Cells, Vol. 11, Pages 65: Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira

Cells doi: 10.3390/cells11010065

Edgar Garza-Lopez
Zer Vue
Prasanna Katti
Kit Neikirk
Michelle Biete
Jacob Lam
Heather K. Beasley
Andrea G. Marshall
Taylor A. Rodman
Trace A. Christensen
Jeffrey L. Salisbury
Larry Vang
Margaret Mungai
Salma AshShareef
Sandra A. Murray
Jianqiang Shao
Jennifer Streeter
Brian Glancy
Renata O. Pereira
E. Dale Abel
Antentor Hinton

High-resolution 3D images of organelles are of paramount importance in cellular biology. Although light microscopy and transmission electron microscopy (TEM) have provided the standard for imaging cellular structures, they cannot provide 3D images. However, recent technological advances such as serial block-face scanning electron microscopy (SBF-SEM) and focused ion beam scanning electron microscopy (FIB-SEM) provide the tools to create 3D images for the ultrastructural analysis of organelles. Here, we describe a standardized protocol using the visualization software, Amira, to quantify organelle morphologies in 3D, thereby providing accurate and reproducible measurements of these cellular substructures. We demonstrate applications of SBF-SEM and Amira to quantify mitochondria and endoplasmic reticulum (ER) structures.

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