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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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Documentation


Additional information


http://biii.eu/node/49

Spot Detector citations

 (52)
call_split

Estimation of diffusion constants from single molecular measurement without explicit tracking

2018
BMC Syst Biol
PMCID: 5907143
PMID: 29671388
DOI: 10.1186/s12918-018-0526-5
call_split See protocol

[…] 512 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 see […]

call_split

The tobacco carcinogen NNK drives accumulation of DNMT1 at the GR promoter thereby reducing GR expression in untransformed lung fibroblasts

2018
Sci Rep
PMCID: 5861118
PMID: 29559689
DOI: 10.1038/s41598-018-23309-2
call_split See protocol

[…] ns. 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. […]

library_books

C terminal calcium binding of α synuclein modulates synaptic vesicle interaction

2018
Nat Commun
PMCID: 5818535
PMID: 29459792
DOI: 10.1038/s41467-018-03111-4

[…] ations 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 […]

library_books

Mapping molecular assemblies with fluorescence microscopy and object based spatial statistics

2018
Nat Commun
PMCID: 5814551
PMID: 29449608
DOI: 10.1038/s41467-018-03053-x

[…] ntional 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 as positio […]

library_books

Fluorogenic RNA Mango aptamers for imaging small non coding RNAs in mammalian cells

2018
Nat Commun
PMCID: 5811451
PMID: 29440634
DOI: 10.1038/s41467-018-02993-8

[…] Images were processed using FIJI and spot detection analysis was performed on each maximum projection by the spot detector plugin in the ICY image analysis software, which detects significant foci with a pixel area ≥3 × 3 pixels and intensity ≥300 a.u. A lower threshold of ≥150 a.u. was used to create a popu […]

library_books

Characterisation of Casein Kinase 1.1 in Leishmania donovani Using the CRISPR Cas9 Toolkit

2017
Biomed Res Int
PMCID: 5733176
PMID: 29333442
DOI: 10.1155/2017/4635605

[…] m early stationary phase were filmed for 10 s (200 frames) with a Leica DMI 4000B microscope, using a 40x objective and an Evolv EMCCD camera, with Metaview software. Tracking was performed using the Spot Detector and Spot Tracking tools from Icy software [], with defaults settings and the following modifications: Spot Detector: Scale 3, Sensitivity 80 (~7 pix); size filtering: min = 10 – max = 30 […]

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