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Icy specifications

Information


Unique identifier OMICS_06572
Name Icy
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

Subtool


  • BioFlow

Versioning


No version available

Maintainer


  • person_outline Fabrice de Chaumont

Publications for Icy

Icy citations

 (131)
library_books

Concepts in Light Microscopy of Viruses

2018
Viruses
PMCID: 5923496
PMID: 29670029
DOI: 10.3390/v10040202

[…] nables simple implementation of additional nodes, strengthening the core functionalities by features, such as Java/R/Python/MATLAB/ImageJ compatibility, machine learning or expanded workflow control. Icy (http://icy.bioimageanalysis.org/) combines both image and data analysis. While slightly less intuitive to use compared to CellProfiler/KNIME, Icy provides great segmentation quality even for nois […]

call_split

Cytokinin stabilizes WUSCHEL by acting on the protein domains required for nuclear enrichment and transcription

2018
PLoS Genet
PMCID: 5919686
PMID: 29659567
DOI: 10.1371/journal.pgen.1007351
call_split See protocol

[…] Images from confocal microscopy were loaded into the Icy Bioimage software [] (http://icy.bioimageanalysis.org) and isolated for the eGFP or dsRed-N7 channel. The HK Means and Active Contour plugins were used to detect cell counts. For fluorescence quan […]

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

[…] d time course image data of single molecular measurements. For this purpose, we utilize the image data generator provided as a plugin “ISBI Challenge Track Generator” [] of an open platform software “ICY” [] for bioimage analysis.We set the parameters of the plugin software as follows; SNR = 4, sequence length = 10, particle density = 100, 500 and 1000, sigma = 1, 2, 3, 5, 7 and 10 in the particle […]

library_books

Robust Phagocyte Recruitment Controls the Opportunistic Fungal Pathogen Mucor circinelloides in Innate Granulomas In Vivo

2018
MBio
PMCID: 5874920
PMID: 29588406
DOI: 10.1128/mBio.02010-17

[…] s at 509 nm (excitation, 488 nm), 610 nm (excitation, 587 nm), and 465 nm (excitation, 353 nm), respectively. Images were taken and processed with the open community platform for BioImage informatics Icy (), and figures were compiled in Illustrator C3 (Adobe Systems, San Jose, CA, United States). For cell tracking analysis, movies were analyzed using Volocity software (Improvision, Coventry, Unite […]

library_books

Application of the Mesolens for subcellular resolution imaging of intact larval and whole adult Drosophila

2018
J Microsc
PMCID: 5947746
PMID: 29570774
DOI: 10.1111/jmi.12693

[…] tating display, shown in Movie S1, was made by constructing a series of projections at different angles (2 degrees, through 360 degrees of rotation) using a maximum brightness projection algorithm in Icy (de Chaumont et al., ), which effectively eliminated all but the exoskeletal signal. However, colour depth‐coding of the same data (Fig. ) did not eliminate the weaker staining and showed interior […]

library_books

Structural centrosome aberrations promote non‐cell‐autonomous invasiveness

2018
PMCID: 5920242
PMID: 29567643
DOI: 10.15252/embj.201798576

[…] s Remote manager 3.3.0‐rc9, and z‐projections of the maximum intensities of the whole stacks were performed using Fiji software. E‐cadherin signals were processed to determine an E‐cadherin JSI using Icy software (http://icy.bioimageanalysis.org/). Briefly, E‐cadherin signals were segmented into three classes, termed background, junctions, and speckles/aggregates, by using k‐means to define two th […]

Citations

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Icy institution(s)
Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France

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