Evidence map›Paper›PMID 40738261›Full record

ArticleJournal of neuroscience methods2025

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

Bryson Gray, Andrew W Smith, Allan MacKenzie-Graham, David W Shattuck, Daniel J Tward

Abstract readValidation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of neuroscience methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Bryson GrayUniversity of California, Los Angeles, Ahmanson-Lovelace Brain Mapping Center, 635 Charles E Young Dr S, Los Angeles, CA 90095, USA.
Andrew W SmithUniversity of California, Los Angeles, Ahmanson-Lovelace Brain Mapping Center, 635 Charles E Young Dr S, Los Angeles, CA 90095, USA.
Allan MacKenzie-GrahamUniversity of California, Los Angeles, Ahmanson-Lovelace Brain Mapping Center, 635 Charles E Young Dr S, Los Angeles, CA 90095, USA.
David W ShattuckUniversity of California, Los Angeles, Ahmanson-Lovelace Brain Mapping Center, 635 Charles E Young Dr S, Los Angeles, CA 90095, USA.
Daniel J TwardUniversity of California, Los Angeles, Ahmanson-Lovelace Brain Mapping Center, 635 Charles E Young Dr S, Los Angeles, CA 90095, USA. Electronic address: dtward@mednet.ucla.edu.

Funding

Tool and Technology Development CoreU19MH114821 · NIMH · COLD SPRING HARBOR LABORATORY · PI ARLOTTA, PAOLA, HUANG, Z JOSH · 2017 to 2021
$64.5M
A 3D multimodal micron-scale human brain atlas bridging single cell data, neuropathology and neuroradiologyRF1MH128875 · NIMH · COLD SPRING HARBOR LABORATORY · PI MITRA, PARTHA PRATIM, ZHANG, JIANGYANG · 2021 to 2021
$5.3M
A Toolkit for Analysis and Visualization of Preclinical Rodent Neuroimaging ExperimentsR01NS121761 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Allan James MacKenzie-Graham, David W Shattuck · 2022 to 2026
$3.1M
Bringing CLARITY to EAER01NS086981 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI MACKENZIE-GRAHAM, ALLAN JAMES · 2015 to 2018
$1.3M
The Mechanism of Gray Matter Atrophy in Experimental Autoimmune EncephalomyelitisR21NS121806 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI MACKENZIE-GRAHAM, ALLAN JAMES · 2021 to 2021
$429k
NIMH NIH HHS RF1 MH128875NIMH NIH HHS U19 MH114821NINDS NIH HHS R01 NS086981NINDS NIH HHS R01 NS121761NINDS NIH HHS R21 NS121806
6 · The paper itself

Abstract

backgroundAccurate localization of white matter pathways using diffusion MRI is critical to investigating brain connectivity, but the accuracy of current methods is not thoroughly understood. A fruitful approach to validating accuracy is to consider microscopy data that have been co-registered with MRI of post mortem samples. In this setting, structure tensor analysis is a standard approach to computing local orientations. However, structure tensor analysis itself has not been well-validated and is subject to uncertainty in its angular resolution, and selectivity to specific spatial scales. NEW

methodHere, we conducted a simulation study to investigate the accuracy of using structure tensors to estimate the orientations of fibers arranged in configurations with and without crossings.

resultsWe examined a range of simulated conditions, with a focus on investigating the method's behavior on images with anisotropic resolution, which is particularly common in microscopy data acquisition. We also analyzed 2D and 3D optical microscopy data. COMPARISON WITH EXISTING

methodsOur results show that parameter choice in structure tensor analysis has relatively little effect on accuracy for estimating single orientations, although accuracy decreases with increasing resolution anisotropy. On the other hand, when estimating the orientations of crossing fibers, the choice of parameters becomes critical, and poor choices result in orientation estimates that are essentially random.

conclusionsThis work provides a set of recommendations for researchers seeking to apply structure tensor analysis effectively in the study of axonal orientations in brain imaging data and quantifies the method's limitations, particularly in the case of anisotropic data.

Indexed as

BrainDiffusion Tensor ImagingImage Processing, Computer-AssistedMicroscopyWhite MatterAnisotropyComputer SimulationHumansImaging, Three-DimensionalAxon orientationBrain connectivityDiffusion MRIStructure tensor analysisTractographyValidationWhite matter

Identifiers

PMID40738261
PMCPMC12903131

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.