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.

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 Semi-automated Root Image Analysis (saRIA)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Narendra Narisetti ◽  
Michael Henke ◽  
Christiane Seiler ◽  
Rongli Shi ◽  
Astrid Junker ◽  
...  
Keyword(s):  
Image Analysis ◽  
Image Segmentation ◽  
Root System ◽  
System Architecture ◽  
Ground Truth ◽  
Automated Analysis ◽  
Root System Architecture ◽  
Automated Image Analysis ◽  
Projection Area ◽  
Ground Truth Data

AbstractQuantitative characterization of root system architecture and its development is important for the assessment of a complete plant phenotype. To enable high-throughput phenotyping of plant roots efficient solutions for automated image analysis are required. Since plants naturally grow in an opaque soil environment, automated analysis of optically heterogeneous and noisy soil-root images represents a challenging task. Here, we present a user-friendly GUI-based tool for semi-automated analysis of soil-root images which allows to perform an efficient image segmentation using a combination of adaptive thresholding and morphological filtering and to derive various quantitative descriptors of the root system architecture including total length, local width, projection area, volume, spatial distribution and orientation. The results of our semi-automated root image segmentation are in good conformity with the reference ground-truth data (mean dice coefficient = 0.82) compared to IJ_Rhizo and GiAroots. Root biomass values calculated with our tool within a few seconds show a high correlation (Pearson coefficient = 0.8) with the results obtained using conventional, pure manual segmentation approaches. Equipped with a number of adjustable parameters and optional correction tools our software is capable of significantly accelerating quantitative analysis and phenotyping of soil-, agar- and washed root images.

scholarly journals Determination of Foam Stability in Lager Beers Using Digital Image Analysis of Images Obtained Using RGB and 3D Cameras

Fermentation ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 46
Author(s):  
Emmanuel Karlo Nyarko ◽  
Hrvoje Glavaš ◽  
Kristina Habschied ◽  
Krešimir Mastanjević
Keyword(s):  
Image Analysis ◽  
Production Process ◽  
Foam Stability ◽  
Raw Materials ◽  
Foam Height ◽  
Automated Analysis ◽  
Automated Image Analysis ◽  
Unique Contribution ◽  
Important Indicator ◽  
3D Camera

Foam stability and retention is an important indicator of beer quality and freshness. A full, white head of foam with nicely distributed small bubbles of CO2 is appealing to the consumers and the crown of the production process. However, raw materials, production process, packaging, transportation, and storage have a big impact on foam stability, which marks foam stability monitoring during all these stages, from production to consumer, as very important. Beer foam stability is expressed as a change of foam height over a certain period. This research aimed to monitor the foam stability of lager beers using image analysis methods on two different types of recordings: RGB and depth videos. Sixteen different commercially available lager beers were subjected to analysis. The automated image analysis method based only on the analysis of RGB video images proved to be inapplicable in real conditions due to problems such as reflection of light through glass, autofocus, and beer lacing/clinging, which make it impossible to accurately detect the actual height of the foam. A solution to this problem, representing a unique contribution, was found by introducing the use of a 3D camera in estimating foam stability. According to the results, automated analysis of depth images obtained from a 3D camera proved to be a suitable, objective, repeatable, reliable, and sufficiently sensitive method for measuring foam stability of lager beers. The applied model proved to be suitable for predicting changes in foam retention of lager beers.

A methodology for the systematic and quantitative study of cell contact guidance in oriented collagen gels. Correlation of fibroblast orientation and gel birefringence

1993 ◽  
Vol 105 (2) ◽  
pp. 317-331 ◽  
Author(s):  
S. Guido ◽  
R.T. Tranquillo
Keyword(s):  
Magnetic Field ◽  
Image Analysis ◽  
Collagen Gel ◽  
Time Lapse ◽  
Automated Image Analysis ◽  
Contact Guidance ◽  
Cell Contact ◽  
Collagen Gels ◽  
Cell Orientation ◽  
Observation Chamber

Despite the likely role of contact guidance in every physiological process involving cell migration, its study in a three-dimensional tissue-equivalent environment has been precluded, heretofore, by inherent difficulties in systematically preparing well-defined contact guidance fields and quantifying the resultant contact guidance. Here, we describe a novel use of a magnetic field to orient collagen fibrils during fibrillogenesis, entrapping cells dispersed in the collagen solution. Using computer-controlled staging and image analysis, we show from automated birefringence measurements of the resultant slab of cell-populated gel contained in a specially designed observation chamber that the fibril orientation is biased along the long axis of the chamber uniformly throughout the chamber. Further, we show that the degree of fibril orientation, and consequently the elicited contact guidance, can be controlled by independently varying the magnetic field strength or temperature during fibrillogenesis. We characterize the contact guidance response to the imposed contact guidance field by measuring cell orientation relative to the axis of fibril orientation from still images obtained in time-lapse via automated image analysis. We present the first quantitative correlation of contact guidance (based on cell orientation) with collagen fibril orientation (based on birefringence) for human foreskin fibroblasts cultured in a collagen gel, by using gels of varying orientation resulting from different magnetic field strengths and temperatures during fibrillogenesis, and by using sufficiently low cell concentrations and early observation times.

