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Data Acceptance for Automated Leukocyte Tracking Through Segmentation of Spatiotemporal Images

N. Ray, S.T. Acton
2005 IEEE Transactions on Biomedical Engineering  
The proposed method first generates a spatiotemporal image from the cell locations given by a tracking method; then, it segments the spatiotemporal image to detect the presence or absence of a leukocyte  ...  In this paper, we propose a validation technique that accepts or rejects the output of automated tracking methods.  ...  Data Acceptance for Automated Leukocyte Tracking Through Segmentation of Spatiotemporal Images Nilanjan Ray, Member, IEEE and Scott T.  ... 
doi:10.1109/tbme.2005.855718 pmid:16235656 fatcat:7o6i7e2exffhpgzcqb4dzd774e

Automated Processing of Zebrafish Imaging Data: A Survey

Ralf Mikut, Thomas Dickmeis, Wolfgang Driever, Pierre Geurts, Fred A. Hamprecht, Bernhard X. Kausler, María J. Ledesma-Carbayo, Raphaël Marée, Karol Mikula, Periklis Pantazis, Olaf Ronneberger, Andres Santos (+3 others)
2013 Zebrafish  
We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection  ...  Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines  ...  Acknowledgments The authors acknowledge all participants of the Satellite Workshop ''Future image processing platforms'' of the 2nd European Zebrafish Principal Investigator Meeting in Karlsruhe, 108  ... 
doi:10.1089/zeb.2013.0886 pmid:23758125 pmcid:PMC3760023 fatcat:k23sufo6dbdpjj6mqaflrfxbni

Integrative analysis of T cell motility from multi-channel microscopy data using TIAM

Viveka Mayya, Willie Neiswanger, Ricardo Medina, Chris H. Wiggins, Michael L. Dustin
2015 JIM - Journal of Immunological Methods  
We have implemented algorithms for detecting, tracking, and analyzing cell motility from multi-channel time-lapse microscopy data.  ...  Cell positions are used to perform local segmentation for extracting features from transmitted light, reflection and fluorescence channels and associating them with cells and cell-tracks to facilitate  ...  We thank Michael Dewar for the initial inspiration to embark on developing TIAM. Assistance of the Light Microscopy Core Facility at the NYU Medical Center is also acknowledged.  ... 
doi:10.1016/j.jim.2014.11.004 pmid:25445324 pmcid:PMC4323926 fatcat:cu7sefccs5dybegmxw2gpkolby

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.  ...  The goal of this review is to illustrate that, when combined with modern imaging platforms and labeling techniques, automated image analysis methods can provide such quantitative information.  ...  Methods for image registration and the automated segmentation of multichannel data are presented in Section 2.  ... 
doi:10.1146/annurev-bioeng-070909-105235 pmid:20482277 fatcat:izhecr6bdzdapmxnnvzhmbpssa

Mapping flow velocity in the human retinal capillary network with pixel intensity cross correlation

Phillip Bedggood, Andrew Metha, Ireneusz Grulkowski
2019 PLoS ONE  
Here we compare measurements derived from PIX to two other state-of-the-art algorithms (particle image velocimetry and the spatiotemporal kymograph), as well as to manually tracked cell data.  ...  The time-shifted pixel which most resembles the reference pixel is deemed to be a 'source' or 'destination' of flow information for that pixel.  ...  Acknowledgments The authors would like to thank students who assisted with image acquisition and manual labelling of cells: Srividya Neriyanuri (PhD candidate), Natalie Kostoski, Sofia Liacopoulos, Moleshri  ... 
doi:10.1371/journal.pone.0218918 pmid:31237930 pmcid:PMC6592569 fatcat:wvxhhe5f35g2jjrpfsntt5mluy

Time‐Lapse Imaging [chapter]

Erik Meijering, Ihor Smal, Oleh Dzyubachyk, Jean‐Christophe Olivo‐Marin
2008 Microscope Image Processing  
and time frames) can be acquired before the specimen is completely photobleached or damaged [49], where "acceptable" means having the minimum SNR required by automated image analysis techniques (discussed  ...  Regardless of the imaging technique used, a careful design of the microscope setup is imperative, as shortcomings may require additional pre-or postprocessing of the resulting image data or, worse, may  ...  , for providing the image data used in this chapter for illustrational purposes.  ... 
doi:10.1016/b978-0-12-372578-3.00015-5 fatcat:vxjehymji5arjocka3k7sw56sm

Snakes on a Plane: A perfect snap for bioimage analysis

Ricard Delgado-Gonzalo, Virginie Uhlmann, Daniel Schmitter, Michael Unser
2015 IEEE Signal Processing Magazine  
The versatile nature of snakes makes them suitable for problems that combine segmentation and tracking (Leukocyte tracking [55] , motility analysis [56] ), organelle tracking (microtubule tracking),  ...  These data often cannot be analyzed manually because the manpower required would be too extensive, which calls for automated methods for the analysis of biomedical images.  ... 
doi:10.1109/msp.2014.2344552 fatcat:lngeqoc2aff6tawege2rx27w5q

Systems microscopy approaches to understand cancer cell migration and metastasis

Sylvia E. Le Dévédec, Kuan Yan, Hans de Bont, Veerander Ghotra, Hoa Truong, Erik H. Danen, Fons Verbeek, Bob van de Water
2010 Cellular and Molecular Life Sciences (CMLS)  
In this review, we provide an overview of recent advanced imaging strategies together with quantitative image analysis that can be implemented to understand the dynamics of matrix adhesions and its molecular  ...  Although these processes are essential for cancer metastasis, little is known about the molecular mechanisms that regulate adhesion dynamics during tumour cell migration.  ...  Acknowledgments The authors would like to thank Leo Price for technical support for the 3D invasion assays.  ... 
doi:10.1007/s00018-010-0419-2 pmid:20556632 pmcid:PMC2933849 fatcat:trma5xtygffmze6jn32zjiz7si

