Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Electron Microscope Tomography and Single-particle Reconstruction

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...

You might also read

Related Articles

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

Sort by

Same author

Relative contribution of gonads and sex chromosomes to sex differences in cell-type gene expression in the mouse medial septum and sex-biased disease risk.

bioRxiv : the preprint server for biology·2025

Same author

Neuronal PAC1 deletion impairs structural plasticity.

Life sciences·2025

Same author

Validation of Structure Tensor Analysis for Orientation Estimation in Brain Tissue Microscopy.

bioRxiv : the preprint server for biology·2025

Same author

Mouse Brain Extractor: Brain segmentation of mouse MRI using global positional encoding and SwinUNETR.

bioRxiv : the preprint server for biology·2024

Same author

Estrogen receptor beta in astrocytes modulates cognitive function in mid-age female mice.

Nature communications·2023

Same author

Neuroprotection in Cerebral Cortex Induced by the Pregnancy Hormone Estriol.

Laboratory investigation; a journal of technical methods and pathology·2023

Search research articles

Related Experiment Video

Updated: Sep 13, 2025

Diffusion Tensor Magnetic Resonance Imaging in the Analysis of Neurodegenerative Diseases

Diffusion Tensor Magnetic Resonance Imaging in the Analysis of Neurodegenerative Diseases

Published on: July 28, 2013

Validation of structure tensor analysis for orientation estimation in brain tissue microscopy.

Bryson Gray¹, Andrew Smith¹, Allan MacKenzie-Graham¹

¹University of California, Los Angeles, Ahmanson-Lovelace Brain Mapping Center, 635 Charles E Young Dr S, Los Angeles, CA 90095, USA.

Journal of Neuroscience Methods

|July 30, 2025

Summary

This summary is machine-generated.

Structure tensor analysis accurately estimates single fiber orientations but struggles with crossings, especially in anisotropic microscopy data. Parameter choices are critical for crossing fibers to avoid random orientation estimates.

Keywords:

Axon orientation Brain connectivity Diffusion MRI Structure tensor analysis Tractography Validation White matter

More Related Videos

Patient-specific Modeling of the Heart: Estimation of Ventricular Fiber Orientations

Patient-specific Modeling of the Heart: Estimation of Ventricular Fiber Orientations

Published on: January 8, 2013

Three-Dimensional Shape Modeling and Analysis of Brain Structures

Three-Dimensional Shape Modeling and Analysis of Brain Structures

Published on: November 14, 2019

Related Experiment Videos

Last Updated: Sep 13, 2025

Diffusion Tensor Magnetic Resonance Imaging in the Analysis of Neurodegenerative Diseases

Diffusion Tensor Magnetic Resonance Imaging in the Analysis of Neurodegenerative Diseases

Published on: July 28, 2013

Patient-specific Modeling of the Heart: Estimation of Ventricular Fiber Orientations

Patient-specific Modeling of the Heart: Estimation of Ventricular Fiber Orientations

Published on: January 8, 2013

Three-Dimensional Shape Modeling and Analysis of Brain Structures

Three-Dimensional Shape Modeling and Analysis of Brain Structures

Published on: November 14, 2019

Area of Science:

Neuroimaging
Diffusion MRI
Microscopy

Background:

Accurate white matter pathway localization via diffusion MRI is crucial for brain connectivity research.
Current diffusion MRI methods require validation, often using co-registered microscopy data from post-mortem samples.
Structure tensor analysis is a standard method for computing local orientations but lacks thorough validation and has uncertainties in angular resolution and spatial scale selectivity.

Purpose of the Study:

To investigate the accuracy of structure tensor analysis for estimating fiber orientations.
To evaluate the method's performance on simulated fiber configurations with and without crossings.
To assess the impact of anisotropic resolution, common in microscopy, on structure tensor accuracy.

Main Methods:

Conducted a simulation study to assess structure tensor accuracy.
Examined various simulated conditions, including anisotropic image resolution.
Analyzed 2D and 3D optical microscopy data.

Main Results:

Parameter choice has minimal impact on single orientation estimation accuracy.
Accuracy decreases with increasing resolution anisotropy.
Parameter choice is critical for estimating crossing fiber orientations; poor choices lead to random estimates.

Conclusions:

Provides recommendations for effective application of structure tensor analysis in brain imaging.
Quantifies the limitations of structure tensor analysis, particularly with anisotropic data.
Highlights the critical role of parameter selection when analyzing complex fiber architectures.