm that our new method yields results in line with those obtained using the standard DNA quantification method and that it is successful for both lung and heart tissues. We are also able to accurately obtain a timeline of decreasing DNA content with increased incubation time with a decellularizing agent. Finally, the identified masks can also be applied to additional fluorescence images of immunostained proteins such as collagen or elastin, thus allowing further image-based tissue characterization.
JTD Keywords: decellularization, differentiation, fluorescence image, image processing, microscopic image, Decellularization, Fluorescence image, Image processing, Matrix, Microscopic image, Segmentation
Xu D, Hu J, Pan X, Sánchez S, Yan X, Ma X, (2021). Enzyme-Powered Liquid Metal Nanobots Endowed with Multiple Biomedical Functions Acs Nano 15, 11543-11554
Catalytically powered micro/nanobots (MNBs) can perform active movement by harnessing energy from in situ chemical reactions and show tremendous potential in biomedical applications. However, the development of imageable MNBs that are driven by bioavailable fuels and possess multiple therapeutic functions remains challenging. To resolve such issues, we herein propose enzyme (urease) powered liquid metal (LM) nanobots that are naturally of multiple therapeutic functions and imaging signals. The main body of the nanobot is composed of a biocompatible LM nanoparticle encapsulated by polydopamine (PDA). Urease enzyme needed for the powering and desired drug molecules, e.g., cefixime trihydrate antibiotic, are grafted on external surfaces of the PDA shell. Such a chemical composition endows the nanobots with dual-mode ultrasonic (US) and photoacoustic (PA) imaging signals and favorable photothermal effect. These LM nanobots exhibit positive chemotaxis and therefore can be collectively guided along a concentration gradient of urea for targeted transportation. When exposed to NIR light, the LM nanobots would deform and complete the function change from active drug carriers to photothermal reagents, to achieve synergetic antibacterial treatment by both photothermal and chemotherapeutic effects. The US and PA properties of the LM nanoparticle can be used to not only track and monitor the active movement of the nanobots in a microfluidic vessel model but also visualize their dynamics in the bladder of a living mouse in vivo. To conclude, the LM nanobots demonstrated herein represent a proof-of-concept therapeutic nanosystem with multiple biomedical functionalities, providing a feasible tool for preclinical studies and clinical trials of MNB-based imaging-guided therapy.
JTD Keywords: cell, chemo-photothermal therapy, chemotaxis, image tracking, liquid metal nanobots, nanomotors, tracking, Chemo-photothermal therapy, Chemotaxis, Image tracking, Liquid metal nanobots, Nanomotors
Abramov A, Maiti B, Keridou I, Puiggalí J, Reiser O, Díaz DD, (2021). A pH-Triggered Polymer Degradation or Drug Delivery System by Light-Mediated Cis/Trans Isomerization of o-Hydroxy Cinnamates Macromolecular Rapid Communications 42,
A new methodology for the pH-triggered degradation of polymers or for the release of drugs under visible light irradiation based on the cyclization of ortho-hydroxy-cinnamates (oHC) to coumarins is described. The key oHC structural motif can be readily incorporated into the rational design of novel photocleavable polymers via click chemistry. This main-chain moiety undergoes a fast photocleavage when irradiated with 455 nm light provided that a suitable base is added. A series of polyethylene glycol-alt-ortho-hydroxy cinnamate (polyethylene glycol (PEG)(n)-alt-oHC)-based polymers are synthesized and the time-dependent visible-light initiated cleavage of the photoactive monomer and polymer is investigated in solution by a variety of spectroscopic and chromatographic techniques. The photo-degradation behavior of the water-soluble poly(PEG(2000)-alt-oHC) is investigated within a broad pH range (pH = 2.1-11.8), demonstrating fast degradation at pH 11.8, while the stability of the polymer is greatly enhanced at pH 2.1. Moreover, the neat polymer shows long-term stability under daylight conditions, thus allowing its storage without special precautions. In addition, two water-soluble PEG-based drug-carrier molecules (mPEG(2000)-oHC-benzhydrol/phenol) are synthesized and used for drug delivery studies, monitoring the process by UV-vis spectroscopy in an ON/OFF intermittent manner.
