Skip to main content

Main menu

  • HOME
  • CONTENT
    • Early Release
    • Featured
    • Current Issue
    • Issue Archive
    • Blog
    • Collections
    • Podcast
  • TOPICS
    • Cognition and Behavior
    • Development
    • Disorders of the Nervous System
    • History, Teaching and Public Awareness
    • Integrative Systems
    • Neuronal Excitability
    • Novel Tools and Methods
    • Sensory and Motor Systems
  • ALERTS
  • FOR AUTHORS
  • ABOUT
    • Overview
    • Editorial Board
    • For the Media
    • Privacy Policy
    • Contact Us
    • Feedback
  • SUBMIT

User menu

Search

  • Advanced search
eNeuro
eNeuro

Advanced Search

 

  • HOME
  • CONTENT
    • Early Release
    • Featured
    • Current Issue
    • Issue Archive
    • Blog
    • Collections
    • Podcast
  • TOPICS
    • Cognition and Behavior
    • Development
    • Disorders of the Nervous System
    • History, Teaching and Public Awareness
    • Integrative Systems
    • Neuronal Excitability
    • Novel Tools and Methods
    • Sensory and Motor Systems
  • ALERTS
  • FOR AUTHORS
  • ABOUT
    • Overview
    • Editorial Board
    • For the Media
    • Privacy Policy
    • Contact Us
    • Feedback
  • SUBMIT
PreviousNext
Research ArticleMethods/New Tools, Novel Tools and Methods

HNCcorr: A Novel Combinatorial Approach for Cell Identification in Calcium-Imaging Movies

Quico Spaen, Roberto Asín-Achá, Selmaan N. Chettih, Matthias Minderer, Christopher Harvey and Dorit S. Hochbaum
eNeuro 20 March 2019, 6 (2) ENEURO.0304-18.2019; https://doi.org/10.1523/ENEURO.0304-18.2019
Quico Spaen
1Department of Industrial Engineering & Operations Research, University of California, Berkeley, CA 94720-2284
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Quico Spaen
Roberto Asín-Achá
2Department of Computer Science, Universidad de Concepción, Concepción, Chile
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Roberto Asín-Achá
Selmaan N. Chettih
3Department of Neurobiology, Harvard Medical School, Boston, MA 02115
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Selmaan N. Chettih
Matthias Minderer
3Department of Neurobiology, Harvard Medical School, Boston, MA 02115
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Matthias Minderer
Christopher Harvey
3Department of Neurobiology, Harvard Medical School, Boston, MA 02115
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Christopher Harvey
Dorit S. Hochbaum
1Department of Industrial Engineering & Operations Research, University of California, Berkeley, CA 94720-2284
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Dorit S. Hochbaum
  • Article
  • Figures & Data
  • Info & Metrics
  • eLetters
  • PDF
Loading

Article Information

DOI 
https://doi.org/10.1523/ENEURO.0304-18.2019
PubMed 
31058211
Published By 
Society for Neuroscience
History 
  • Received August 6, 2018
  • Revision received February 14, 2019
  • Accepted February 25, 2019
  • Published online March 20, 2019.
Copyright & Usage 
Copyright © 2019 Spaen 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. Quico Spaen1,
  2. Roberto Asín-Achá2,
  3. Selmaan N. Chettih3,
  4. Matthias Minderer3,
  5. Christopher Harvey3 and
  6. Dorit S. Hochbaum1
  1. 1Department of Industrial Engineering & Operations Research, University of California, Berkeley, CA 94720-2284
  2. 2Department of Computer Science, Universidad de Concepción, Concepción, Chile
  3. 3Department of Neurobiology, Harvard Medical School, Boston, MA 02115
  1. Correspondence should be addressed to Dorit S. Hochbaum at Hochbaum{at}ieor.berkeley.edu.
View Full Text

Author contributions

  1. Author contributions: C.H. and D.S.H. designed research; Q.S. and R.A. performed research; S.N.C. and M.M. contributed unpublished reagents/analytic tools; Q.S., R.A., and D.S.H. wrote the paper.

Disclosures

  • The authors declare no competing financial interests.

  • This research was supported by the Department of Health and Human Services (HHS) | National Institutes of Health (NIH) | National Institute of Mental Health: R01MH107620; HHS | NIH | National Institute of Neurological Disorders and Stroke (NINDS): R01NS089521; National Science Foundation (NSF) | Directorate for Engineering | Division of Civil, Mechanical and Manufacturing Innovation (CMMI): CMMI 1760102; a Boehringer Ingelheim Fund fellowship; a Herchel Smith graduate fellowship; a NSF graduate fellowship; the New York Stem Cell Foundation; and UC Berkeley | UC Berkeley Library | Berkeley Research Impact Initiative.

Funding

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

    R01MH107620
  • HHS | NIH | National Institute of Neurological Disorders and Stroke (NINDS)

    R01NS089521
  • NSF | ENG | Division of Civil, Mechanical and Manufacturing Innovation (CMMI)

    CMMI 1760102
  • Boehringer Ingelheim Fonds (BIF)

  • Herchel Smith graduate fellowship

  • NSF graduate fellowship

  • New York Stem Cell Foundation (NYSCF)

Other Version

  • You are viewing the most recent version of this article.
  • previous version (March 20, 2019).

