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Protocols

bUnwarpJ specifications

Information


Unique identifier OMICS_25606
Name bUnwarpJ
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data An image.
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 2.6.9
Stability Stable
Requirements
ImageJ
Maintained Yes

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bUnwarpJ citations

 (14)
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miR200 regulated CXCL12β promotes fibroblast heterogeneity and immunosuppression in ovarian cancers

2018
Nat Commun
PMCID: 5849633
PMID: 29535360
DOI: 10.1038/s41467-018-03348-z
call_split See protocol

[…] SMA, FSP1) and of CD3 staining from the same tumor areas in representative tumors were further analyzed. Images were first aligned by applying an elastic transformation using a Fiji software plugin (bUnwarpJ). The plugin uses landmarks, defined by the user, and haematoxilin and eosin (H&E) staining from the different sections to compute the best correlation between images. The software next appli […]

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Effects of mutating α tubulin lysine 40 on sensory dendrite development

2017
PMCID: 5769580
PMID: 29122984
DOI: 10.1242/jcs.210203
call_split See protocol

[…] ). Briefly, z-stack images of neurons expressing CD4::GFP in larvae at 48 h AEL were acquired 15 min apart. Maximum projections of images taken at both time points were aligned in ImageJ by using the bUnwarpJ plugin and then overlaid in Metamorph. The first image (t=0) was pseudo-colored red and the second image (t=15 min) was pseudo-colored green. Overlaid images were manually scored for red and […]

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Visualization of Radial Peripapillary Capillaries Using Optical Coherence Tomography Angiography: The Effect of Image Averaging

2017
PLoS One
PMCID: 5222511
PMID: 28068370
DOI: 10.1371/journal.pone.0169385
call_split See protocol

[…] cted as the reference image; the other nine OCTAs were registered to this reference image using the Register Virtual Stack Slices plug-in on Image J; we employed a rigid extraction model with elastic bUnwarpJ splines registration []. For sets of images in which registration failed using the superficial OCTA slab due to low contrast, a deeper layer with larger blood vessels (vitreous to 150 μm belo […]

library_books

Multicenter Evaluation of Geometric Accuracy of MRI Protocols Used in Experimental Stroke

2016
PLoS One
PMCID: 5014410
PMID: 27603704
DOI: 10.1371/journal.pone.0162545

[…] ane resolution for proper comparison. Subsequently, rigid transformation was used to align MRI images over corresponding reference CT data and a non-rigid b-splines transformation algorithm using the bUnwarpJ plugin in ImageJ was applied to produce a precise match []. This tool produces a file containing the horizontal and vertical displacement values induced on each pixel of the MRI images; this […]

library_books

Fully automatic and robust 3D registration of serial section microscopic images

2015
Sci Rep
PMCID: 4598826
PMID: 26449756
DOI: 10.1038/srep15051

[…] thod using least squares (linear feature correspondence), an elastic b-spline model for biological images (UnwarpJ), an improved bi-directional b-spline model for histopathological section alignment (bUnwarpJ) and an elastic volume reconstruction method, and the four benchmark registration methods are tested with four different transformation parameters, including translation, rigid, similarity an […]

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Rapid and Localized Mechanical Stimulation and Adhesion Assay: TRPM7 Involvement in Calcium Signaling and Cell Adhesion

2015
PLoS One
PMCID: 4422584
PMID: 25946314
DOI: 10.1371/journal.pone.0126440
call_split See protocol

[…] ize the vibration, images from the fast camera were analyzed using an ImageJ (available at http://rsb.info.nih.gov/ij; developed by Wayne Rasband, National Institutes of Health, Bethesda, MD) plugin, bUnwarpJ []. This plugin was used to compare the position of the beads between two frames: a frame displaced by the probe motion and a reference frame with the probe merely positioned but not moving. […]


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