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Protocols

DeconvolutionLab specifications

Information


Unique identifier OMICS_25417
Name DeconvolutionLab
Alternative name DeconvolutionLab2
Software type Application/Script, Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2
Stability Stable
Maintained Yes

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Versioning


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Maintainers


  • person_outline Daniel Sage
  • person_outline Laurene Donati
  • person_outline Ferreol Soulez
  • person_outline Denis Fortun

Publication for DeconvolutionLab

DeconvolutionLab citations

 (20)
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Hookworm Secreted Extracellular Vesicles Interact With Host Cells and Prevent Inducible Colitis in Mice

2018
Front Immunol
PMCID: 5936971
PMID: 29760697
DOI: 10.3389/fimmu.2018.00850
call_split See protocol

[…] a laser scanning confocal microscope (Zeiss 780 NLO, Zeiss, Oberkochen, Germany). Confocal image deconvolution was performed in ImageJ using the plugins “Diffraction PSF 3D” for PSF calculation and “DeconvolutionLab” with the Tikhonov–Miller algorithm for 2D deconvolution (). […]

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Wnt/β catenin signaling stimulates the expression and synaptic clustering of the autism associated Neuroligin 3 gene

2018
PMCID: 5835496
PMID: 29503438
DOI: 10.1038/s41398-018-0093-y
call_split See protocol

[…] 400; Molecular Probes, Eugene, OR, USA) for secondary staining. Samples were examined on a LSM780 confocal microscopy (Carl Zeiss, Jena, Germany). Images were deconvolved using the ImageJ/FIJI plugin DeconvolutionLab using theoretical point spread functions. Total Nlgn3 fluorescence intensity was measured as arbitrary units in all dendritic processes with clear signal of MAP2 in 15 µm segments tha […]

library_books

Aberration corrected cryoimmersion light microscopy

2018
Proc Natl Acad Sci U S A
PMCID: 5819432
PMID: 29358380
DOI: 10.1073/pnas.1717282115

[…] sis were carried out by using Fiji (). FWHM values were measured by using the plugin GDSC SMLN after running an inverted deconvolution run for correcting for finite size of the beads using the plugin Deconvolutionlab2 (). […]

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Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

2018
J Extracell Vesicles
PMCID: 5795766
PMID: 29410780
DOI: 10.1080/20013078.2018.1428004

[…] peated to perform laser scanning confocal imaging on a 780 NLO microscope (Zeiss). Confocal image deconvolution was performed in ImageJ using the plugins “Diffraction PSF 3D” for PSF calculation and “DeconvolutionLab” with the Richardson–Lucy algorithm for 3D deconvolution and Tikhonov–Miller algorithm for 2D deconvolution []. […]

library_books

Revealing chiral cell motility by 3D Riesz transform differential interference contrast microscopy and computational kinematic analysis

2017
Nat Commun
PMCID: 5736583
PMID: 29259161
DOI: 10.1038/s41467-017-02193-w

[…] d low-frequency components for flat-field correction. The transformed images were post-processed for noise reduction and voxel interpolation. All 3D images were deconvoluted with open-source software DeconvolutionLab2 with theoretical point spread function (PSF) based on Born–Wolf model generated by PSF Generator. Both 2D and 3D images were smoothed with a Gaussian filter along the X, Y, and time […]

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Increased signaling by the autism related Engrailed 2 protein enhances dendritic branching and spine density, alters synaptic structural matching, and exaggerates protein synthesis

2017
PLoS One
PMCID: 5557355
PMID: 28809922
DOI: 10.1371/journal.pone.0181350
call_split See protocol

[…] ial deconvolution: point spread functions (PSF) were calculated using the ImageJ’s plugin PSF Generator [] and the deconvolution was performed using the Richardson-Lucy algorithm implemented into the DeconvolutionLab ImageJ’s plugin []. These two freeware programs were provided by the Biomedical Imaging Group of the EPFL (Ecole Polytechnique Fédérale de Lausanne; Switzerland). To simplify the anal […]


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DeconvolutionLab institution(s)
Biomedical Imaging Group, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland; Center for Biomedical Imaging - Signal Processing Core (CIBM-SP), Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland; BioImaging and Optics Platform, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
DeconvolutionLab funding source(s)
Supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 692726 ”GlobalBioIm: Global integrative framework for computational bio-imaging”).

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