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Pattern recognition tools for proteomics

Virginio Cantoni
2014 The European Physical Journal Plus  
The first step is the segmentation, performed by classical operators of mathematical morphology, of the protein "solvent-excluded surface" in concavity and convexity regions.  ...  protein representation and morphological analysis.  ...  The first step is the segmentation, performed by classical operators of mathematical morphology, of the protein "solvent-excluded surface" in concavity and convexity regions.  ... 
doi:10.1140/epjp/i2014-14130-3 fatcat:sddaw3sbo5eb7mkkib6o23hpge

Multidisciplinary bioimaging approach to study plant morphogenesis

Saiko Yoshida, Sören Strauss, Milad Adibi
2021 PLANT MORPHOLOGY  
We mainly focus on protocols for imaging plant structures by confocal laser scanning microscopes, followed by quantitative analysis based on 3D segmentation of cells layers/tissues, and computational modelling  ...  Morphology of plants is controlled by coordinated patterns of cell division and growth.  ...  Analyses of (A) cell volume, (B) cell surface area, (C, D) division wall on a 3D meshes and (E) visualization of corner localized protein by MorphoGraphX In A and B, cell volumes or cell surface areas  ... 
doi:10.5685/plmorphol.33.15 fatcat:zgvsojo2m5ffbapzaerg7onviq

Quantifying Modes of 3D Cell Migration

Meghan K. Driscoll, Gaudenz Danuser
2015 Trends in Cell Biology  
Since cell migration is a dynamic process, it is usually studied via microscopy, but 3D movies of 3D processes are difficult to interpret by visual inspection.  ...  environments in vivo, we are only now beginning to use experimental workflows that yield images with sufficient spatiotemporal resolution to study the molecular processes governing cell migration in 3D  ...  Figure 3 .Trends 3 Computer science and mathematics of 3D cell morphology. (A) Part of the surface of a primary melanoma cell represented as a triangle mesh.  ... 
doi:10.1016/j.tcb.2015.09.010 pmid:26603943 pmcid:PMC4663125 fatcat:kx5jit4fgraevjhfiskhxtahiy

A univocal definition of the neuronal soma morphology using Gaussian mixture models

Sergio Luengo-Sanchez, Concha Bielza, Ruth Benavides-Piccione, Isabel Fernaud-Espinosa, Javier DeFelipe, Pedro Larrañaga
2015 Frontiers in Neuroanatomy  
In this paper, we provide a mathematical definition and an automatic segmentation method to delimit the neuronal soma.  ...  We concluded that there were no significant differences between automatically and manually segmented somata, i.e., the proposed procedure segments the neurons similarly to how a neuroanatomist does.  ...  Brain Project initiative from EPFL); Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED, CB06/05/0066, Spain); TIN2013-41592-P projects, by the Regional Government of Madrid through  ... 
doi:10.3389/fnana.2015.00137 pmid:26578898 pmcid:PMC4630289 fatcat:utw3lqnyqrel7izi7knu3s6gni

Correlative 3D Imaging and Microfluidic Modelling of Human Pulmonary Lymphatics using Immunohistochemistry and High-resolution μCT

Stephanie K. Robinson, Jonathan J. Ramsden, Jane Warner, Peter M. Lackie, Tiina Roose
2019 Scientific Reports  
Image-based 3D mathematical modelling of pulmonary lymphatic microfluidics has been limited by the lack of accurate and representative image geometries.  ...  mathematical modelling of human lung microfluidics at micrometre resolution.  ...  Data Availability All connected data to this manuscript will be made available through the following DOI (https://doi.org/10.5258/ SOTON/D0310).  ... 
doi:10.1038/s41598-019-42794-7 pmid:31015547 pmcid:PMC6478691 fatcat:nal5jpojwfh6nktyqtyvs4he3e

An automatically initialized level-set approach for the segmentation of proteomics images

Michalis A. Savelonas, Eleftheria A. Mylona, Dimitris Maroulis
2011 2011 10th International Workshop on Biomedical Engineering  
The proposed initialization process is based on the formation of a level-set surface of multiple cones, which are centered at regional intensity maxima positions, associated with protein spots.  ...  Level-set methods are natural candidates for this segmentation task, since their topological adaptability is a prerequisite to identify the boundaries of thousands of protein spots present.  ...  Aivaliotis for the provision of segmentation results obtained by the application of PDQuest 8.0.1 and Delta 2D image analysis software packages on real proteomics images respectively.  ... 
doi:10.1109/iwbe.2011.6079033 fatcat:oh7odp4ja5b6bguza3lypwem2e

Quantification and its Applications in Fluorescent Microscopy Imaging

Nicholas Hamilton
2009 Traffic : the International Journal of Intracellular Transport  
Further, 2D and 3D video microscopy are giving important insights into the dynamics of protein localization and transport.  ...  Here we outline and give entry points to the literature on approaches to quantification such as segmentation, tracking, automated classification and data visualization.  ...  Using segmentation techniques such as gradient flows and coupled active surfaces nuclei may readily be segmented and quantified from 3D fluorescent imaging (15, 16) .  ... 
doi:10.1111/j.1600-0854.2009.00938.x pmid:19500318 fatcat:jg63yjjtone5tj7fe6aorjb7dm

Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis

Ville Härmä, Hannu-Pekka Schukov, Antti Happonen, Ilmari Ahonen, Johannes Virtanen, Harri Siitari, Malin Åkerfelt, Jyrki Lötjönen, Matthias Nees, Olivier de Wever
2014 PLoS ONE  
The spectrum of different multicellular morphologies formed in 3D is a sensitive indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression  ...  indirect modulators of the actin cytoskeleton which induce systematic changes in spheroid morphology and differentiation versus invasion.  ...  Morphologies formed in 3D vary in shape, size, geometry, density, surface features, and internal textures.  ... 
doi:10.1371/journal.pone.0096426 pmid:24810913 pmcid:PMC4014501 fatcat:xfubpehmkfaibnmkmymybyubia

