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Research ArticleOpen Source Tools and Methods, Novel Tools and Methods

RapID Cell Counter: Semi-Automated and Mid-Throughput Estimation of Cell Density within Diverse Cortical Layers

Aarthi Sekar, Thiago M. Sanches, Keiko Hino, Matangi Kumar, Juliann Wang, Elisa Ha, Blythe Durbin-Johnson, Sergi Simó and Megan Y. Dennis
eNeuro 1 November 2021, 8 (6) ENEURO.0185-21.2021; https://doi.org/10.1523/ENEURO.0185-21.2021
Aarthi Sekar
1Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616
2Department of Biochemistry and Molecular Medicine, MIND Institute, University of California, Davis, CA, 95616
3Genome Center, University of California, Davis, CA, 95616
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Thiago M. Sanches
1Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616
4Department of Animal Sciences, University of California, Davis, CA, 95616
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Keiko Hino
5Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616
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Matangi Kumar
3Genome Center, University of California, Davis, CA, 95616
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Juliann Wang
3Genome Center, University of California, Davis, CA, 95616
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Elisa Ha
3Genome Center, University of California, Davis, CA, 95616
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Blythe Durbin-Johnson
6Department of Public Health Sciences, University of California, Davis, CA, 95616
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Sergi Simó
5Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616
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Megan Y. Dennis
1Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616
2Department of Biochemistry and Molecular Medicine, MIND Institute, University of California, Davis, CA, 95616
3Genome Center, University of California, Davis, CA, 95616
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Article Information

DOI 
https://doi.org/10.1523/ENEURO.0185-21.2021
PubMed 
34725102
Published By 
Society for Neuroscience
History 
  • Received April 23, 2021
  • Revision received September 23, 2021
  • Accepted October 25, 2021
  • Published online November 1, 2021.
Copyright & Usage 
Copyright © 2021 Sekar 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. Aarthi Sekar1,2,3,*,
  2. Thiago M. Sanches1,4,*,
  3. Keiko Hino5,
  4. Matangi Kumar3,
  5. Juliann Wang3,
  6. Elisa Ha3,
  7. Blythe Durbin-Johnson6,
  8. Sergi Simó5 and
  9. Megan Y. Dennis1,2,3
  1. 1Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616
  2. 2Department of Biochemistry and Molecular Medicine, MIND Institute, University of California, Davis, CA, 95616
  3. 3Genome Center, University of California, Davis, CA, 95616
  4. 4Department of Animal Sciences, University of California, Davis, CA, 95616
  5. 5Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616
  6. 6Department of Public Health Sciences, University of California, Davis, CA, 95616
  1. Correspondence should be addressed to Megan Y. Dennis at mydennis{at}ucdavis.edu or Sergi Simó at ssimo{at}ucdavis.edu.
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Author contributions

  1. Author contributions: A.S., T.M.S., S.S., and M.Y.D. designed research; A.S., T.M.S., K.H., M.K., J.W., and E.H. performed research; A.S., T.M.S., B.D.-J., S.S., and M.Y.D. analyzed data; A.S., T.M.S., S.S., and M.Y.D. wrote the paper.

  2. ↵* A.S. and T.M.S. contributed equally to this work.

Disclosures

  • The authors declare no competing financial interests.

  • This work was supported by National Institutes of Health National Institutes of General Medicine T32 Predoctoral Training Program in Molecular and Cellular Biology at University of California Davis Grant GM007377 (to A.S.), Eunice Kennedy Shriver National Institute of Child Health and Human Development funded MIND Institute Intellectual and Developmental Disabilities Research Center Grant P50HD103526 (to B.D.-J.), National Center for Advancing Translational Sciences Grant UL1TR001860 (to B.D.-J.), National Institute of Neurological Disorders and Stroke Grant R01NS120961 (to S.S.), National Institute of Neurological Disorders and Stroke Grant R00NS083627 (to M.Y.D.), and NIH Director’s New Innovator Award administered by the National Institute of Mental Health DP2OD025824 (to M.Y.D.). This work was also supported by the Alfred P. Sloan Foundation Fellowship FG-2016-6814 (to M.Y.D.).

Funding

  • HHS | NIH | National Institute of General Medical Sciences (NIGMS)

    GM007377
  • HHS | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)

    P50HD103526
  • HHS | NIH | National Institute of Neurological Disorders and Stroke (NINDS)

    R01NS120961; R00NS083627
  • HHS | NIH | NIH Office of the Director (OD)

    DP2OD025824
  • Alfred P. Sloan Foundation

    FG-2016-6814

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  • previous version (November 01, 2021).

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Total 202535555140
Total117345091823
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RapID Cell Counter: Semi-Automated and Mid-Throughput Estimation of Cell Density within Diverse Cortical Layers
Aarthi Sekar, Thiago M. Sanches, Keiko Hino, Matangi Kumar, Juliann Wang, Elisa Ha, Blythe Durbin-Johnson, Sergi Simó, Megan Y. Dennis
eNeuro 1 November 2021, 8 (6) ENEURO.0185-21.2021; DOI: 10.1523/ENEURO.0185-21.2021

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RapID Cell Counter: Semi-Automated and Mid-Throughput Estimation of Cell Density within Diverse Cortical Layers
Aarthi Sekar, Thiago M. Sanches, Keiko Hino, Matangi Kumar, Juliann Wang, Elisa Ha, Blythe Durbin-Johnson, Sergi Simó, Megan Y. Dennis
eNeuro 1 November 2021, 8 (6) ENEURO.0185-21.2021; DOI: 10.1523/ENEURO.0185-21.2021
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Keywords

  • Automated
  • brain imaging
  • cell quantification
  • fluorescence
  • microscopy

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