JTD Keywords: coumarins, drug delivery, e/z-double bond isomerization, o-hydroxy cinnamates, polymer degradation, Aliphatic compounds, Antioxidant activity, Antitumor, Chromatographic techniques, Chromatography, Cis/trans isomerization, Controlled drug delivery, Coumarin derivatives, Coumarins, Drug delivery, Drug delivery system, E/z-double bond isomerization, Films, Hydrogels, Image enhancement, Light, Long term stability, O-hydroxy cinnamates, Particles, Photoactive monomers, Photodegradation, Polyethylene glycols, Polyethylenes, Polymer degradation, Responsive polymers, Salts, Structural motifs, Synthesis (chemical), Targeted drug delivery, Visible light photocatalysis, Visible-light irradiation
Vouloutsi, Vasiliki, Mura, Anna, Tauber, F., Speck, T., Prescott, T. J., Verschure, P., (2020). Biomimetic and Biohybrid Systems 9th International Conference, Living Machines 2020, Freiburg, Germany, July 28–30, 2020, Proceedings , Springer, Cham (Lausanne, Switzerland) 12413, 1-428
This book constitutes the proceedings of the )th International Conference on Biomimetic and Biohybrid Systems, Living Machines 2020, held in Freiburg, Germany, in July 2020. Due to COVID-19 pandemic the conference was held virtually. The 32 full and 7 short papers presented in this volume were carefully reviewed and selected from 45 submissions. They deal with research on novel life-like technologies inspired by the scientific investigation of biological systems, biomimetics, and research that seeks to interface biological and artificial systems to create biohybrid systems.
JTD Keywords: Artificial intelligence, Soft robotics, Biomimetics, Insect navigation, Synthetic nervous system, Computer vision, Bio-inspired materials, Visual homing, Locomotion+, Image processing, Intelligent robots, Human-robot interaction, Machine learning, Snake robot, Mobile robots, Robotic systems, Drosophila, Robots, Sensors, Signal processing
Mas, S., Torro, A., Bec, N., Fernández, L., Erschov, G., Gongora, C., Larroque, C., Martineau, P., de Juan, A., Marco, S., (2019). Use of physiological information based on grayscale images to improve mass spectrometry imaging data analysis from biological tissues Analytica Chimica Acta 1074, 69-79
The characterization of cancer tissues by matrix-assisted laser desorption ionization-mass spectrometry images (MALDI-MSI) is of great interest because of the power of MALDI-MS to understand the composition of biological samples and the imaging side that allows for setting spatial boundaries among tissues of different nature based on their compositional differences. In tissue-based cancer research, information on the spatial location of necrotic/tumoral cell populations can be approximately known from grayscale images of the scanned tissue slices. This study proposes as a major novelty the introduction of this physiologically-based information to help in the performance of unmixing methods, oriented to extract the MS signatures and distribution maps of the different tissues present in biological samples. Specifically, the information gathered from grayscale images will be used as a local rank constraint in Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) for the analysis of MALDI-MSI of cancer tissues. The use of this constraint, setting absence of certain kind of tissues only in clear zones of the image, will help to improve the performance of MCR-ALS and to provide a more reliable definition of the chemical MS fingerprint and location of the tissues of interest. The general strategy to address the analysis of MALDI-MSI of cancer tissues will involve the study of the MCR-ALS results and the posterior use of MCR-ALS scores as dimensionality reduction for image segmentation based on K-means clustering. The resolution method will provide the MS signatures and their distribution maps for each tissue in the sample. Then, the resolved distribution maps for each biological component (MCR scores) will be submitted as initial information to K-means clustering for image segmentation to obtain information on the boundaries of the different tissular regions in the samples studied. MCR-ALS prior to K-means not only provides the desired dimensionality reduction, but additionally resolved non-biological signal contributions are not used and the weight given to the different biological components in the segmentation process can be modulated by suitable preprocessing methods.
