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PID specifications

Information


Unique identifier OMICS_25531
Name PID
Alternative name Parallel iterative deconvolution
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 1.12
Stability Stable
Maintained Yes

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Versioning


No version available

Additional information


https://sites.google.com/site/piotrwendykier/software/deconvolution/paralleliterativedeconvolution

PID citations

 (10)
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Over elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation

2018
Nat Commun
PMCID: 5871873
PMID: 29593297
DOI: 10.1038/s41467-018-03641-x
call_split See protocol

[…] quisition software (Molecular Devices). Images were taken as Z-stacks in a range of 10–14 µm, with a distance between planes of 0.2 μm.Deconvolution in three spatial dimensions was performed with the Parallel Iterative Deconvolution plugin of ImageJ, using the Wiener Filter Preconditioned Landweber algorithm with the following parameters: weiner = 0.001 (expressed as a fraction of the largest Four […]

library_books

Persistent microglial activation and synaptic loss with behavioral abnormalities in mouse offspring exposed to CASPR2 antibodies in utero

2017
Acta Neuropathol
PMCID: 5587616
PMID: 28755208
DOI: 10.1007/s00401-017-1751-5

[…] ified. All image processing and analyses was performed in Fiji. To process images for quantification of synaptic profiles, first z-stacks were deconvolved using the WPL deconvolution algorithm in the Parallel Iterative Deconvolution ImageJ plugin [] based on the Iterative Deconvolve 3D algorithm [] utilizing a theoretical 3D point spread function generated in PSF Lab []. Image stacks were then fil […]

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Nodal/Activin Pathway is a Conserved Neural Induction Signal in Chordates

2017
PMCID: 5540175
PMID: 28782045
DOI: 10.1038/s41559-017-0226-3
call_split See protocol

[…] as undertaken using a rabbit polyclonal anti-pSmad1/5/8 primary antibody (Cell Signaling 9511L, 1:150) and a secondary antibody (1:500) coupled to FITC. Photographs were processed in ImageJ using the Parallel Iterative Deconvolution 2D plug-in. Xenopus embryos or animal caps were processed for in situ hybridization as described in . For quantitative RT-PCR, total RNAs were extracted with the RNeas […]

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Cardiac Light Sheet Fluorescent Microscopy for Multi Scale and Rapid Imaging of Architecture and Function

2016
Sci Rep
PMCID: 4776137
PMID: 26935567
DOI: 10.1038/srep22489
call_split See protocol

[…] ata), to further recover the image from blurring and substantially enhance the resolution. The iterative 3-D deconvolution conducted in this work was run on the open source ImageJ platform using its “parallel iterative deconvolution” plugin, “3-D iterative deconvolution” module. We selected the MRNSD (Modified Residual Norm Steepest Descent) or WPL (Wiener Filter Preconditioned Landweber) option, […]

library_books

Macrophage activation and polarization modify P2X7 receptor secretome influencing the inflammatory process

2016
Sci Rep
PMCID: 4776275
PMID: 26935289
DOI: 10.1038/srep22586

[…] g Alexa 647 donkey anti-mouse (A-31571; Life technologies) as secondary antibody. Images were acquired with a Nikon Eclipse Ti microscope. Image stacks were deconvolved using NIH ImageJ software with Parallel Iterative Deconvolution plugin, and reconstituted maximum-intensity projections images are shown in the results. […]

library_books

Inflammasome dependent IL 1β release depends upon membrane permeabilisation

2016
Cell Death Differ
PMCID: 4946890
PMID: 26868913
DOI: 10.1038/cdd.2015.176

[…] stated above but using a 60 × Plan Apo Vc objective (numerical aperture, 1.40) and a Z optical spacing of 0.2 μm. Images were deconvolved using ImageJ software (US National Institutes of Health) with Parallel Iterative Deconvolution plugin, and maximum-intensity projections images are shown in the results. […]

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