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Title: GitHub - DanuserLab/u-segment3D: Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.

Open Graph Title: GitHub - DanuserLab/u-segment3D: Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.

X Title: GitHub - DanuserLab/u-segment3D: Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.

Description: Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method. - DanuserLab/u-segment3D

Open Graph Description: Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method. - DanuserLab/u-segment3D

X Description: Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method. - DanuserLab/u-segment3D

Mail addresses
felixzhou1@gmail.com

Opengraph URL: https://github.com/DanuserLab/u-segment3D

X: @github

direct link

Domain: patch-diff.githubusercontent.com

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og:image:altGenerate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method. - DanuserLab/u-segment3D
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Universal consensus 3D segmentation of cells from 2D segmented stackshttps://doi.org/10.1038/s41592-025-02887-w
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