JTD Keywords: MCR-ALS, K-means, Local rank constraints, MALDI-MSI, Grayscale images
Martinez-Hernandez, Uriel, Vouloutsi, Vasiliki, Mura, Anna, Mangan, Michael, Asada, Minoru, Prescott, T. J., Verschure, P., (2019). Biomimetic and Biohybrid Systems 8th International Conference, Living Machines 2019, Nara, Japan, July 9–12, 2019, Proceedings , Springer, Cham (Lausanne, Switzerland) 11556, 1-384
This book constitutes the proceedings of the 8th International Conference on Biomimetic and Biohybrid Systems, Living Machines 2019, held in Nara, Japan, in July 2019. The 26 full and 16 short papers presented in this volume were carefully reviewed and selected from 45 submissions. They deal with research on novel life-like technologies inspired by the scientific investigation of biological systems, biomimetics, and research that seeks to interface biological and artificial systems to create biohybrid systems.
JTD Keywords: Artificial intelligence, Biomimetics, Computer architecture, Human robot interaction, Human-Computer Interaction (HCI), Humanoid robot, Image processing, Learning algorithms, Mobile robots, Multipurpose robots, Neural networks, Quadruped robots, Reinforcement learning, Robot learning, Robotics, Robots, Sensor, Sensors, Swarm robotics, User interfaces
Alsaleh, S. M., Aviles, A. I., Sobrevilla, P., Casals, A., Hahn, J. K., (2015). Automatic and robust single-camera specular highlight removal in cardiac images Engineering in Medicine and Biology Society (EMBC) 37th Annual International Conference of the IEEE , IEEE (Milan, Italy) , 675-678
In computer-assisted beating heart surgeries, accurate tracking of the heart's motion is of huge importance and there is a continuous need to eliminate any source of error that might disturb the tracking process. One source of error is the specular reflection that appears on the glossy surface of the heart. In this paper, we propose a robust solution for the detection and removal of specular highlights. A hybrid color attributes and wavelet based edge projection approach is applied to accurately identify the affected regions. These regions are then recovered using a dynamic search-based inpainting with adaptive windowing. Experimental results demonstrate the precision and efficiency of the proposed method. Moreover, it has a real-time performance and can be generalized to various other applications.
JTD Keywords: Heart, Image color analysis, Image edge detection, Surgery, Tracking, Wavelet transforms
Aviles, A. I., Sobrevilla, P., Casals, A., (2014). An approach for physiological motion compensation in robotic-assisted cardiac surgery Experimental & Clinical Cardiology , 20, (11), 6713-6724
The lack of physiological motion compensation is a major problem in robotic-assisted cardiac surgery. Since the heart is beating while the surgeon carried out the procedure, dexterity of the surgeon’s and precision are compromised. Due to the operative space and the visibility of the surgical field are reduced, the most practical solution is the use of computer vision techniques. The lack of efficiency and robustness of the existing proposals make physiological motion compensation to be considered an open problem. In this work a novel solution to solve this problem based on the minimization of an energy functional is presented. It is described in the three-dimensional space using the l1−regularized optimization class in which cubic b-splines are used to represent the changes produced on the heart surface. Moreover, the logarithmic barrier function is applied to create an approximation of the total energy in order to avoid its non-differentiability. According to the results, this proposal is able to deal with complex deformations, requires a short computational time and gives a small error.
JTD Keywords: Beating heart surgery, Image analysis, Motion compensation
Dols-Perez, A., Sisquella, X., Fumagalli, L., Gomila, G., (2013). Optical visualization of ultrathin mica flakes on semitransparent gold substrates Nanoscale Research Letters 8, (1), 1-5
We show that optical visualization of ultrathin mica flakes on metallic substrates is viable using semitransparent gold as substrates. This enables to easily localize mica flakes and rapidly estimate their thickness directly on gold substrates by conventional optical reflection microscopy. We experimentally demonstrate it by comparing optical images with atomic force microscopy images of mica flakes on semitransparent gold. Present results open the possibility for simple and rapid characterization of thin mica flakes as well as other thin sheets directly on metallic substrates.
