Plant Image Analysis Plant Image Analysis


Hanchuan Peng lab
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Scientific article
V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets.
H. Peng, Z. Ruan, F. Long, JH. Simpson, EW. Myers,
2010 , Nat. Biotechnol. , 28(4), 348
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Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model.
H. Peng, Z. Ruan, D. Atasoy, S. Sternson,
2010 , Bioinformatics , 26(12), 0
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Extensible visualization and analysis for multidimensional images using Vaa3D.
H. Peng, A. Bria, Z. Zhou, G. Iannello, F. Long,
2014 , Nat Protoc , 9(1), 193
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Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes Vaa3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, Vaa3D streamlines the workflow of visualization-assisted analysis.

Source: Vaa3D webpage

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Operating system
mac, windows, linux,

freeware, open-source,

Measured variables
3D-reconstruction, surface,

Automation level

Plant requirements

Image requirements

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