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On the digital trail of mobile cells

C. Zimmer, Bo Zhang, A. Dufour, A. Thebaud, S. Berlemont, V. Meas-Yedid, J.-C.O. Marin
<span title="">2006</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/txj4mzfpbne4hhwgo2ku5cycbq" style="color: black;">IEEE Signal Processing Magazine</a> </i> &nbsp;
In this article, we first provide a brief background on the importance of understanding cell movements, then review a selection of current efforts on tracking moving cells, with an emphasis on deformable  ...  Signal processing approaches can contribute significantly to this research, most notably to help analyze the exploding quantity of imaging data produced with standard and new microscopy techniques.  ...  A fully 3-D alternative are active surfaces, as used in [1] , [12] , and [27] to segment cells in 3-D fluorescence microscopy.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/msp.2006.1628878">doi:10.1109/msp.2006.1628878</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tsfrcalgcnaq3lhygz7nyddsmq">fatcat:tsfrcalgcnaq3lhygz7nyddsmq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100415065358/http://www.bioimageanalysis.org:80/publications/zimmer2006j.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fc/8c/fc8cb7c3e29c136e636879c5d6c52133978b83ae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/msp.2006.1628878"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Quantitative Imaging of Pre-mRNA Splicing Factors in Living Cells

Roland Eils, Daniel Gerlich, Wolfgang Tvaruskó, David L. Spector, Tom Misteli, Jennifer Lippincott-Schwartz
<span title="">2000</span> <i title="American Society for Cell Biology (ASCB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/btmjitlxs5by3dntmzk67gakxi" style="color: black;">Molecular Biology of the Cell</a> </i> &nbsp;
Part of this work was performed in collaboration with TILL Photonics. This work was further supported by BMBF grant 01 KW 9621 and Deutsche Forschungsgemeinschaft grant Ja 395/6-2.  ...  The bioinformatics group acknowledges the support by the Federal Ministry of Education, Science, Research and Technology (BMBF) through BioFuture grant AZ 11880.  ...  (D) Detail from C. Live Cell Analysis of Splicing Factors Vol. 11, February 2000 Figure 3 . 3 Quantification and visualization of surface dynamics for speckles in transcriptionally inactive cells.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1091/mbc.11.2.413">doi:10.1091/mbc.11.2.413</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10679003">pmid:10679003</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC14782/">pmcid:PMC14782</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/24tvzpv2tbcnpmoknqjmzhinqa">fatcat:24tvzpv2tbcnpmoknqjmzhinqa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171121213140/https://core.ac.uk/download/pdf/33023274.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e2/da/e2dafc88a853e78c5e85372f5c14924e2865636e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1091/mbc.11.2.413"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC14782" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Quantitative in vivo microscopy: the return from the 'omics'

Rodrigo Fernández-González, Arrate Muñoz–Barrutia, Mary Helen Barcellos-Hoff, Carlos Ortiz-de-Solorzano
<span title="">2006</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/leca7sevx5fbxol36lihhcvvce" style="color: black;">Current Opinion in Biotechnology</a> </i> &nbsp;
Acknowledgements References and recommended reading  ...  [61 ] describe an intelligent algorithmic integration of segmentation and tracking consisting of a full four-dimensional segmentation plus tracking algorithm that uses active contours to detect cells  ...  Once the cells and/or elements of interest have been correctly segmented, cell or organelle dynamics can be measured using algorithmic tracking.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2006.07.005">doi:10.1016/j.copbio.2006.07.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16899361">pmid:16899361</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/udtfndozfjhlvccn77urqh4hgy">fatcat:udtfndozfjhlvccn77urqh4hgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20140616095823/http://www.via.cornell.edu/courses/ece578/project/2014/g2/paper14.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b7/7e/b77e78355071e6cb2c9bddc17659074f5aeb2451.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.copbio.2006.07.005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton

I-Hsuan Wang, Christoph Burckhardt, Artur Yakimovich, Urs Greber
<span title="2018-03-31">2018</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ockrmqzwdnfq3b4pukv44pnfgu" style="color: black;">Viruses</a> </i> &nbsp;
We discuss the methodology enabling researchers to visualize single virions in cells by fluorescence imaging and tracking.  ...  We tdiscuss the methodology enabling researchers to visualize single virions in cells by fluorescence imaging and tracking.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Conflicts of Interest: The authors declare no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/v10040166">doi:10.3390/v10040166</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29614729">pmid:29614729</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5923460/">pmcid:PMC5923460</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/su7pqpusjrbo7jbkulouce5md4">fatcat:su7pqpusjrbo7jbkulouce5md4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719042617/http://www.zora.uzh.ch/id/eprint/150940/8/viruses-10-00166.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d9/6b/d96b54da4f12a6c4ce770197725462abc60203b5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/v10040166"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5923460" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Plasma membrane LAT activation precedes vesicular recruitment defining two phases of early T-cell activation

