scholarly journals Open source software for quantification of cell migration, protrusions, and fluorescence intensities

2015 ◽  
Vol 209 (1) ◽  
pp. 163-180 ◽  
Author(s):  
David J. Barry ◽  
Charlotte H. Durkin ◽  
Jasmine V. Abella ◽  
Michael Way
Keyword(s):  
Cell Migration ◽  
Open Source ◽  
Imaging Techniques ◽  
Automated Analysis ◽  
Spatial And Temporal Scales ◽  
Migration Rates ◽  
Automated Quantification ◽  
Membrane Protrusions ◽  
Automated Tools ◽  
User Friendly

Cell migration is frequently accompanied by changes in cell morphology (morphodynamics) on a range of spatial and temporal scales. Despite recent advances in imaging techniques, the application of unbiased computational image analysis methods for morphodynamic quantification is rare. For example, manual analysis using kymographs is still commonplace, often caused by lack of access to user-friendly, automated tools. We now describe software designed for the automated quantification of cell migration and morphodynamics. Implemented as a plug-in for the open-source platform, ImageJ, ADAPT is capable of rapid, automated analysis of migration and membrane protrusions, together with associated fluorescently labeled proteins, across multiple cells. We demonstrate the ability of the software by quantifying variations in cell population migration rates on different extracellular matrices. We also show that ADAPT can detect and morphologically profile filopodia. Finally, we have used ADAPT to compile an unbiased description of a “typical” bleb formed at the plasma membrane and quantify the effect of Arp2/3 complex inhibition on bleb retraction.

scholarly journals CiliaQ – a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images

2020 ◽  
Author(s):  
Jan Niklas Hansen ◽  
Sebastian Rassmann ◽  
Birthe Stüven ◽  
Nathalie Jurisch-Yaksi ◽  
Dagmar Wachten
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Primary Cilia ◽  
Time Lapse ◽  
High Throughput Analysis ◽  
Ciliary Function ◽  
Automated Quantification ◽  
Membrane Protrusions ◽  
Health And Disease ◽  
2D And 3D

AbstractCilia are hair-like membrane protrusions that emanate from the surface of most vertebrate cells and are classified into motile and primary cilia. Motile cilia move fluid flow or propel cells, while also fulfilling sensory functions. Primary cilia are immotile and act as a cellular antenna, translating environmental cues into cellular responses. Ciliary dysfunction leads to severe diseases, commonly termed ciliopathies. The molecular details underlying ciliopathies and ciliary function are, however, not well understood. Since cilia are small subcellular compartments, imaging-based approaches have been used to study them. However, tools to comprehensively analyze images are lacking. Automatic analysis approaches require commercial software and are limited to 2D analysis and only a few parameters. The widely used manual analysis approaches are time consuming, user-biased, and difficult to compare. Here, we present CiliaQ, a package of open-source, freely-available, and easy-to-use ImageJ plugins. CiliaQ allows high throughput analysis of 2D and 3D, static or time-lapse images of cilia in cell culture or tissues, and outputs a comprehensive list of parameters for ciliary morphology, length, bending, orientation, and fluorescence intensity, making it broadly applicable. We envision CiliaQ as a resource and platform for reproducible and comprehensive analysis of ciliary function in health and disease.

scholarly journals CiliaQ: a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images

2021 ◽  
Vol 44 (2) ◽  
Author(s):  
Jan Niklas Hansen ◽  
Sebastian Rassmann ◽  
Birthe Stüven ◽  
Nathalie Jurisch-Yaksi ◽  
Dagmar Wachten
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Primary Cilia ◽  
Time Lapse ◽  
High Throughput Analysis ◽  
Ciliary Function ◽  
Automated Quantification ◽  
Membrane Protrusions ◽  
Health And Disease ◽  
2D And 3D

Abstract Cilia are hair-like membrane protrusions that emanate from the surface of most vertebrate cells and are classified into motile and primary cilia. Motile cilia move fluid flow or propel cells, while also fulfill sensory functions. Primary cilia are immotile and act as a cellular antenna, translating environmental cues into cellular responses. Ciliary dysfunction leads to severe diseases, commonly termed ciliopathies. The molecular details underlying ciliopathies and ciliary function are, however, not well understood. Since cilia are small subcellular compartments, imaging-based approaches have been used to study them. However, tools to comprehensively analyze images are lacking. Automatic analysis approaches require commercial software and are limited to 2D analysis and only a few parameters. The widely used manual analysis approaches are time consuming, user-biased, and difficult to compare. Here, we present CiliaQ, a package of open-source, freely available, and easy-to-use ImageJ plugins. CiliaQ allows high-throughput analysis of 2D and 3D, static or time-lapse images from fluorescence microscopy of cilia in cell culture or tissues, and outputs a comprehensive list of parameters for ciliary morphology, length, bending, orientation, and fluorescence intensity, making it broadly applicable. We envision CiliaQ as a resource and platform for reproducible and comprehensive analysis of ciliary function in health and disease. Graphic abstract

scholarly journals CellMAPtracer: A user-friendly tracking tool for long-term migratory and proliferating cells

