EM3D specifications


Unique identifier OMICS_27807
Name EM3D
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.0
Stability Stable
Registration required Yes
Maintained Yes


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  • person_outline Uel McMahan <>

Additional information


Publication for EM3D

EM3D in publications

PMCID: 3718691
PMID: 23894473
DOI: 10.1371/journal.pone.0069410

[…] of the luminal assemblies based on the alignment of their surface models was carried out using the icp (iterative closest point) algorithm . surface models generated in the idl version of em3d were exported to the ‘.ply’ data format. individual luminal assemblies were then aligned to form the models starting at 20 degree step points in the x,y,z rotation using the software package […]

PMCID: 3306385
PMID: 22438915
DOI: 10.1371/journal.pone.0033333

[…] to maximize contrast boundary discrimination of the structures under study., structures were segmented from the reconstructions by using a combination of manual and semi-automatic methods in em3d to define individual volumes-of-interest (vois; ). for the presynaptic membrane and synaptic vesicles, which were heavily stained and had a simple geometry, a semi-automatic scheme was used […]

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EM3D institution(s)
Department of Neurobiology, Stanford University School of Medicine, Stanford, CA, USA
EM3D funding source(s)
Supported by NIH training grant 5T32 NS 07158, the M.A Antelman Fund and NIH research grant 2R01 NS 14506.

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