Lakshmi Balagopalan, Jason Yi, Tiffany Nguyen, Katherine M. McIntire, Adam S. Harned, Kedar Narayan, Lawrence E. Samelson
<span title="2018-05-22">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
We propose a model in which cell surface LAT is recruited rapidly and phosphorylated at sites of T-cell activation, while the vesicular pool is subsequently recruited and dynamically interacts with microclusters  ...  Here, we show the sequence of events in LAT microcluster formation and vesicle delivery, using lattice light sheet microscopy to image a T cell from the earliest point of activation.  ...  This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. HHSN261200800001E.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-018-04419-x">doi:10.1038/s41467-018-04419-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29789604">pmid:29789604</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5964120/">pmcid:PMC5964120</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rbnmiuabtradrbzvmgvz7lr6ca">fatcat:rbnmiuabtradrbzvmgvz7lr6ca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208130623/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5964120&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7f/3c/7f3c55b9002cdc1cadef169cba8598b0797ddb6b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-018-04419-x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964120" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Real-time analysis of T cell receptors in naive cells in vitro and in vivo reveals flexibility in synapse and signaling dynamics

Rachel S. Friedman, Peter Beemiller, Caitlin M. Sorensen, Jordan Jacobelli, Matthew F. Krummel
<span title="2010-11-15">2010</span> <i title="Rockefeller University Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ye43mmowdfaidn3yibreupuvq4" style="color: black;">Journal of Cell Biology</a> </i> &nbsp;
Figure 3 . 3 Quantification of OT-I-GFP T cell surface TCR fluorescence in vivo.  ...  (c) Surface volume rendering of an OT-I-GFP cell segmented using the active contour algorithm. (d) Quantification of green fluorescence of OT-I-GFP cells masked on the cell surface voxels.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1083/jcb1914oia9">doi:10.1083/jcb1914oia9</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nseucmmwqjb7zio2nndqlw7key">fatcat:nseucmmwqjb7zio2nndqlw7key</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201108004240/https://escholarship.org/content/qt0kq7c181/qt0kq7c181.pdf?t=qag2ng" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cc/5d/cc5d4242762a6f7b8b438f6d555ffc3827e5245d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1083/jcb1914oia9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Directional Persistence of Cell Migration Coincides with Stability of Asymmetric Intracellular Signaling

Michael C. Weiger, Shoeb Ahmed, Erik S. Welf, Jason M. Haugh
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
In this analysis of phosphoinositide 3-kinase signaling in randomly migrating fibroblasts, we observe that hot spots of intense signaling coincide with localized cell protrusion and endure with characteristic  ...  We further show that distant hot spots are dynamically and stochastically coupled.  ...  live-cell fluorescence microscopy, and how the dynamics of hot spots and other important features of the signaling pattern might be related to local changes in cell motility.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2009.09.051">doi:10.1016/j.bpj.2009.09.051</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20085720">pmid:20085720</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2800965/">pmcid:PMC2800965</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7zmzufvdyjarhfr7qwynx53k7y">fatcat:7zmzufvdyjarhfr7qwynx53k7y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305123022/https://core.ac.uk/download/pdf/81121107.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2c/52/2c529dfc0037af0873335df2c6293933823c4f73.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2009.09.051"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800965" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Visualizing Calcium Flux in Freely Moving Nematode Embryos

Evan L. Ardiel, Abhishek Kumar, Joseph Marbach, Ryan Christensen, Rishi Gupta, William Duncan, Jonathan S. Daniels, Nico Stuurman, Daniel Colón-Ramos, Hari Shroff
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Using light-sheet fluorescence microscopy to address the challenges associated with functional imaging at this developmental stage, we recorded calcium dynamics in muscles and neurons and developed analysis  ...  To identify neuronal correlates of behavior, we monitored brainwide activity with subcellular resolution and identified a particularly active cell associated with muscle contractions.  ...  ACKNOWLEDGMENTS We thank Applied Scientific Instrumentation for lending us a diSPIM frame, Mark Reinhardt and PCO for lending us scientific CMOS cameras, and Lynne Chang and Nikon for lending us objectives  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2017.02.035">doi:10.1016/j.bpj.2017.02.035</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28494967">pmid:28494967</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5425378/">pmcid:PMC5425378</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jf7apf7q2zfcrpgce7d2bkgfhe">fatcat:jf7apf7q2zfcrpgce7d2bkgfhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191027042255/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5425378&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/09/c0/09c010693c277e329b9c984ec9f9141f35641a76.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2017.02.035"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425378" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identification and super-resolution imaging of ligand-activated receptor dimers in live cells

