Evidence map›Paper›PMID 27039972›Full record

ArticleJournal of neuroscience methods2016

A methodological pipeline for serial-section imaging and tissue realignment for whole-brain functional and connectivity assessment.

Lilia Mesina, Aaron A Wilber, Benjamin J Clark, Sutherland Dube, Alexis J Demecha, Craig E L Stark, Bruce L McNaughton

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of neuroscience methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
3.0field-weighted citation impact, top 8% of its field
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

4 citing papers in PubMed, 7 citations in OpenAlex.

  1. Review
  2. Review
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 3 institutions in 2 countries.

Lilia MesinaCanadian Centre for Behavioural Neuroscience, The University of Lethbridge, Lethbridge, AB, Canada. Electronic address: lilia.mesina@uleth.ca.
Aaron A WilberCanadian Centre for Behavioural Neuroscience, The University of Lethbridge, Lethbridge, AB, Canada; Department of Neurobiology and Behavior, University of California, Irvine, CA, USA. Electronic address: awilber@uci.edu.
Benjamin J ClarkDepartment of Psychology, The University of New Mexico, Albuquerque, NM, USA. Electronic address: bnjclark@unm.edu.
Sutherland DubeCanadian Centre for Behavioural Neuroscience, The University of Lethbridge, Lethbridge, AB, Canada.
Alexis J DemechaCanadian Centre for Behavioural Neuroscience, The University of Lethbridge, Lethbridge, AB, Canada.
Craig E L StarkDepartment of Neurobiology and Behavior, University of California, Irvine, CA, USA.
Bruce L McNaughtonCanadian Centre for Behavioural Neuroscience, The University of Lethbridge, Lethbridge, AB, Canada; Department of Neurobiology and Behavior, University of California, Irvine, CA, USA.
University of California, Irvine · USUniversity of Lethbridge · CAUniversity of New Mexico · US

Funding

Parietal-hippocampal network in the triple transgenic mouse model of AlzheimersR00AG049090 · NIA · FLORIDA STATE UNIVERSITY · PI WILBER, AARON A · 2017 to 2019
$747k
Parietal-hippocampal network in the triple transgenic mouse model of AlzheimersK99AG049090 · NIA · UNIVERSITY OF CALIFORNIA-IRVINE · PI WILBER, AARON A · 2015 to 2016
$189k
Phase sequences of posterior parietal cortex ensembles and sequence learningF32MH099682 · NIMH · UNIVERSITY OF CALIFORNIA-IRVINE · PI WILBER, AARON A · 2013 to 2013
$51k
NIA NIH HHS K99 AG049090NIA NIH HHS R00 AG049090NIMH NIH HHS F32 MH099682
6 · The paper itself

Abstract

backgroundUnderstanding the neurobiological basis of cognition and behavior, and disruptions to these processes following injury and disease, requires a large-scale assessment of neural populations, and knowledge of their patterns of connectivity. NEW

methodWe present an analysis platform for large-scale investigation of functional and neuroanatomical connectivity in rodents. Retrograde tracers were injected and in a subset of animals behavioral tests to drive immediate-early gene expression were administered. This approach allows users to perform whole-brain assessment of function and connection in a semi-automated quantitative manner. Brains were cut in the coronal plane, and an image of the block face was acquired. Wide-field fluorescent scans of whole sections were acquired and analyzed using Matlab software.

resultsThe toolkit utilized open-source and custom platforms to accommodate a largely automated analysis pipeline in which neuronal boundaries are automatically segmented, the position of segmented neurons are co-registered with a corresponding image acquired during sectioning, and a 3-D representation of neural tracer (and other products) throughout the entire brain is generated. COMPARISON WITH EXISTING

methodsCurrent whole brain connectivity measures primarily target mice and use anterograde tracers. Our focus on segmented units of interest (e.g., NeuN labeled neurons) and restricting measures to these units produces a flexible platform for a variety of whole brain analyses (measuring activation, connectivity, markers of disease, etc.).

conclusionsThis open-source toolkit allows an investigator to visualize and quantify whole brain data in 3-D, and additionally provides a framework that can be rapidly integrated with user-specific analyses and methodologies.

Indexed as

Gene ExpressionSoftwareAnimalsBrainBrain MappingFemaleGenes, Immediate-EarlyImaging, Three-DimensionalMaleMice, Inbred C57BLNeural PathwaysNeuroanatomical Tract-Tracing TechniquesPattern Recognition, AutomatedRats, Inbred F344Rats, Long-EvansConnectomeFunctional networksImmediate-early genesNeural tracingNeuroimagingTissue realignment

Identifiers

PMID27039972
PMCPMC5695690
OpenAlexW2321517285

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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 OpenQuestion graph.