JTD Keywords: Atomic force, Conductive AFM, Gold substrates, Metallic substrate, Optical image, Optical reflection, Optical visualization, Ultrathin layers, Atomic force microscopy, Geometrical optics, Gold, Mica, Optical microscopy, Substrates
Melchels, Ferry P. W., Tonnarelli, Beatrice, Olivares, Andy L., Martin, Ivan, Lacroix, Damien, Feijen, Jan, Wendt, David J., Grijpma, Dirk W., (2011). The influence of the scaffold design on the distribution of adhering cells after perfusion cell seeding Biomaterials 32, (11), 2878-2884
In natural tissues, the extracellular matrix composition, cell density and physiological properties are often non-homogeneous. Here we describe a model system, in which the distribution of cells throughout tissue engineering scaffolds after perfusion seeding can be influenced by the pore architecture of the scaffold. Two scaffold types, both with gyroid pore architectures, were designed and built by stereolithography: one with isotropic pore size (412 ± 13 [mu]m) and porosity (62 ± 1%), and another with a gradient in pore size (250-500 [mu]m) and porosity (35%-85%). Computational fluid flow modelling showed a uniform distribution of flow velocities and wall shear rates (15-24 s-1) for the isotropic architecture, and a gradient in the distribution of flow velocities and wall shear rates (12-38 s-1) for the other architecture. The distribution of cells throughout perfusion-seeded scaffolds was visualised by confocal microscopy. The highest densities of cells correlated with regions of the scaffolds where the pores were larger, and the fluid velocities and wall shear rates were the highest. Under the applied perfusion conditions, cell deposition is mainly determined by local wall shear stress, which, in turn, is strongly influenced by the architecture of the pore network of the scaffold.
JTD Keywords: Scaffolds, Microstructure, Cell adhesion, Confocal microscopy, Image analysis, Computational fluid dynamics
Casamitjana, M., Pérez, M. C., Aranda, J., Montseny, E., Martin, E. X., (2010). Reliable 3D reconstruction extending pixel-level certainty measures IEEE International Conference on Fuzzy 2010 IEEE World Congress on Computational Intelligence , IEEE (Barcelona, Spain) , 1-7
A new method for obtaining a three-dimensional volumetric reconstruction from a set of views improving the classical Shape from Silhouette method (SFS) is presented. SFS approaches can be easily accelerated through hardware and software techniques but they are very sensible to errors arising during calibration and segmentation processes so they present difficulties when dealing with real images. This paper proposes a new algorithm which uses the information about pixel segmentation uncertainty contained in each view in order to get a reliable 3D reconstruction of the scene. Aggregation of the projected uncertainties permits to classify scene's voxels by means of a decision rule but also makes it possible to create a three-dimensional confidence map of the scene. As a consequence, the regions where more information is needed can be foreseen. Sample reconstructions from real image sets are presented and evaluated.
JTD Keywords: Calibration, Image classification, Image reconstruction, Image segmentation, 3D reconstruction, Calibration process, Decision rule, Hardware technique, Pixel segmentation, Pixel-level certainty measures, Scene voxel classification, Segmentation process, Shape from silhouette method, Software technique, Three-dimensional confidence map, Three-dimensional volumetric reconstruction
Muñoz, Luis Miguel, Casals, Alícia, Amat, Josep, Puig-Vidal, Manel, Samitier, Josep, (2005). Improved AFM scanning methodology with adaptation to the target shape C3 - Proceedings - IEEE International Conference on Robotics and Automation ICRA 2005 2005 IEEE International Conference on Robotics and Automation , IEEE (Barcelona, Spain) , 1529-1534
This paper presents a manipulation and measurement aid for tasks carried out in micro-nano environments operating with scanning AFM. In teleoperated manipulation or measurement over a given point of the target, where a slow and precise movement is necessary, the developed system increases the accuracy in this point producing a space deformation. In automatic scanning, the adjusted selection of the target, through assisted image segmentation, enables to reduce the working time.
JTD Keywords: Assisted teleoperation, Image segmentation, Micro-nano manipulation, Workspace deformation