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A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells
JoVE Journal
Neuroscience
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JoVE Journal Neuroscience
A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

DOI:
10.3791/59444-v

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12:49 min

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September 28, 2019

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, , , , , ,
1Biological and Environmental Sciences and Engineering Division,King Abdullah University of Science and Technology, 2Visual Computing Center,King Abdullah University of Science and Technology

Chapters

  • 00:04Title
  • 01:02Image Processing Using Fiji
  • 03:58Segmentation (Semi-Automated) and Reconstruction Using Ilastik 1.3.2
  • 07:433D Analysis
  • 09:41Results: 3D Reconstruction and Virtual Reality Analysis
  • 11:40Conclusion

Summary

Automatic Translation

Automatic Translation

The described pipeline is designed for the segmentation of electron microscopy datasets larger than gigabytes, to extract whole-cell morphologies. Once the cells are reconstructed in 3D, customized software designed around individual needs can be used to perform a qualitative and quantitative analysis directly in 3D, also using virtual reality to overcome view occlusion.

Tags

Keywords: 3D ReconstructionVirtual Reality AnalysisGlial CellsNeuronal CellsAutomated Serial Section Electron MicroscopyImage ProcessingSegmentationTrakEM2Ilastik3D ModelingStructural ImpairmentsDiagnostic StrategyImage StitchingImage Downsampling

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