Spot Detector protocols

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Spot Detector specifications

Information


Unique identifier OMICS_18872
Name Spot Detector
Software type Package/Module
Interface Graphical user interface
Restrictions to use License purchase required
Input data Some current sequences or a batch of file.
Output data Some exports detection or images with detection markers and binary image for control.
Output format Excel
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 1.9.2.1
Stability Beta
Source code URL http://www.bioimageanalysis.org/icy/repository/getJarFile.php?pluginId=52&beta=0
Maintained Yes

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http://biii.eu/node/49

Spot Detector in pipelines

 (3)
2017
PMCID: 5474736
PMID: 28607494
DOI: 10.1038/ncomms15835

[…] were acquired under electron microscopes, as described above., endogenous rab6 fluorescent structures (number and intensity) in proximity with melanosomes were quantified using icy software (plugin spot detector) by delineating melanosomes with circles (15 pixels diameter)—which overlap the tyrp1 labelling at melanosomes. linescan analysis was performed using metamorph. pearson’s correlation […]

2017
PMCID: 5551700
PMID: 28687665
DOI: 10.1083/jcb.201607074

[…] slices per level were analyzed. the rms was manually delineated with dapi counterstaining. automated countings were performed in four rms regions with icy bioimage analysis software using the spot detector plugin. all values are given as the mean of the number of calretinin+ cells per rms ± sem, and a mann-whitney test was performed., for gfap quantification in the rms, four control […]

2013
PMCID: 3753654
PMID: 23814183
DOI: 10.1093/nar/gkt561

[…] objective. after acquisition, sequential images were opened in imaris (bitplane llc, south windsor, ct) and saved as an .avi file., single rna transcripts were identified in 3d image stacks using a spot detector 3d laplacian of gaussian plug-in available for nih imagej (version 1.45 b) (). all images were subject to a rolling-ball background subtraction before spot detection. to quantify […]


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Spot Detector in publications

 (84)
PMCID: 5907143
PMID: 29671388
DOI: 10.1186/s12918-018-0526-5

[…] pixels. the other parameters (except for seeds) are set to default, which means the extinction rate of each particle is 0.05. the particles in generated image data are detected by another plugin “spot detector” of the icy software. the detection of bright spots by spot detector plugin is performed with default parameters. the simulation is repeated 3 times for each condition with different […]

PMCID: 5900057
PMID: 29686621
DOI: 10.3389/fphys.2018.00307

[…] (1:100) at 37°c for 1 h, followed by secondary antibodies conjugated to alexa fluor 488. the fluorescence signals were visualized with a tcs sp2 confocal fluorescence microscope (leica). the spot detector bioapplication (thermo fisher scientific) was used to acquire and analyze the images after optimization. images of 500–1,000 cells for each treatment group were analyzed to obtain […]

PMCID: 5861118
PMID: 29559689
DOI: 10.1038/s41598-018-23309-2

[…] the cells were then fixed with cold methanol (merck) and stained with 0.5% crystal violet (merck). images of the dishes were captured and the numbers of spots/colonies were determined using icy - spot detector., mrc-5 cells were harvested from days 29 and 106 of the chronic treatment. cells were prepared for comet assay analyses as per weber et al.. comet slides were visualised using a nikon […]

PMCID: 5818535
PMID: 29459792
DOI: 10.1038/s41467-018-03111-4

[…] at the same mean density. the maximum distance value of the normalized histogram then yields a measure for the radius of the localization clusters. for image analysis of synaptic vesicles, the spot detector plugin of the image analysis software icy was used to identify vesicles,, followed by analysis using an in-house matlab script to calculate the number of vesicles within a 250 nm radius […]

PMCID: 5814551
PMID: 29449608
DOI: 10.1038/s41467-018-03053-x

[…] microscopy images (fig. ), we use a robust and automatic algorithm based on a wavelet transformation of the image and statistical thresholding of wavelet coefficients (implemented as a plugin spot detector in the open-source image analysis software icy (http://icy.bioimageanalysis.org/)). these spots correspond to clusters of molecules where centre of mass (or intensity) is used […]


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