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MorphoLibJ specifications


Unique identifier OMICS_12377
Name MorphoLibJ
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes




No version available

Publication for MorphoLibJ

MorphoLibJ citations


A Potential Compensatory Role of Panx3 in the VNO of a Panx1 Knock Out Mouse Model

PMCID: 5946002
PMID: 29780304
DOI: 10.3389/fnmol.2018.00135

[…] fluorescence protocol was created using a collection of plugins built into the ImageJ software. At the start, separated channels were background subtracted. A morphological segmentation tool from the MorphoLibJ plugin library was applied to segment images based on the watershed algorithm, creating new images based on watershed lines. These images were inverted to analyze particles, and the resulti […]


Automated brightfield morphometry of 3D organoid populations by OrganoSeg

Sci Rep
PMCID: 5871765
PMID: 29593296
DOI: 10.1038/s41598-017-18815-8

[…] ure batch variation stemming from different hydrogel lots and brightfield imaging setups. The images were manually traced as a standard reference with which to compare OrganoSeg against CellProfiler, MorphoLibJ, and ImageJ. The existing platforms each implemented the segmentation pipeline to the extent possible, but all lacked the multi-window local adaptive thresholding of OrganoSeg (Fig. ). Comp […]


A tension adhesion feedback loop in plant epidermis

PMCID: 5963923
PMID: 29683428
DOI: 10.7554/eLife.34460.027

[…] Original images were confocal Z-stacks. We used the MorphoGraphX software () to recover only the outer epidermal cortical microtubules signal. Further analysis was performed in 2D using the imageJ morpholibJ library (), to segment cells, the analyze particle tool to define ROIs and an automated version the FibrilTool macro () to analyze the principal orientation (θM) and anisotropy of the CMT a […]


Histological quantification of maize stem sections from FASGA stained images

Plant Methods
PMCID: 5664815
PMID: 29118822
DOI: 10.1186/s13007-017-0225-z
call_split See protocol

[…] The whole image processing workflow was developed within the ImageJ/Fiji plateform [], using the MorphoLibJ library []. The whole workflow was implemented as an ImageJ/Fiji plugin, freely available on the Internet []. The plugin provides the possibility to finely tune the different parameters use […]


Characterizing microglia activation: a spatial statistics approach to maximize information extraction

Sci Rep
PMCID: 5431479
PMID: 28484229
DOI: 10.1038/s41598-017-01747-8
call_split See protocol

[…] (Step 1) Image analysis was performed using Fiji (ImageJ, v1.51 h, 64 bit Windows) software with MorphoLibJ (v1.3.1) integrated library and plugin. Quantification of Iba-1 labelled microglia in retinal whole-mounts was achieved using a multi-step algorithm. First, segmentation of Iba-1 labelled m […]


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MorphoLibJ institution(s)
UR1268 Biopolymers, Interactions and Assemblies, INRA, Nantes, France; Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France; UMR782 Food Process Engineering and Microbiology, INRA, AgroParisTech, Thiverval-Grignon, France; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Computer Science and Artificial Intelligence Department, Basque Country University (UPV/EHU), Donostia-San Sebastian, Spain; Donostia International Physics Center (DIPC), Donostia-San Sebastian, Spain; Sorbonne Universités, UPMC Univ Paris UFR 927, Paris, France
MorphoLibJ funding source(s)
The TEFOR Infrastructure under the Investments for the Future program of the French National Research Agency (Grant #ANR-11-INBS-0014)

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