scholarly journals Development of a lab bioimage informatics system for fluorescence microscopy data, with application to experimental studies of RhoGAP regulation of calcium signaling and actomyosin contractility

2019 ◽  
Author(s):  
Jeffrey Alan Bouffard
Keyword(s):  
Fluorescence Microscopy ◽  
Calcium Signaling ◽  
Experimental Studies ◽  
Bioimage Informatics ◽  
Informatics System ◽  
Actomyosin Contractility ◽  
Microscopy Data

Systematic Analysis of Jurkat T-Cell Deformation in Fluorescence Microscopy Data

2017 ◽  
pp. 275-280 ◽  
Author(s):  
Sven-Thomas Antoni ◽  
Omar M. F. Ismail ◽  
Daniel Schetelig ◽  
Björn-Philipp Diercks ◽  
René Werner ◽  
...  
Keyword(s):  
T Cell ◽  
Fluorescence Microscopy ◽  
Cell Deformation ◽  
Systematic Analysis ◽  
Jurkat T Cell ◽  
Microscopy Data

scholarly journals Live cell imaging of macrophage/bacterium interaction demonstrates cell lysis induced by Corynebacterium diphtheriae and Corynebacterium ulcerans

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Dulanthi Weerasekera ◽  
Jonas Hahn ◽  
Martin Herrmann ◽  
Andreas Burkovski
Keyword(s):  
Fluorescence Microscopy ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Time Lapse ◽  
Corynebacterium Diphtheriae ◽  
Live Cell ◽  
Human Macrophage ◽  
Data Description ◽  
Corynebacterium Ulcerans ◽  
Microscopy Data

Abstract Objectives In frame of a study to characterize the interaction of human macrophage-like cells with pathogenic corynebacteria, Corynebacterium diphtheriae and Corynebacterium ulcerans, live cell imaging experiments were carried out and time lapse fluorescence microscopy videos were generated, which are presented here. Data description The time lapse fluorescence microscopy data revealed new insights in the interaction of corynebacteria with human macrophage-like THP-1 cells. In contrast to uninfected cells and infections with non-pathogenic C. glutamicum used as a control, pathogenic C. diphtheriae and C. ulcerans showed highly detrimental effects towards human cells and induction of cell death of macrophages.

scholarly journals Deciphering tissue morphodynamics using bioimage informatics

2017 ◽  
Vol 372 (1720) ◽  
pp. 20150512 ◽  
Author(s):  
Alexandre C. Dufour ◽  
Anneliene H. Jonker ◽  
Jean-Christophe Olivo-Marin
Keyword(s):  
Developmental Biology ◽  
Image Analysis ◽  
Fluorescence Microscopy ◽  
Automated Analysis ◽  
Tissue Level ◽  
Bioimage Informatics ◽  
Software Packages ◽  
Introductory Overview ◽  
To Come ◽  
Microscopy Techniques

In recent years developmental biology has greatly benefited from the latest advances in fluorescence microscopy techniques. Consequently, quantitative and automated analysis of this data is becoming a vital first step in the quest for novel insights into the various aspects of development. Here we present an introductory overview of the various image analysis methods proposed for developmental biology images, with particular attention to openly available software packages. These tools, as well as others to come, are rapidly paving the way towards standardized and reproducible bioimaging studies at the whole-tissue level. Reflecting on these achievements, we discuss the remaining challenges and the future endeavours lying ahead in the post–image analysis era. This article is part of the themed issue ‘Systems morphodynamics: understanding the development of tissue hardware’.

Pre-Meeting Congress on Opportunities, Artifacts and Interpretation of Aberration-Corrected Electron Microscopy Data

2011 ◽  
Vol 17 (S1) ◽  
pp. 20-20
Author(s):  
Philip Batson ◽  
David Muller ◽  
Lawrence Allard ◽  
Paul Voyles ◽  
Miofang Chi ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Experimental Studies ◽  
Soft Materials ◽  
Subject Line ◽  
Practical Experiences ◽  
Microscopy Data ◽  
Poster Presentations ◽  
Image Collection ◽  
Difficult Situations ◽  
Aberration Corrected

This one-day pre-meeting congress, organized by the MSA Aberration-Corrected Electron Microscopy (ACEM) FIG, will be a forum for the discussion of the latest advances and solutions to problems associated with application of aberration correction technology. There will be platform presentations by both invited and contributed speakers, with poster presentations during a working lunch. Invited speakers will introduce innovations and issues, while contributors will highlight practical experiences and solutions to problems encountered during the application of ACEM to on-going experimental studies. This workshop includes: image collection/interpretation, new spectroscopies or other signals, artifacts and practical experiences in applications of ACEM to difficult situations such as hard/soft materials and in-situ experiments. All platform presentations will be intentionally kept short (∼15–20 minutes) to allow the maximum amount of interaction and information flow among attendees. Please send one page abstracts, including figures, to [email protected] with the subject line: M&M PMC Abstract.

scholarly journals Quantifying cellular interaction dynamics in 3D fluorescence microscopy data

2009 ◽  
Vol 4 (9) ◽  
pp. 1305-1311 ◽  
Author(s):  
Frederick Klauschen ◽  
Masaru Ishii ◽  
Hai Qi ◽  
Marc Bajénoff ◽  
Jackson G Egen ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Cellular Interaction ◽  
Interaction Dynamics ◽  
3D Fluorescence Microscopy ◽  
Microscopy Data

scholarly journals ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data

2019 ◽  
Author(s):  
Jochem H. Smit ◽  
Yichen Li ◽  
Eliza M. Warszawik ◽  
Andreas Herrmann ◽  
Thorben Cordes
Keyword(s):  
Data Analysis ◽  
Fluorescence Microscopy ◽  
Single Molecule ◽  
Statistical Significance ◽  
Reproducible Research ◽  
Cellular Processes ◽  
Analysis Package ◽  
Microscopy Data ◽  
The Cost ◽  
Single Molecule Localization Microscopy

AbstractSingle-molecule fluorescence microscopy studies of bacteria provide unique insights into the mechanisms of cellular processes and protein machineries in ways that are unrivalled by any other technique. With the cost of microscopes dropping and the availability of fully automated microscopes, the volume of microscopy data produced has increased tremendously. These developments have moved the bottleneck of throughput from image acquisition and sample preparation to data analysis. Furthermore, requirements for analysis procedures have become more stringent given the requirement of various journals to make data and analysis procedures available. To address this we have developed a new data analysis package for analysis of fluorescence microscopy data of rod-like cells. Our software ColiCoords structures microscopy data at the single-cell level and implements a coordinate system describing each cell. This allows for the transformation of Cartesian coordinates of both cellular images (e.g. from transmission light or fluorescence microscopy) and single-molecule localization microscopy (SMLM) data to cellular coordinates. Using this transformation, many cells can be combined to increase the statistical significance of fluorescence microscopy datasets of any kind. Coli-Coords is open source, implemented in the programming language Python, and is extensively documented. This allows for modifications for specific needs or to inspect and publish data analysis procedures. By providing a format that allows for easy sharing of code and associated data, we intend to promote open and reproducible research.The source code and documentation can be found via the project’s GitHub page.

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