Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Junctophilin-2-orchestrated calcium signalosome regulates brown adipocyte thermogenesis and energy metabolism.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

3D EM uncovers mitochondrial network remodeling in residual triple negative breast cancer after conventional chemotherapy treatments.

iScience·2026
Same author

Annexin A6 Modulates the Secretion of Pro-Inflammatory Cytokines and Exosomes via Interaction with SNAP23 in Triple-Negative Breast Cancer Cells.

Cells·2026
Same author

Clinicopathologic characteristics of early-onset breast cancer among unselected young Black women.

Cancer·2026
Same author

Aging Remodels Mitochondrial Architecture Across the Male Reproductive Axis.

Research square·2026
Same author

Adipose Tissue Plasticity, Lipoprotein Metabolism, and Cardiovascular Risk: The Emerging Role of the GLP-1 Axis.

Circulation research·2026

Related Experiment Video

Updated: Oct 7, 2025

Three-dimensional Characterization of Interorganelle Contact Sites in Hepatocytes using Serial Section Electron Microscopy
09:12

Three-dimensional Characterization of Interorganelle Contact Sites in Hepatocytes using Serial Section Electron Microscopy

Published on: June 9, 2022

5.9K

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

Edgar Garza-Lopez1, Zer Vue2, Prasanna Katti3

  • 1Hinton and Garza Lopez Family Consulting Company, Iowa City, IA 52246, USA.

Cells
|January 11, 2022
PubMed
Summary

New 3D imaging techniques like SBF-SEM and FIB-SEM enable ultrastructural analysis of organelles. This study presents a standardized protocol using Amira software for reproducible 3D quantification of organelle morphology.

Keywords:
3D imaging3D reconstructionAmiraFIB-SEMSBF-SEMmitochondrial imagingorganellessegmentationvolume analysis

More Related Videos

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
12:08

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Published on: August 13, 2014

24.7K
Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps
08:59

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps

Published on: October 28, 2018

7.2K

Related Experiment Videos

Last Updated: Oct 7, 2025

Three-dimensional Characterization of Interorganelle Contact Sites in Hepatocytes using Serial Section Electron Microscopy
09:12

Three-dimensional Characterization of Interorganelle Contact Sites in Hepatocytes using Serial Section Electron Microscopy

Published on: June 9, 2022

5.9K
From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
12:08

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Published on: August 13, 2014

24.7K
Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps
08:59

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps

Published on: October 28, 2018

7.2K

Area of Science:

  • Cellular Biology
  • Microscopy
  • Biotechnology

Background:

  • High-resolution 3D imaging is crucial for understanding organelle structure and function.
  • Traditional methods like light microscopy and transmission electron microscopy (TEM) lack 3D capabilities.
  • Emerging techniques such as serial block-face scanning electron microscopy (SBF-SEM) and focused ion beam scanning electron microscopy (FIB-SEM) offer 3D ultrastructural insights.

Purpose of the Study:

  • To establish a standardized protocol for quantifying organelle morphology in 3D.
  • To demonstrate the application of SBF-SEM and Amira software for accurate and reproducible 3D measurements.
  • To analyze the 3D morphology of mitochondria and endoplasmic reticulum (ER).

Main Methods:

  • Utilized serial block-face scanning electron microscopy (SBF-SEM) for high-resolution 3D data acquisition.
  • Employed Amira visualization software for standardized 3D image processing and analysis.
  • Quantified morphological parameters of mitochondria and endoplasmic reticulum (ER) structures.

Main Results:

  • Developed and validated a reproducible protocol for 3D organelle quantification.
  • Successfully applied SBF-SEM and Amira to analyze complex organelle structures.
  • Obtained accurate measurements of mitochondrial and ER morphologies in three dimensions.

Conclusions:

  • The presented protocol enables precise and reproducible 3D quantification of organelle morphology.
  • SBF-SEM combined with Amira software is a powerful tool for ultrastructural analysis in cellular biology.
  • This approach advances the study of organelle dynamics and cellular substructures.