High resolution 3-Dimensional imaging of the human cardiac conduction system from microanatomy to mathematical modeling

Robert S. Stephenson, Andrew Atkinson, Petros Kottas, Filip Perde, Fatemeh Jafarzadeh, Mike Bateman, Paul A. Iaizzo, Jichao Zhao, Henggui Zhang, Robert H. Anderson, Jonathan C. Jarvis, Halina Dobrzynski
2017 Scientific Reports  
Although experimental data exist on the remodelling of the conduction system in disease at a cellular and protein level 52 , little is known on how the 3D morphology is affected.  ...  It shows the 3D extent and location of the segmented atrioventricular conduction axis across the upper surface of the interventricular septum (e).  ... 
doi:10.1038/s41598-017-07694-8 pmid:28775383 pmcid:PMC5543124 fatcat:6qho27y7a5a5fob3syhakopv6q

Molecular Image Analysis: Quantitative Description and Classification of the Nuclear Lamina in Human Mesenchymal Stem Cells

Christiaan H. Righolt, Vered Raz, Bart J. Vermolen, Roeland W. Dirks, Hans J. Tanke, Ian T. Young
2011 International Journal of Molecular Imaging  
We have developed an image processing methodology that finds and quantifies the 3D structure of the nuclear lamina.  ...  We show that measurements on such images can be used for cell classification and provide information concerning protein spatial localization in this structure.  ...  These curvatures provide a mathematical description of the way the surface bends.  ... 
doi:10.1155/2011/723283 pmid:21490732 pmcid:PMC3065845 fatcat:5jahnl4jsnfldbur4up2ochv4m

Three-Dimensional Image Quantification as a New Morphometry Method for Tissue Engineering

Julie A. Rytlewski, Laura R. Geuss, Chinedu I. Anyaeji, Evan W. Lewis, Laura J. Suggs
2012 Tissue Engineering. Part C, Methods  
The quantification method is based on collecting and segmenting fluorescent confocal z-stacks into 3D models with 3D Slicer, an open-source magnetic resonance imaging/computed tomography analysis program  ...  Additionally, the statistical outcomes of 3D morphological quantification agreed with our initial qualitative observations among different test groups.  ...  Fibrinogen from human plasma (50%-70% protein, ‡ 80% clottable), thrombin from human plasma ( ‡ 1,000NIH units/mg protein), collagen-coated Sigma-Solohill MCBs, and 37% formaldehyde were obtained from  ... 
doi:10.1089/ten.tec.2011.0417 pmid:22224751 pmcid:PMC3381293 fatcat:wbsj67j3lzauhgb5vbfnzrui6u

Characterization of Biological Processes through Automated Image Analysis

Jens Rittscher
2010 Annual Review of Biomedical Engineering  
The text includes a review of image registration and image segmentation methods, as well as algorithms that enable the analysis of cellular architecture, cell morphology, and tissue organization.  ...  (94) improved segmentation performance by formulating the segmentation problem as a quest to find a deformable cutting surface, which is defined in a 3D mesh.  ...  They propose to design specific segmentation algorithms for each of these object morphologies. By extending the idea of watershed segmentation into 3D, Lin et al.  ... 
doi:10.1146/annurev-bioeng-070909-105235 pmid:20482277 fatcat:izhecr6bdzdapmxnnvzhmbpssa

Non-invasive single-cell morphometry in living bacterial biofilms

Mingxing Zhang, Ji Zhang, Yibo Wang, Jie Wang, Alecia M. Achimovich, Scott T. Acton, Andreas Gahlmann
2020 Nature Communications  
In this work, we present Bacterial Cell Morphometry 3D (BCM3D), an image analysis workflow that combines deep learning with mathematical image analysis to accurately segment and classify single bacterial  ...  cells in 3D fluorescence images.  ...  based on the cell arrangements in a. c XY slice through the 3D simulated fluorescence image in b (upper panel shows cells expressing cytosolic fluorescent proteins, lower panel shows cells stained with  ... 
doi:10.1038/s41467-020-19866-8 pmid:33262347 fatcat:ph54slrhojezjccpizcnw7p4uu

A computational image analysis glossary for biologists

A. H. K. Roeder, A. Cunha, M. C. Burl, E. M. Meyerowitz
2012 Development  
Watershed A method developed within mathematical morphology to allow for segmentation of grayscale images.  ...  Based on the corners selected, surfaces are drawn through the cube.  ... 
doi:10.1242/dev.076414 pmid:22872081 fatcat:kl7qwh5ojfflvejlfuevmzgwvy

Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments

Erik S. Welf, Meghan K. Driscoll, Kevin M. Dean, Claudia Schäfer, Jun Chu, Michael W. Davidson, Michael Z. Lin, Gaudenz Danuser, Reto Fiolka
2016 Developmental Cell  
We leverage the nearly isotropic resolution of meSPIM to quantify the local concentration of actin and phosphatidylinositol 3-kinase signaling on the surfaces of cells deep within 3D collagen matrices  ...  Highlights d meSPIM allows microenvironmentally conscious 3D imaging/ analysis of subcellular biology d Precisely controlled microenvironments reveal diverse morphological phenotypes d Isotropic resolution  ...  Effects of 2D and 3D Microenvironments on Cell Morphology It is well documented that cells behave very differently in 3D microenvironments than on 2D surfaces, and even embedded within a 3D matrix, cells  ... 
doi:10.1016/j.devcel.2016.01.022 pmid:26906741 pmcid:PMC4784259 fatcat:vanrgow56vfhbhpe6pv4hsctj4
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