scholarly journals Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays

2007 ◽  
Vol 1 (1) ◽  
Author(s):  
Najaf A Shah ◽  
Richard J Laws ◽  
Bradley Wardman ◽  
Lue Ping Zhao ◽  
John L Hartman
Keyword(s):  
Cell Proliferation ◽  
Image Analysis ◽  
Time Lapse ◽  
Automated Image Analysis ◽  
Yeast Culture ◽  
Proliferation Kinetics ◽  
Time Lapse Imaging

scholarly journals SynActJ: Easy-to-Use Automated Analysis of Synaptic Activity

2021 ◽  
Vol 3 ◽  
Author(s):  
Christopher Schmied ◽  
Tolga Soykan ◽  
Svenja Bolz ◽  
Volker Haucke ◽  
Martin Lehmann
Keyword(s):  
Image Analysis ◽  
Organic Dyes ◽  
Calcium Influx ◽  
Glutamate Release ◽  
Automated Analysis ◽  
Time Lapse ◽  
Synaptic Activity ◽  
Automated Image Analysis ◽  
Batch Mode ◽  
Fluorescent Intensity

Neuronal synapses are highly dynamic communication hubs that mediate chemical neurotransmission via the exocytic fusion and subsequent endocytic recycling of neurotransmitter-containing synaptic vesicles (SVs). Functional imaging tools allow for the direct visualization of synaptic activity by detecting action potentials, pre- or postsynaptic calcium influx, SV exo- and endocytosis, and glutamate release. Fluorescent organic dyes or synapse-targeted genetic molecular reporters, such as calcium, voltage or neurotransmitter sensors and synapto-pHluorins reveal synaptic activity by undergoing rapid changes in their fluorescence intensity upon neuronal activity on timescales of milliseconds to seconds, which typically are recorded by fast and sensitive widefield live cell microscopy. The analysis of the resulting time-lapse movies in the past has been performed by either manually picking individual structures, custom scripts that have not been made widely available to the scientific community, or advanced software toolboxes that are complicated to use. For the precise, unbiased and reproducible measurement of synaptic activity, it is key that the research community has access to bio-image analysis tools that are easy-to-apply and allow the automated detection of fluorescent intensity changes in active synapses. Here we present SynActJ (Synaptic Activity in ImageJ), an easy-to-use fully open-source workflow that enables automated image and data analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active synapses in time-lapse movies via an interactive seeded watershed segmentation that can be easily adjusted and applied to a dataset in batch mode. The extracted intensity traces of each synaptic bouton are automatically processed, analyzed, and plotted using an R Shiny workflow. We validate the workflow on time-lapse images of stimulated synapses expressing the SV exo-/endocytosis reporter Synaptophysin-pHluorin or a synapse-targeted calcium sensor, Synaptophysin-RGECO. We compare the automatic workflow to manual analysis and compute calcium-influx and SV exo-/endocytosis kinetics and other parameters for synaptic vesicle recycling under different conditions. We predict SynActJ to become an important tool for the analysis of synaptic activity and synapse properties.

Mother machine image analysis with MM3

2019 ◽  
Author(s):  
John T. Sauls ◽  
Jeremy W. Schroeder ◽  
Steven D. Brown ◽  
Guillaume Le Treut ◽  
Fangwei Si ◽  
...  
Keyword(s):  
Image Analysis ◽  
Phase Contrast ◽  
Time Lapse ◽  
Command Line ◽  
Throughput Time ◽  
Analysis Pipeline ◽  
Machine Experiment ◽  
Command Line Tool ◽  
Time Lapse Imaging ◽  
Machine Image

The mother machine is a microfluidic device for high-throughput time-lapse imaging of microbes. Here, we present MM3, a complete and modular image analysis pipeline. MM3 turns raw mother machine images, both phase contrast and fluorescence, into a data structure containing cells with their measured features. MM3 employs machine learning and non-learning algorithms, and is implemented in Python. MM3 is easy to run as a command line tool with the occasional graphical user interface on a PC or Mac. A typical mother machine experiment can be analyzed within one day. It has been extensively tested, is well documented and publicly available via Github.

scholarly journals Quantifying endothelial cell proliferation in the zebrafish embryo

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 1032
Author(s):  
George Bowley ◽  
Timothy JA Chico ◽  
Jovana Serbanovic-Canic ◽  
Paul C Evans
Keyword(s):  
Cell Proliferation ◽  
Endothelial Cell ◽  
Zebrafish Embryo ◽  
Time Lapse ◽  
Endothelial Cell Proliferation ◽  
Small Scale ◽  
Zebrafish Embryos ◽  
Time Lapse Imaging

