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Research ArticleOpen Source Tools and Methods, Novel Tools and Methods

A Semi-Automated Workflow for Brain Slice Histology Alignment, Registration, and Cell Quantification (SHARCQ)

Kristoffer Lauridsen, Annie Ly, Emily D. Prévost, Connor McNulty, Dillon J. McGovern, Jian Wei Tay, Joseph Dragavon and David H. Root
eNeuro 8 April 2022, 9 (2) ENEURO.0483-21.2022; DOI: https://doi.org/10.1523/ENEURO.0483-21.2022
Kristoffer Lauridsen
1Department of Psychology and Neuroscience, University of Colorado, Boulder, CO 80301
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Annie Ly
1Department of Psychology and Neuroscience, University of Colorado, Boulder, CO 80301
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Emily D. Prévost
1Department of Psychology and Neuroscience, University of Colorado, Boulder, CO 80301
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Connor McNulty
1Department of Psychology and Neuroscience, University of Colorado, Boulder, CO 80301
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Dillon J. McGovern
1Department of Psychology and Neuroscience, University of Colorado, Boulder, CO 80301
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Jian Wei Tay
2BioFrontiers Institute, University of Colorado, Boulder, CO 80303
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Joseph Dragavon
2BioFrontiers Institute, University of Colorado, Boulder, CO 80303
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David H. Root
1Department of Psychology and Neuroscience, University of Colorado, Boulder, CO 80301
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Article Information

DOI 
https://doi.org/10.1523/ENEURO.0483-21.2022
PubMed 
35396257
Published By 
Society for Neuroscience
History 
  • Received November 16, 2021
  • Revision received April 1, 2022
  • Accepted April 4, 2022
  • Published online April 8, 2022.
Copyright & Usage 
Copyright © 2022 Lauridsen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.

Author Information

  1. Kristoffer Lauridsen1,*,
  2. Annie Ly1,*,
  3. Emily D. Prévost1,
  4. Connor McNulty1,
  5. Dillon J. McGovern1,
  6. Jian Wei Tay2,
  7. Joseph Dragavon2 and
  8. David H. Root1
  1. 1Department of Psychology and Neuroscience, University of Colorado, Boulder, CO 80301
  2. 2BioFrontiers Institute, University of Colorado, Boulder, CO 80303
  1. Correspondence should be addressed to David H. Root at david.root{at}colorado.edu.
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Author contributions

  1. Author contributions: K.L., A.L., E.D.P., C.M., and J.W.T. performed research; A.L., E.D.P., J.D., and D.H.R. designed research; A.L., E.D.P., and D.J.M. analyzed data; A.L. and D.H.R. wrote the paper.

  2. ↵* K.L. and A.L. contributed equally to this work.

Disclosures

  • The authors declare no competing financial interests.

  • This work was supported by National Institute on Drug Abuse of the National Institutes of Health (NIH) Awards R01DA047443 (to D.H.R.) and F31MH125569 (to D.J.M.), the Webb-Waring Biomedical Research Award from the Boettcher Foundation, a 2020 National Alliance for Research on Schizophrenia and Depression Young Investigator grant from the Brain and Behavior Research Foundation, an Anonymous benefactor, and The University of Colorado (D.H.R.). Imaging was performed at the BioFrontiers Institute Advanced Light Microscopy Core (RRID: SCR_018302). The PerkinElmer Opera Phenix is supported by the NIH Grant 1S10OD025072.

Funding

  • HHS | NIH | National Institute on Drug Abuse (NIDA)

    DA047443
  • Boettcher Foundation

    Webb-Waring Award
  • Brain and Behavior Research Foundation (Brain & Behavior Research Foundation)

    NARSAD
  • HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)

    1S10OD025072
  • HHS | NIH | National Institute of Mental Health (NIMH)

    MH125569

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A Semi-Automated Workflow for Brain Slice Histology Alignment, Registration, and Cell Quantification (SHARCQ)
Kristoffer Lauridsen, Annie Ly, Emily D. Prévost, Connor McNulty, Dillon J. McGovern, Jian Wei Tay, Joseph Dragavon, David H. Root
eNeuro 8 April 2022, 9 (2) ENEURO.0483-21.2022; DOI: 10.1523/ENEURO.0483-21.2022

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A Semi-Automated Workflow for Brain Slice Histology Alignment, Registration, and Cell Quantification (SHARCQ)
Kristoffer Lauridsen, Annie Ly, Emily D. Prévost, Connor McNulty, Dillon J. McGovern, Jian Wei Tay, Joseph Dragavon, David H. Root
eNeuro 8 April 2022, 9 (2) ENEURO.0483-21.2022; DOI: 10.1523/ENEURO.0483-21.2022
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Keywords

  • atlas registration
  • brain mapping
  • cell-type

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