Evidence map›Paper›PMID 37900100›Full record

ArticleBio-protocol2023

Princeton RAtlas: A Common Coordinate Framework for Fully cleared, Whole

Emily Jane Dennis, Peter Bibawi, Zahra M Dhanerawala, Laura A Lynch, Samuel S-H Wang, Carlos D Brody

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

Article in Bio-protocol, 2023. 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, top 87% 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

1 citing paper in PubMed, 0 citations in OpenAlex.

  1. Brain-wide coordination of internal signals during decision-making.bioRxiv : the preprint server for biology · 2025
    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

6 authors at 3 institutions in 1 country.

Emily Jane DennisPrinceton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
Peter BibawiPrinceton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
Zahra M DhanerawalaPrinceton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
Laura A LynchPrinceton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
Samuel S-H WangPrinceton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
Carlos D BrodyPrinceton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
Princeton University · USHoward Hughes Medical Institute · USUniversity of Pennsylvania · US

Funding

Subcortical Neural Coding and DynamicsU19NS104648 · NINDS · PRINCETON UNIVERSITY · PI SEUNG, HYUNJUNE SEBASTIAN · 2017 to 2021
$15.3M
Imaging adaptive cerebellar processing at cellular resolution in awake miceR01NS045193 · NINDS · PRINCETON UNIVERSITY · PI WANG, SAMUEL SHENG-HUNG · 2003 to 2024
$7.5M
A web-based framework for multi-modal visualization and annotation of neuroanatomical dataRF1MH128776 · NIMH · PRINCETON UNIVERSITY · PI KLEINFELD, DAVID, WANG, SAMUEL SHENG-HUNG · 2021 to 2021
$1.6M
NIMH NIH HHS RF1 MH128776NINDS NIH HHS R01 NS045193NINDS NIH HHS U19 NS104648
6 · The paper itself

Abstract

Whole-brain clearing and imaging methods are becoming more common in mice but have yet to become standard in rats, at least partially due to inadequate clearing from most available protocols. Here, we build on recent mouse-tissue clearing and light-sheet imaging methods and develop and adapt them to rats. We first used cleared rat brains to create an open-source, 3D rat atlas at 25 μm resolution. We then registered and imported other existing labeled volumes and made all of the code and data available for the community (https://github.com/emilyjanedennis/PRA) to further enable modern, whole-brain neuroscience in the rat. Key features • This protocol adapts iDISCO (Renier et al., 2014) and uDISCO (Pan et al., 2016) tissue-clearing techniques to consistently clear rat brains. • This protocol also decreases the number of working hours per day to fit in an 8 h workday. Graphical overview.

Indexed as

iDISCOImage registrationLight-sheet imagingNeuroscienceRatRattus norvegicusTissue clearinguDISCO

Identifiers

PMID37900100
PMCPMC10603261
OpenAlexW4387830677

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.