Introduction: Endothelial cell (EC) proliferation is a fundamental determinant of vascular development and homeostasis, and contributes to cardiovascular disease by increasing vascular permeability to blood-borne lipoproteins. Rodents have been traditionally used to analyse EC proliferation mechanisms in vascular health and disease; however, alternative models such as the zebrafish embryo allow researchers to conduct small scale screening studies in a physiologically relevant vasculature whilst reducing the use of mammals in biomedical research. In vitro models of EC proliferation are valuable but do not fully recapitulate the complexity of the in vivo situation. Several groups have used zebrafish embryos for vascular biology research because they offer the advantages of an in vivo model in terms of complexity but are also genetically manipulable and optically transparent. Methods: Here we investigated whether zebrafish embryos can provide a suitable model for the study of EC proliferation. We explored the use of antibody, DNA labelling, and time-lapse imaging approaches. Results: Antibody and DNA labelling approaches were of limited use in zebrafish due to the low rate of EC proliferation combined with the relatively narrow window of time in which they can label proliferating nuclei. By contrast, time-lapse imaging of fluorescent proteins localised to endothelial nuclei was a sensitive method to quantify EC proliferation in zebrafish embryos. Discussion: We conclude that time-lapse imaging is suitable for analysis of endothelial cell proliferation in zebrafish, and that this method is capable of capturing more instances of EC proliferation than immunostaining or cell labelling alternatives. This approach is relevant to anyone studying endothelial cell proliferation for screening genes or small molecules involved in EC proliferation. It offers greater biological relevance than existing in vitro models such as HUVECs culture, whilst reducing the overall number of animals used for this type of research.

scholarly journals Cell Tracking Profiler – a user-driven analysis framework for evaluating 4D live-cell imaging data

2020 ◽  
Vol 133 (22) ◽  
pp. jcs241422
Author(s):  
Claire Mitchell ◽  
Lauryanne Caroff ◽  
Jose Alonso Solis-Lemus ◽  
Constantino Carlos Reyes-Aldasoro ◽  
Alessandra Vigilante ◽  
...  
Keyword(s):  
Image Analysis ◽  
Cell Tracking ◽  
Cell Function ◽  
Ground Truth ◽  
Time Lapse ◽  
Automated Image Analysis ◽  
Imaging Data ◽  
Cell Behaviour ◽  
Muscle Stem Cell

ABSTRACTAccurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo. Here, by using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm, we established a ‘ground truth’ for muSC behaviour. This revealed that segmentation and tracking algorithms from commonly used programs are error-prone, leading us to develop a fast semi-automated image analysis pipeline that allows user-defined parameters for segmentation and correction of cell tracking. Cell Tracking Profiler (CTP) is a package that runs two existing programs, HK Means and Phagosight within the Icy image analysis suite, to enable user-managed cell tracking from 3D time-lapse datasets to provide measures of cell shape and movement. We demonstrate how CTP can be used to reveal changes to cell behaviour of muSCs in response to manipulation of the cell cytoskeleton by small-molecule inhibitors. CTP and the associated tools we have developed for analysis of outputs thus provide a powerful framework for analysing complex cell behaviour in vivo from 4D datasets that are not amenable to straightforward analysis.

scholarly journals Time-Lapse Imaging of Ag3Sn Thermal Coarsening in Sn-3Ag-0.5Cu Solder Joints

2020 ◽  
Author(s):  
J. W. Xian ◽  
S. A. Belyakov ◽  
C. M. Gourlay
Keyword(s):  
Image Analysis ◽  
Size Distribution ◽  
Ostwald Ripening ◽  
Solder Joints ◽  
Time Lapse ◽  
Ripening Process ◽  
Large Particles ◽  
Coarsening Kinetics ◽  
Time Lapse Imaging ◽  
Best Fit

Abstract The coarsening of Ag3Sn particles occurs during the operation of joints and plays an important role in failure. Here, Ag3Sn coarsening is studied at 125°C in the eutectic regions of Sn-3Ag-0.5Cu/Cu solder joints by SEM-based time-lapse imaging. Using multi-step thresholding segmentation and image analysis, it is shown that coalescence of Ag3Sn particles is an important ripening process in addition to LSW-like Ostwald ripening. About 10% of the initial Ag3Sn particles coalesced during ageing, coalescence occurred uniformly across eutectic regions, and the scaled size distribution histograms contained large particles that can be best fit by the Takajo model of coalescence ripening. Similar macroscopic coarsening kinetics were measured between the surface and bulk Ag3Sn particles. Tracking of individual surface particles showed an interplay between the growth/shrinkage and coalescence of Ag3Sn.

Determining transaminase activity in bacterial libraries by time-lapse imaging

2019 ◽  
Vol 55 (90) ◽  
pp. 13538-13541 ◽  
Author(s):  
Carlos J. C. Rodrigues ◽  
João M. Sanches ◽  
Carla C. C. R. de Carvalho
Keyword(s):  
Image Analysis ◽  
Kinetic Parameters ◽  
Substrate Concentration ◽  
Time Lapse ◽  
Transaminase Activity ◽  
Time Lapse Imaging

Transaminase activity was determined by time-lapse imaging using a colourimetric reaction and image analysis. The correlation between substrate concentration and luminance allows the screening of biocatalysts and determination of kinetic parameters.

Sign in / Sign up

Export Citation Format

Share Document