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Article

Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira

1
Hinton and Garza Lopez Family Consulting Company, Iowa City, IA 52246, USA
2
Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
3
National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
4
Department of Biology, University of Hawaii at Hilo, Hilo, HI 96720, USA
5
Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN 37208, USA
7
Microscopy and Cell Analysis Core Facility, Mayo Clinic, Rochester, MN 55905, USA
8
Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 52013, USA
10
Central Microscopy Research Facility, University of Iowa, Iowa City, IA 52242, USA
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Fraternal Order of Eagles Diabetes Research Center, Iowa City, IA 52242, USA
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
These authors share senior authorship.
Academic Editor: Alexander E. Kalyuzhny
Cells 2022, 11(1), 65; https://doi.org/10.3390/cells11010065
Received: 25 September 2021 / Revised: 18 December 2021 / Accepted: 22 December 2021 / Published: 27 December 2021
(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Techniques)
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. View Full-Text
Keywords: Amira; SBF-SEM; FIB-SEM; segmentation; organelles; 3D reconstruction; 3D imaging; mitochondrial imaging; volume analysis Amira; SBF-SEM; FIB-SEM; segmentation; organelles; 3D reconstruction; 3D imaging; mitochondrial imaging; volume analysis
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MDPI and ACS Style

Garza-Lopez, E.; Vue, Z.; Katti, P.; Neikirk, K.; Biete, M.; Lam, J.; Beasley, H.K.; Marshall, A.G.; Rodman, T.A.; Christensen, T.A.; Salisbury, J.L.; Vang, L.; Mungai, M.; AshShareef, S.; Murray, S.A.; Shao, J.; Streeter, J.; Glancy, B.; Pereira, R.O.; Abel, E.D.; Hinton, A., Jr. Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira. Cells 2022, 11, 65. https://doi.org/10.3390/cells11010065

AMA Style

Garza-Lopez E, Vue Z, Katti P, Neikirk K, Biete M, Lam J, Beasley HK, Marshall AG, Rodman TA, Christensen TA, Salisbury JL, Vang L, Mungai M, AshShareef S, Murray SA, Shao J, Streeter J, Glancy B, Pereira RO, Abel ED, Hinton A Jr. Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira. Cells. 2022; 11(1):65. https://doi.org/10.3390/cells11010065

Chicago/Turabian Style

Garza-Lopez, Edgar, 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. D. Abel, and Antentor Hinton Jr. 2022. "Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira" Cells 11, no. 1: 65. https://doi.org/10.3390/cells11010065

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