Evidence map›Paper›PMID 34644582›Full record

ArticleCell reports2021

NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images.

Oleh Krupa, Giulia Fragola, Ellie Hadden-Ford, Jessica T Mory, Tianyi Liu, Zachary Humphrey, Benjamin W Rees, Ashok Krishnamurthy, William D Snider, Mark J Zylka and 3 more

Abstract readVideo-Audio Media
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

  1. Article
  2. bioRxiv : the preprint server for biology · 2026
    Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images.IEEE/ACM transactions on computational biology and bioinformatics
    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

13 authors.

Oleh KrupaJoint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27514, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Giulia FragolaUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Ellie Hadden-FordUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Jessica T MoryUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Tianyi LiuUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Zachary HumphreyUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Benjamin W ReesUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Ashok KrishnamurthyRenaissance Computing Institute, Chapel Hill, NC 27517, USA; Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
William D SniderUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Mark J ZylkaUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
Guorong WuDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
Lei XingUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address: lxing@email.unc.edu.
Jason L SteinUNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address: jason_stein@med.unc.edu.

Funding

Virology Research Program (Program 4)P30CA016086 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI David Darr · 1985 to 2026
$201.5M
UNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Stephanie Engel · 2001 to 2026
$36.3M
UNC Neuroscience Center Research Cores: MicroscopyP30NS045892 · NINDS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI ZYLKA, MARK J. · 2003 to 2022
$11.5M
Preclinical CoreP50HD103573 · NICHD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI GABRIEL S DICHTER · 2020 to 2026
$9.7M
Environmental-use chemicals that target pathways linked to autism and other neurodevelopmental disordersR35ES028366 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Mark J. Zylka · 2019 to 2026
$6.8M
The influence of common genetic variation on brain overgrowth pathwaysR01MH120125 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI STEIN, JASON LOUIS · 2019 to 2023
$2.5M
pathQTL: Integrative Multi-Omics Causal Inference of Molecular Mechanisms Leading to Neuropsychiatric IllnessR01MH118349 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI LOVE, MICHAEL ISAIAH, STEIN, JASON LOUIS · 2019 to 2023
$2.4M
Quantifying the developmental trajectory of autism-associated brain overgrowth using 3D cellular resolution imagingR01MH121433 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI STEIN, JASON LOUIS · 2019 to 2023
$2.2M
A Scalable Platform for Exploring and Analyzing Whole Brain Tissue Cleared ImagesR01NS110791 · NINDS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI WU, GUORONG · 2019 to 2023
$1.9M
Transcription-associated DNA damage and neurodegenerationR56AG058663 · NIA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI MCCONNELL, MICHAEL J., ZYLKA, MARK J. · 2018 to 2018
$709k
NCI NIH HHS P30 CA016086NIA NIH HHS R56 AG058663NICHD NIH HHS P50 HD103573NIEHS NIH HHS P30 ES010126NIEHS NIH HHS R35 ES028366NIMH NIH HHS R01 MH118349NIMH NIH HHS R01 MH120125NIMH NIH HHS R01 MH121433NINDS NIH HHS P30 NS045892NINDS NIH HHS R01 NS110791
6 · The paper itself

Abstract

Tissue-clearing methods allow every cell in the mouse brain to be imaged without physical sectioning. However, the computational tools currently available for cell quantification in cleared tissue images have been limited to counting sparse cell populations in stereotypical mice. Here, we introduce NuMorph, a group of analysis tools to quantify all nuclei and nuclear markers within the mouse cortex after clearing and imaging by light-sheet microscopy. We apply NuMorph to investigate two distinct mouse models: a Topoisomerase 1 (Top1) model with severe neurodegenerative deficits and a Neurofibromin 1 (Nf1) model with a more subtle brain overgrowth phenotype. In each case, we identify differential effects of gene deletion on individual cell-type counts and distribution across cortical regions that manifest as alterations of gross brain morphology. These results underline the value of whole-brain imaging approaches, and the tools are widely applicable for studying brain structure phenotypes at cellular resolution.

Indexed as

Histocytological Preparation TechniquesNerve DegenerationNeuroimagingAnimalsCell NucleusCerebral CortexDNA Topoisomerases, Type IGene DeletionGenes, Neurofibromatosis 1Image Processing, Computer-AssistedMiceMice, KnockoutNeurogliaNeuronsPhenotypeSupport Vector MachineDNA Topoisomerases, Type Iimage analysisneurofibromatosistissue clearingwhole-brain imaging

Identifiers

PMID34644582
PMCPMC8530274

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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 OpenQuestion graph.