Pascale Winckler, Lydia Lartigue, Gregory Giannone, Francesca De Giorgi, François Ichas, Jean-Baptiste Sibarita, Brahim Lounis, Laurent Cognet
<span title="2013-08-08">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
The nanometric dimensions and the dynamic nature of the interactions make their investigations complex in live cells.  ...  While super-resolution fluorescence microscopies offer live-cell molecular imaging with sub-wavelength resolutions, they lack specificity for distinguishing interacting molecule populations.  ...  Single molecule fluorescent spots were localized in each image frame and tracked over time using a combination of wavelet segmentation 36 and simulated annealing algorithms 37, 38 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep02387">doi:10.1038/srep02387</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23925048">pmid:23925048</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3737505/">pmcid:PMC3737505</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kkvhkn32z5bgxdcucnipvyx3ee">fatcat:kkvhkn32z5bgxdcucnipvyx3ee</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223113824/http://pdfs.semanticscholar.org/4ee0/310baeb71b9b8b1c5e69f9ca98de7cf672e2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4e/e0/4ee0310baeb71b9b8b1c5e69f9ca98de7cf672e2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep02387"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737505" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Extracting neuronal activity signals from microscopy recordings of contractile tissue: a cell tracking approach using B-spline Explicit Active Surfaces (BEAS) [article]

Youcef Kazwiny, Joao M. Pedroso, Zhiqing Zhang, Werend Boesmans, Jan D'hooge, Pieter Vanden Berghe
<span title="2020-12-15">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Ca 2+ imaging is a widely used microscopy technique to simultaneously study cellular activity in multiple cells.  ...  The desired information consists of cell-specific time series of pixel intensity values, in which the fluorescence intensity represents cellular activity.  ...  Acknowledgements 448 The authors thank Tobie Martens for manual cell delineation and ROI selection on Ca 2+ recordings.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.12.15.422837">doi:10.1101/2020.12.15.422837</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ynby4ivxtzebhl4nka2nnis63i">fatcat:ynby4ivxtzebhl4nka2nnis63i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429033954/https://www.biorxiv.org/content/biorxiv/early/2020/12/15/2020.12.15.422837.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c2/17/c217b831e16b7a7a5e5510d32cfe795f2066f7e6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.12.15.422837"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Longitudinal label-free tracking of cell death dynamics in living engineered human skin tissue with a multimodal microscope

Youbo Zhao, Marina Marjanovic, Eric J. Chaney, Benedikt W. Graf, Ziad Mahmassani, Marni D. Boppart, Stephen A. Boppart
<span title="2014-09-19">2014</span> <i title="The Optical Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fxa4hwkh5vf4nejqcsg3pblm5u" style="color: black;">Biomedical Optics Express</a> </i> &nbsp;
We demonstrate real-time, longitudinal, label-free tracking of apoptotic and necrotic cells in living tissue using a multimodal microscope.  ...  The integrated imaging platform combines multi-photon microscopy (MPM, based on two-photon excitation fluorescence), optical coherence microscopy (OCM), and fluorescence lifetime imaging microscopy (FLIM  ...  We also thank Matek, Inc. for their technical assistance with the engineered human skin equivalents used in this study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1364/boe.5.003699">doi:10.1364/boe.5.003699</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25360383">pmid:25360383</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4206335/">pmcid:PMC4206335</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6ezysf6biva3rpvajg2r5ncfya">fatcat:6ezysf6biva3rpvajg2r5ncfya</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200207171416/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4206335&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/51/9d/519dec25822b3323d4264cd63faf75e1a4fd6e28.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1364/boe.5.003699"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4206335" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Real-time analysis of T cell receptors in naive cells in vitro and in vivo reveals flexibility in synapse and signaling dynamics

