Protocols for generating surfaces and measuring 3d organelle morphology using amira

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

doi:10.3390/cells11010065

Protocols for generating surfaces and measuring 3d organelle morphology using amira

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 AbelAntentor Hinton

Biochemistry and Molecular Biology

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Article number	65
Journal	Cells
Volume	11
Issue number	1
DOIs	https://doi.org/10.3390/cells11010065
State	Published - Jan 1 2022

Keywords

3D imaging
3D reconstruction
Amira
FIB-SEM
Mitochondrial imaging
Organelles
SBF-SEM
Segmentation
Volume analysis

ASJC Scopus subject areas

Medicine(all)

Access to Document

10.3390/cells11010065

Cite this

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., ... Hinton, A. (2022). Protocols for generating surfaces and measuring 3d organelle morphology using amira. Cells, 11(1), Article 65. https://doi.org/10.3390/cells11010065

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 2022, 'Protocols for generating surfaces and measuring 3d organelle morphology using amira', Cells, vol. 11, no. 1, 65. https://doi.org/10.3390/cells11010065

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title = "Protocols for generating surfaces and measuring 3d organelle morphology using amira",

abstract = "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.",

keywords = "3D imaging, 3D reconstruction, Amira, FIB-SEM, Mitochondrial imaging, Organelles, SBF-SEM, Segmentation, Volume analysis",

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

note = "Funding Information: Funding: This work was supported by T32 HL007121, the UNCF/BMS EE Just Postgraduate Fellowship, Ford Foundation Postdoctoral Fellowship, Burroughs Wellcome Fund CASI Award, Burroughs Welcome Fund Ad-hoc Award, NIH SRP Subaward to #5R25HL106365-12 from the NIH PRIDE Program, DK020593, Vanderbilt Diabetes and Research Training Center for DRTC Alzheimer{\textquoteright}s Disease Pilot & Feasibility Program, UNCF/BMS EE Just Faculty Fund Grant awarded to A.H.J.; NSF grant MCB #2011577I and NIH T32 5T32GM133353 to S.A.M., NIH grants R01HL108379 and R01DK092065 to E.D.A. H.K.B. is supported by 2U54CA 163069-07 from NCI and R25 GM059994/GM/NIGMS NIH. Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2022",

month = jan,

day = "1",

doi = "10.3390/cells11010065",

language = "English (US)",

volume = "11",

journal = "Cells",

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T1 - Protocols for generating surfaces and measuring 3d organelle morphology using amira

AU - Garza-Lopez, Edgar

AU - Vue, Zer

AU - Katti, Prasanna

AU - Neikirk, Kit

AU - Biete, Michelle

AU - Lam, Jacob

AU - Beasley, Heather K.

AU - Marshall, Andrea G.

AU - Rodman, Taylor A.

AU - Christensen, Trace A.

AU - Salisbury, Jeffrey L.

AU - Vang, Larry

AU - Mungai, Margaret

AU - Ashshareef, Salma

AU - Murray, Sandra A.

AU - Shao, Jianqiang

AU - Streeter, Jennifer

AU - Glancy, Brian

AU - Pereira, Renata O.

AU - Abel, E. Dale

AU - Hinton, Antentor

N1 - Funding Information: Funding: This work was supported by T32 HL007121, the UNCF/BMS EE Just Postgraduate Fellowship, Ford Foundation Postdoctoral Fellowship, Burroughs Wellcome Fund CASI Award, Burroughs Welcome Fund Ad-hoc Award, NIH SRP Subaward to #5R25HL106365-12 from the NIH PRIDE Program, DK020593, Vanderbilt Diabetes and Research Training Center for DRTC Alzheimer’s Disease Pilot & Feasibility Program, UNCF/BMS EE Just Faculty Fund Grant awarded to A.H.J.; NSF grant MCB #2011577I and NIH T32 5T32GM133353 to S.A.M., NIH grants R01HL108379 and R01DK092065 to E.D.A. H.K.B. is supported by 2U54CA 163069-07 from NCI and R25 GM059994/GM/NIGMS NIH. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2022/1/1

Y1 - 2022/1/1

N2 - 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.

AB - 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.

KW - 3D imaging

KW - 3D reconstruction

KW - Amira

KW - FIB-SEM

KW - Mitochondrial imaging

KW - Organelles

KW - SBF-SEM

KW - Segmentation

KW - Volume analysis

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DO - 10.3390/cells11010065

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SN - 2073-4409

VL - 11

JO - Cells

JF - Cells

IS - 1

M1 - 65

ER -

Protocols for generating surfaces and measuring 3d organelle morphology using amira

Abstract

Keywords

ASJC Scopus subject areas

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