Spatiotemporal Segmentation for Validation of Rolling Leukocyte Tracking Data

N. Ray, S.T. Acton
Proceedings. (ICASSP '05). IEEE International Conference on Acoustics, Speech, and Signal Processing, 2005.  
However, for any automated tracking method to be successful, an automated validation process must exist to accept or reject the output of tracking.  ...  In this paper, we propose an automated validation technique that first generates a spatiotemporal image from the cell locations output by a tracking method; then, it segments the spatiotemporal image to  ...  Since the goal of any automated tracking technique is to avoid the manual data collection, the automated tracker outputs must be validated as a part of an automated data acceptance process in the absence  ... 
doi:10.1109/icassp.2005.1415358 dblp:conf/icassp/RayA05 fatcat:6ayy23zjdbgezaz3wlfh64ulg4

CellGeo: A computational platform for the analysis of shape changes in cells with complex geometries

Denis Tsygankov, Colleen G. Bilancia, Eric A. Vitriol, Klaus M. Hahn, Mark Peifer, Timothy C. Elston
2014 Journal of Cell Biology  
444 445 Computational analysis of cell shape with CellGeo • Tsygankov et al.  ...  Tsygankov), and National Institutes of Health F31 fellowship 5F31NS062487 (E.A. Vitriol). The authors declare no competing financial interests. Submitted: 12 June 2013 Accepted: 10 December 2013  ...  This work was supported by grants from National Institutes of Health R01 GM47857 (M. Peifer), R01 GM057464 (K.M.  ... 
doi:10.1083/jcb.201306067 pmid:24493591 pmcid:PMC3912527 fatcat:5ribaze4tbeqjlrhnw2zhbcz5u

Visualizing pyrazinamide action by live single cell imaging of phagosome acidification and Mycobacterium tuberculosis pH homeostasis [article]

Pierre Santucci, Beren Aylan, Laure Botella, Elliott M Bernard, Claudio Bussi, Enrica Pellegrino, Natalia Athanasiadi, Maximiliano G Gutierrez
2021 bioRxiv   pre-print
By using Mtb mutants, we confirmed that intracellular acidification is a prerequisite for PZA efficacy in cellulo.  ...  Here, we describe a live dual-imaging approach to monitor host subcellular acidification and Mtb intrabacterial pH.  ...  For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.  ... 
doi:10.1101/2021.12.20.473466 fatcat:s7asqxx5pjfbdnt6eris2e33ou

F-actin bundles direct the initiation and orientation of lamellipodia through adhesion-based signaling

Heath E. Johnson, Samantha J. King, Sreeja B. Asokan, Jeremy D. Rotty, James E. Bear, Jason M. Haugh
2015 Journal of Cell Biology  
Ratiometric imaging reveals that F-actin bundles/filopodia play both structural and signaling roles, as they prime the activation of PI3K signaling mediated by integrins and focal adhesion kinase.  ...  internal reflection fluorescence microscopy to monitor cytoskeletal and signaling dynamics in migrating cells, we show that peripheral F-actin bundles/filopodia containing fascin-1 serve as templates for  ...  Haugh) and National Institutes of Health grant GM083035 (J.E. Bear). The authors declare no competing financial interests. Submitted: 24 June 2014 Accepted: 3 January 2015  ... 
doi:10.1083/jcb.201406102 pmid:25666809 pmcid:PMC4332254 fatcat:v6s6bbhwevd7hjnxj3sfuu3ege

Image-based characterization of thrombus formation in time-lapse DIC microscopy

Nicolas Brieu, Nassir Navab, Jovana Serbanovic-Canic, Willem H. Ouwehand, Derek L. Stemple, Ana Cvejic, Martin Groher
2012 Medical Image Analysis  
Two approaches are introduced for the segmentation of dynamic textures.  ...  Our key idea is to perform segmentation of the thrombus by distinguishing different motion patterns in image time-series rather than by performing a standard image segmentation task in each frame.  ...  Tracking in Microscopy Images In time-lapse data, tracking replaces the aforementioned segmentation problem.  ... 
doi:10.1016/ pmid:22482997 pmcid:PMC3740235 fatcat:dvg3ync4ejg5deeofot6mhs5hy

Vascular surveillance by haptotactic blood platelets in inflammation and infection

Leo Nicolai, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, Charlotte Marx, Andreas Ehrlich, Joachim Pircher, Zhe Zhang, Inas Saleh (+18 others)
2020 Nature Communications  
Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand  ...  Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation.  ...  Acknowledgements We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical discussions  ... 
doi:10.1038/s41467-020-19515-0 pmid:33188196 pmcid:PMC7666582 fatcat:ockmn54hb5bcrhkphnnj2tqtl4

Integrin-dependent actomyosin contraction regulates epithelial cell scattering

Johan de Rooij, Andre Kerstens, Gaudenz Danuser, Martin A. Schwartz, Clare M. Waterman-Storer
2005 Journal of Cell Biology  
Time-lapse imaging T suggests that tension on cell-cell junctions may disrupt cell-cell adhesion.  ...  he scattering of Madin-Darby canine kidney cells in vitro mimics key aspects of epithelial-mesenchymal transitions during development, carcinoma cell invasion, and metastasis.  ...  for extensive help with image acquisition and processing; Michael Adams for technical assistance with respect to microscopes; and the Waterman laboratory members for helpful discussion.  ... 
doi:10.1083/jcb.200506152 pmid:16216928 pmcid:PMC2171213 fatcat:tui2azedsvdnhigz76sypztgse
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