Rachel S. Friedman, Peter Beemiller, Caitlin M. Sorensen, Jordan Jacobelli, Matthew F. Krummel
<span title="2010-11-01">2010</span> <i title="Rockefeller University Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hlxgij3xe5gajfxq2e74j7itlu" style="color: black;">Journal of Experimental Medicine</a> </i> &nbsp;
These in vivo observations demonstrate that varied TCR trafficking and cell arrest dynamics occur during early T cell activation.  ...  To enable imaging of TCR dynamics in naive T cells in the lymph node, we enhanced signal detection of the fluorescent TCR fusion protein and used volumetric masking with a second fluorophore to mark the  ...  (c) Surface volume rendering of an OT-I-GFP cell segmented using the active contour algorithm. (d) Quantification of green fluorescence of OT-I-GFP cells masked on the cell surface voxels. .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1084/jem.20091201">doi:10.1084/jem.20091201</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21041455">pmid:21041455</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2989766/">pmcid:PMC2989766</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7kfjhyfwinf53fy5nxdtl37wkq">fatcat:7kfjhyfwinf53fy5nxdtl37wkq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224151927/http://pdfs.semanticscholar.org/59db/c9b7bc55a51ea90fe90c8a20f735f2df7f1e.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/59/db/59dbc9b7bc55a51ea90fe90c8a20f735f2df7f1e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1084/jem.20091201"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989766" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Quantification and its Applications in Fluorescent Microscopy Imaging

Nicholas Hamilton
<span title="">2009</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/236hwyqxjnai3lw6lzbpgsalpq" style="color: black;">Traffic : the International Journal of Intracellular Transport</a> </i> &nbsp;
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.  ...  Acknowledgments The author would like to thank Dr Rohan D. Teasdale (UQ) and Dr Markus C. Kerr (UQ) for their help in the editing and preparation of this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1600-0854.2009.00938.x">doi:10.1111/j.1600-0854.2009.00938.x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19500318">pmid:19500318</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jg63yjjtone5tj7fe6aorjb7dm">fatcat:jg63yjjtone5tj7fe6aorjb7dm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190607005308/https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-0854.2009.00938.x" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b6/31/b631205fc7feb5a1079f500adc9b94d8595cc47d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1600-0854.2009.00938.x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Live imaging of root–bacteria interactions in a microfluidics setup

Hassan Massalha, Elisa Korenblum, Sergey Malitsky, Orr H. Shapiro, Asaph Aharoni
<span title="2017-03-27">2017</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
Using dual inoculation experiments, we further show active exclusion of Escherichia coli cells from the root surface after B. subtilis colonization, suggesting a possible protection mechanism against root  ...  Nevertheless, current approaches for studying root-bacteria interactions are limited in their capacity to track changes in bacterial colonization of the root surface over space and time and even more to  ...  Benfey for cell layer reporters and the root mutants. We also thank the Adelis Foundation, the Leona M. and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1618584114">doi:10.1073/pnas.1618584114</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28348235">pmid:28348235</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5410799/">pmcid:PMC5410799</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/66mmpkpqabh4fmegjjymk4jvk4">fatcat:66mmpkpqabh4fmegjjymk4jvk4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219204434/http://pdfs.semanticscholar.org/1a6b/fd37cb5921a70189e1c26603dfc22172ed16.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1a/6b/1a6bfd37cb5921a70189e1c26603dfc22172ed16.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1618584114"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5410799" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Characterization of Proprioceptive System Dynamics in Behaving Drosophila Larvae Using High-Speed Volumetric Microscopy

Rebecca D. Vaadia, Wenze Li, Venkatakaushik Voleti, Aditi Singhania, Elizabeth M.C. Hillman, Wesley B. Grueber
<span title="2019-03-07">2019</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/waxwzq3cnbet3cmwccpuk4bel4" style="color: black;">Current Biology</a> </i> &nbsp;
This sequential activity was related to the dynamics of each neuron's terminal processes, and could endow each proprioceptor with a specific role in monitoring different aspects of body-wall deformation  ...  Here we used high-speed volumetric swept confocally aligned planar excitation (SCAPE) microscopy in crawling Drosophila larvae to simultaneously track the position, deformation, and intracellular calcium  ...  Calculating segment and dendrite dynamics-To relate calcium dynamics to segmental contraction and extension phases, changes in inter-cell distances were calculated from the tracked cell coordinates -defined  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cub.2019.01.060">doi:10.1016/j.cub.2019.01.060</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30853438">pmid:30853438</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6624193/">pmcid:PMC6624193</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u5res5d22fedvpxjmjhm5ijthe">fatcat:u5res5d22fedvpxjmjhm5ijthe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200330085901/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6624193&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cub.2019.01.060"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624193" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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