2020 ◽  
Author(s):  
Salim Ghannoum ◽  
Kamil Antos ◽  
Waldir Leoncio Netto ◽  
Alvaro Köhn-Luque ◽  
Hesso Farhan
Keyword(s):  
Cell Cycle ◽  
Cell Migration ◽  
Cell Biology ◽  
Imaging Techniques ◽  
Software Tool ◽  
Terminal Phase ◽  
Proliferating Cells ◽  
Dividing Cells ◽  
User Friendly

AbstractBackgroundCell migration is a fundamental cell biological process of key importance in health and disease. Advances in imaging techniques have paved the way to monitor cells motility. An ever-growing collection of computational tools to track cells has improved our ability to analyze moving cells. However, few if any tools let the user supervise and correct cell tracks that are automatically detected. Thus, we developed CellMAPtracer, a tool to track cells in a semi-automated supervised fashion, thereby improving the accuracy and facilitating the long term tracking of migratory and dividing cells. CellMAPtracer is available with a user-friendly graphical user interface and does not require any coding or programming skills.ResultsWe used CellMAPtracer to track fluorescently-labelled BT549 breast cancer cells. It allowed us to track dividing cells and determine the fate of the daughter cells with respect to migration speed or directionality and cell cycle length. Of note, we were able to track multi-daughter divisions, wherein a cell divides and gives rise to more than two cells. We also identified a not previously described speed change in the terminal phase of the cell cycle.ConclusionCellMAPtracer is a software tool for tracking cell migration and proliferation through a user-friendly interface that has a great potential to facilitate new discoveries in cell biology.

scholarly journals GIANI: open-source software for automated analysis of 3D microscopy images

2020 ◽  
Author(s):  
David J. Barry ◽  
Claudia Gerri ◽  
Donald M. Bell ◽  
Rocco D’Antuono ◽  
Kathy K. Niakan
Keyword(s):  
Protein Expression ◽  
Open Source ◽  
Cell Fate ◽  
Open Source Software ◽  
High Performance ◽  
Three Dimensional ◽  
Automated Analysis ◽  
Large Numbers ◽  
User Friendly ◽  
High Performance Computing Cluster

AbstractThe study of cellular and developmental processes in physiologically relevant three-dimensional (3D) systems facilitates an understanding of mechanisms underlying cell fate, disease and injury. While cutting-edge microscopy technologies permit the routine acquisition of 3D datasets, there is currently a lack of user-friendly, open-source software to analyse such images. Here we describe GIANI (djpbarry.github.io/Giani), new software for the analysis of 3D images, implemented as a plugin for the popular FIJI platform. The design primarily facilitates segmentation of nuclei and cells, followed by quantification of morphology and protein expression. GIANI enables routine and reproducible batch-processing of large numbers of images and also comes with scripting and command line tools, such that users can incorporate its functionality into their own scripts and easily run GIANI on a high-performance computing cluster. We demonstrate the utility of GIANI by quantifying cell morphology and protein expression in mouse early embryos. More generally, we anticipate that GIANI will be a useful tool for researchers in a variety of biomedical fields.

MackDroid - An Android based Application to monitor devices

2016 ◽  
Vol 9 ◽  
pp. 1
Author(s):  
Maaz Sirkhot ◽  
Ekta Sirwani ◽  
Aishwarya Kourani ◽  
Akshit Batheja ◽  
Kajal Jethanand Jewani
Keyword(s):  
Operating System ◽  
Open Source ◽  
Vital Role ◽  
Mobile Users ◽  
Android Application ◽  
Web Page ◽  
Technological World ◽  
Monitoring Service ◽  
User Friendly

In this technological world, smartphones can be considered as one of the most far-reaching inventions. It plays a vital role in connecting people socially. The number of mobile users using an Android based smartphone has increased rapidly since last few years resulting in organizations, cyber cell departments, government authorities feeling the need to monitor the activities on certain targeted devices in order to maintain proper functionality of their respective jobs. Also with the advent of smartphones, Android became one of the most popular and widely used Operating System. Its highlighting features are that it is user friendly, smartly designed, flexible, highly customizable and supports latest technologies like IoT. One of the features that makes it exclusive is that it is based on Linux and is Open Source for all the developers. This is the reason why our project Mackdroid is an Android based application that collects data from the remote device, stores it and displays on a PHP based web page. It is primarily a monitoring service that analyzes the contents and distributes it in various categories like Call Logs, Chats, Key logs, etc. Our project aims at developing an Android application that can be used to track, monitor, store and grab data from the device and store it on a server which can be accessed by the handler of the application.

scholarly journals An Interactive WebGIS Framework for Coastal Erosion Risk Management

