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Research ArticleMethods/New Tools, Novel Tools and Methods

Automatic Cell Segmentation by Adaptive Thresholding (ACSAT) for Large-Scale Calcium Imaging Datasets

Simon P. Shen, Hua-an Tseng, Kyle R. Hansen, Ruofan Wu, Howard J. Gritton, Jennie Si and Xue Han
eNeuro 4 September 2018, 5 (5) ENEURO.0056-18.2018; https://doi.org/10.1523/ENEURO.0056-18.2018
Simon P. Shen
1Department of Physics, Harvard University, Cambridge, MA 02138
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Hua-an Tseng
2Biomedical Engineering Department, Boston University, Boston, MA 02215
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Kyle R. Hansen
2Biomedical Engineering Department, Boston University, Boston, MA 02215
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Ruofan Wu
3School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287
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Howard J. Gritton
2Biomedical Engineering Department, Boston University, Boston, MA 02215
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  • ORCID record for Howard J. Gritton
Jennie Si
3School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287
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Xue Han
2Biomedical Engineering Department, Boston University, Boston, MA 02215
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Article Information

DOI 
https://doi.org/10.1523/ENEURO.0056-18.2018
PubMed 
30221189
Published By 
Society for Neuroscience
History 
  • Received February 3, 2018
  • Revision received August 16, 2018
  • Accepted August 23, 2018
  • Published online September 4, 2018.
Copyright & Usage 
Copyright © 2018 Shen 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. Simon P. Shen1,*,
  2. Hua-an Tseng2,*,
  3. Kyle R. Hansen2,
  4. Ruofan Wu3,
  5. Howard J. Gritton2,
  6. Jennie Si3 and
  7. Xue Han2
  1. 1Department of Physics, Harvard University, Cambridge, MA 02138
  2. 2Biomedical Engineering Department, Boston University, Boston, MA 02215
  3. 3School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287
  1. Correspondence to either of the following: Jennie Si, Arizona State University Goldwater Center #351, 650 E Tyler Mall, Tempe, AZ85287. E-mail: si{at}asu.edu; or Xue Han, Boston University, 44 Cummington Mall, Room 401, Boston, MA 02215. E-mail: xuehan{at}bu.edu.
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Author contributions

  1. Author contributions: S.P.S. designed research, performed research, contributed unpublished reagents/analytic tools, analyzed data, and wrote the paper; H.T. performed research, analyzed data, and wrote the paper; K.R.H. performed research; R.W. analyzed data; H.G. performed research; J.S. and X.H. designed research and wrote the paper.

Disclosures

  • The authors declare no competing financial interests.

  • X.H. acknowledges funding from National Institutes of Health Director’s new innovator award (1DP2NS082126), Pew Foundation, DARPA Young Faculty Award, National Science Foundation (EEC-1647837), Boston University Biomedical Engineering Department. K.R.H. is supported by a National Science Foundation Graduate Research Fellowship (DGE-1247312).

  • ↵* S.P.S. and H.T. are co-first authors.

Funding

  • NIH Director's new innovator award

    1DP2NS082126
  • Pew Foundation

  • DARPA Young Faculty Award

  • Boston University Biomedical Engineering Department

  • National Science Foundation Graduate Research Fellowship

    DGE-1247312

Other Version

  • You are viewing the most recent version of this article.
  • previous version (September 04, 2018).

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Sep 2018773186117
Oct 201827113140
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Jun 20203175
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Sep 202079712
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Apr 20214606
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Total 20252226864
Total153870471405
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Automatic Cell Segmentation by Adaptive Thresholding (ACSAT) for Large-Scale Calcium Imaging Datasets
Simon P. Shen, Hua-an Tseng, Kyle R. Hansen, Ruofan Wu, Howard J. Gritton, Jennie Si, Xue Han
eNeuro 4 September 2018, 5 (5) ENEURO.0056-18.2018; DOI: 10.1523/ENEURO.0056-18.2018

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Automatic Cell Segmentation by Adaptive Thresholding (ACSAT) for Large-Scale Calcium Imaging Datasets
Simon P. Shen, Hua-an Tseng, Kyle R. Hansen, Ruofan Wu, Howard J. Gritton, Jennie Si, Xue Han
eNeuro 4 September 2018, 5 (5) ENEURO.0056-18.2018; DOI: 10.1523/ENEURO.0056-18.2018
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Keywords

  • GCaMP6
  • genetically encoded calcium sensors
  • in vivo Imaging
  • adaptive thresholding
  • ROI segmentation
  • automated image analysis
  • wide-field imaging
  • two-photon imaging
  • neural network

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