scholarly journals Automated Image Analysis for High-Content Screening and Analysis

2010 ◽  
Vol 15 (7) ◽  
pp. 726-734 ◽  
Author(s):  
Aabid Shariff ◽  
Joshua Kangas ◽  
Luis Pedro Coelho ◽  
Shannon Quinn ◽  
Robert F. Murphy
Keyword(s):  
Machine Learning ◽  
Image Processing ◽  
Image Analysis ◽  
Cell Biology ◽  
Image Data ◽  
Automated Analysis ◽  
Image Features ◽  
Automated Image Analysis ◽  
High Content Screening ◽  
Spatial Transformation

The field of high-content screening and analysis consists of a set of methodologies for automated discovery in cell biology and drug development using large amounts of image data. In most cases, imaging is carried out by automated microscopes, often assisted by automated liquid handling and cell culture. Image processing, computer vision, and machine learning are used to automatically process high-dimensional image data into meaningful cell biological results. The key is creating automated analysis pipelines typically consisting of 4 basic steps: (1) image processing (normalization, segmentation, tracing, tracking), (2) spatial transformation to bring images to a common reference frame (registration), (3) computation of image features, and (4) machine learning for modeling and interpretation of data. An overview of these image analysis tools is presented here, along with brief descriptions of a few applications.

Automated Image Analysis Of Nuclear And Cytoplasmic Changes In Exfoliated Cells From Tracheas Treated With Carcinogen

1977 ◽  
Vol 35 ◽  
pp. 220-221
Author(s):  
S.F. Stinson ◽  
J.C. Lilga ◽  
M.B. Sporn
Keyword(s):  
Image Analysis ◽  
Pattern Analysis ◽  
Relative Proportion ◽  
Automated Image Analysis ◽  
Image Analyzer ◽  
Cross Sectional ◽  
Exfoliated Cells ◽  
Neoplastic Lesions ◽  
Analysis System ◽  
Morphologic Criterion

Increased nuclear size, resulting in an increase in the relative proportion of nuclear to cytoplasmic sizes, is an important morphologic criterion for the evaluation of neoplastic and pre-neoplastic cells. This paper describes investigations into the suitability of automated image analysis for quantitating changes in nuclear and cytoplasmic cross-sectional areas in exfoliated cells from tracheas treated with carcinogen.Neoplastic and pre-neoplastic lesions were induced in the tracheas of Syrian hamsters with the carcinogen N-methyl-N-nitrosourea. Cytology samples were collected intra-tracheally with a specially designed catheter (1) and stained by a modified Papanicolaou technique. Three cytology specimens were selected from animals with normal tracheas, 3 from animals with dysplastic changes, and 3 from animals with epidermoid carcinoma. One hundred randomly selected cells on each slide were analyzed with a Bausch and Lomb Pattern Analysis System automated image analyzer.

Progress In The Practical Application Of Automated Image Analysis To Tem Negatives

1977 ◽  
Vol 35 ◽  
pp. 214-217
Author(s):  
F. A. Heckman ◽  
E. Redman ◽  
J.E. Connolly
Keyword(s):  
Image Analysis ◽  
Image Quality ◽  
Exposure Time ◽  
Image Contrast ◽  
Automated Image Analysis ◽  
Practical Application ◽  
Factors Affecting ◽  
High Image Quality ◽  
Qualitative Evidence ◽  
Comprehensive Study

In our initial publication on this subject1) we reported results demonstrating that contrast is the most important factor in producing the high image quality required for reliable image analysis. We also listed the factors which enhance contrast in order of the experimentally determined magnitude of their effect. The two most powerful factors affecting image contrast attainable with sheet film are beam intensity and KV. At that time we had only qualitative evidence for the ranking of enhancing factors. Later we carried out the densitometric measurements which led to the results outlined below.Meaningful evaluations of the cause-effect relationships among the considerable number of variables in preparing EM negatives depend on doing things in a systematic way, varying only one parameter at a time. Unless otherwise noted, we adhered to the following procedure evolved during our comprehensive study:Philips EM-300; 30μ objective aperature; magnification 7000- 12000X, exposure time 1 second, anti-contamination device operating.

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