2021 ◽  
Vol 9 (6) ◽  
pp. 567
Author(s):  
Alessandra Capolupo ◽  
Cristina Monterisi ◽  
Alessandra Saponieri ◽  
Fabio Addona ◽  
Leonardo Damiani ◽  
...  
Keyword(s):  
Open Source ◽  
3D Visualization ◽  
Erosion Risk ◽  
Innovative Strategies ◽  
Web Mapping ◽  
Natural Processes ◽  
Multi Scale ◽  
Interactive Interface ◽  
Multi Temporal ◽  
User Friendly

The Italian coastline stretches over about 8350 km, with 3600 km of beaches, representing a significant resource for the country. Natural processes and anthropic interventions keep threatening its morphology, moulding its shape and triggering soil erosion phenomena. Thus, many scholars have been focusing their work on investigating and monitoring shoreline instability. Outcomes of such activities can be largely widespread and shared with expert and non-expert users through Web mapping. This paper describes the performances of a WebGIS prototype designed to disseminate the results of the Italian project Innovative Strategies for the Monitoring and Analysis of Erosion Risk, known as the STIMARE project. While aiming to include the entire national coastline, three study areas along the regional coasts of Puglia and Emilia Romagna have already been implemented as pilot cases. This WebGIS was generated using Free and Open-Source Software for Geographic information systems (FOSS4G). The platform was designed by combining Apache http server, Geoserver, as open-source server and PostgreSQL (with PostGIS extension) as database. Pure javascript libraries OpenLayers and Cesium were implemented to obtain a hybrid 2D and 3D visualization. A user-friendly interactive interface was programmed to help users visualize and download geospatial data in several formats (pdf, kml and shp), in accordance with the European INSPIRE directives, satisfying both multi-temporal and multi-scale perspectives.

scholarly journals Amikacin Suppresses Human Breast Cancer Cell MDA-MB-231 Migration and Invasion

Toxics ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 108
Author(s):  
Yun-Hsin Wang ◽  
Yau-Hung Chen ◽  
Wen-Hao Shen
Keyword(s):  
Wound Healing ◽  
Cell Migration ◽  
Western Blotting ◽  
Bacterial Infections ◽  
Aminoglycoside Antibiotic ◽  
Migration And Invasion ◽  
Interacting Protein ◽  
Migration Rates ◽  
Thioredoxin Interacting Protein ◽  
Sirna Knockdown

(1) Background: Amikacin is an aminoglycoside antibiotic used for treating gram-negative bacterial infections in cancer patients. In this study, our aims are to investigate the migratory inhibition effects of amikacin in human MDA-MB-231 cells. (2) Methods: We used a wound-healing assay, trans-well analysis, Western blotting, immunostaining and siRNA knockdown approaches to investigate how amikacin influenced MDA-MB-231 cell migration and invasion. (3) Results: Wound healing showed that the MDA-MB-231 cell migration rates decreased to 44.4% in the presence of amikacin. Trans-well analysis showed that amikacin treatment led to invasion inhibition. Western blotting demonstrated that amikacin induced thioredoxin-interacting protein (TXNIP) up-regulation. TXNIP was knocked down using siRNA in MDA-MB-231 cell. Using immunostaining analysis, we found that inhibition of TXNIP expression led to MDA-MB-231 pseudopodia extension; however, amikacin treatment attenuated the cell extension formation. (4) Conclusions: We observed inhibition of migration and invasion in MDA-MB-231 cells treated with amikacin. This suggests inhibition might be mediated by up-regulation of TXNIP.

scholarly journals Subcellular optogenetic activation of Cdc42 controls local and distal signaling to drive immune cell migration

2016 ◽  
Vol 27 (9) ◽  
pp. 1442-1450 ◽  
Author(s):  
Patrick R. O’Neill ◽  
Vani Kalyanaraman ◽  
N. Gautam
Keyword(s):  
Cell Migration ◽  
Intracellular Signaling ◽  
Immune Cell ◽  
Leading Edge ◽  
Signaling Networks ◽  
Membrane Protrusions ◽  
A Cell ◽  
Immune Cell Migration ◽  
Directional Cell Migration ◽  
Rhoa Signaling

Migratory immune cells use intracellular signaling networks to generate and orient spatially polarized responses to extracellular cues. The monomeric G protein Cdc42 is believed to play an important role in controlling the polarized responses, but it has been difficult to determine directly the consequences of localized Cdc42 activation within an immune cell. Here we used subcellular optogenetics to determine how Cdc42 activation at one side of a cell affects both cell behavior and dynamic molecular responses throughout the cell. We found that localized Cdc42 activation is sufficient to generate polarized signaling and directional cell migration. The optically activated region becomes the leading edge of the cell, with Cdc42 activating Rac and generating membrane protrusions driven by the actin cytoskeleton. Cdc42 also exerts long-range effects that cause myosin accumulation at the opposite side of the cell and actomyosin-mediated retraction of the cell rear. This process requires the RhoA-activated kinase ROCK, suggesting that Cdc42 activation at one side of a cell triggers increased RhoA signaling at the opposite side. Our results demonstrate how dynamic, subcellular perturbation of an individual signaling protein can help to determine its role in controlling polarized cellular responses.

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