Online Impact

 

Article usage

Select a custom date range for the past year
E.g., 2025-06-16
to
E.g., 2025-06-16

Article usage: March 2019 to May 2025

AbstractFullPdf
Mar 2019170051
Apr 201956499107
May 20196718635
Jun 2019499016
Jul 2019239429
Aug 2019124716
Oct 201974210
Nov 201983715
Dec 2019176117
Total 2019917656296
Jan 20205326
Feb 202084825
Mar 202055717
May 20204297
Jun 20203487
Jul 202022714
Aug 20203304
Sep 202014717
Oct 202047516
Nov 202037110
Dec 202016910
Total 202039533133
Jan 202145912
Feb 202115213
Mar 20213608
Apr 202157917
May 202157321
Jun 20211518
Jul 202115325
Aug 202155113
Sep 20210589
Oct 202115420
Nov 202125019
Dec 202117018
Total 202129710183
Jan 202234910
Feb 20222318
Mar 202266020
Apr 202214414
May 202229547
Jun 202234610
Jul 20224652
Aug 202204411
Sep 202222518
Oct 202212313
Nov 202212510
Dec 202212912
Total 202226536175
Jan 202323210
Feb 202304111
Mar 20230448
Apr 20230447
May 202323216
Jun 20230508
Jul 202344320
Aug 2023114127
Sep 202334515
Oct 2023310414
Nov 2023419913
Dec 2023116716
Total 202340742165
Jan 2024114722
Feb 2024166322
Mar 202485314
Apr 2024174720
May 202446013
Jun 202495711
Jul 202474718
Aug 202455216
Sep 202456714
Oct 20242549
Nov 20244548
Dec 20242609
Total 202490661176
Jan 202546515
Feb 202538713
Mar 202525021
Apr 202525815
May 20251334
Total 20251229368
Total115341311196
Back to top

In this issue

eneuro: 6 (2)
eNeuro
Vol. 6, Issue 2
March/April 2019
  • Table of Contents
  • Index by author
  • Ed Board (PDF)
Email

Thank you for sharing this eNeuro article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
HNCcorr: A Novel Combinatorial Approach for Cell Identification in Calcium-Imaging Movies
(Your Name) has forwarded a page to you from eNeuro
(Your Name) thought you would be interested in this article in eNeuro.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Print
View Full Page PDF
Citation Tools
HNCcorr: A Novel Combinatorial Approach for Cell Identification in Calcium-Imaging Movies
Quico Spaen, Roberto Asín-Achá, Selmaan N. Chettih, Matthias Minderer, Christopher Harvey, Dorit S. Hochbaum
eNeuro 20 March 2019, 6 (2) ENEURO.0304-18.2019; DOI: 10.1523/ENEURO.0304-18.2019

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Respond to this article
Share
HNCcorr: A Novel Combinatorial Approach for Cell Identification in Calcium-Imaging Movies
Quico Spaen, Roberto Asín-Achá, Selmaan N. Chettih, Matthias Minderer, Christopher Harvey, Dorit S. Hochbaum
eNeuro 20 March 2019, 6 (2) ENEURO.0304-18.2019; DOI: 10.1523/ENEURO.0304-18.2019
Twitter logo Facebook logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Jump to section

  • Article
    • Abstract
    • Significance Statement
    • Introduction
    • Materials and Methods
    • Results
    • Discussion
    • Footnotes
    • References
    • Synthesis
  • Figures & Data
  • Info & Metrics
  • eLetters
  • PDF

Keywords

  • calcium imaging
  • cell identification
  • clustering
  • combinatorial optimization
  • graph methods

Responses to this article

Respond to this article

Jump to comment:

No eLetters have been published for this article.

Related Articles

Cited By...

More in this TOC Section

Methods/New Tools

  • A Toolbox of Criteria for Distinguishing Cajal–Retzius Cells from Other Neuronal Types in the Postnatal Mouse Hippocampus
  • Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain
  • Assessment of Spontaneous Neuronal Activity In Vitro Using Multi-Well Multi-Electrode Arrays: Implications for Assay Development
Show more Methods/New Tools

Novel Tools and Methods

  • A Toolbox of Criteria for Distinguishing Cajal–Retzius Cells from Other Neuronal Types in the Postnatal Mouse Hippocampus
  • Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain
  • Assessment of Spontaneous Neuronal Activity In Vitro Using Multi-Well Multi-Electrode Arrays: Implications for Assay Development
Show more Novel Tools and Methods

Subjects

  • Novel Tools and Methods
  • Home
  • Alerts
  • Follow SFN on BlueSky
  • Visit Society for Neuroscience on Facebook
  • Follow Society for Neuroscience on Twitter
  • Follow Society for Neuroscience on LinkedIn
  • Visit Society for Neuroscience on Youtube
  • Follow our RSS feeds

Content

  • Early Release
  • Current Issue
  • Latest Articles
  • Issue Archive
  • Blog
  • Browse by Topic

Information

  • For Authors
  • For the Media

About

  • About the Journal
  • Editorial Board
  • Privacy Notice
  • Contact
  • Feedback
(eNeuro logo)
(SfN logo)

Copyright © 2025 by the Society for Neuroscience.
eNeuro eISSN: 2373-2822

The ideas and opinions expressed in eNeuro do not necessarily reflect those of SfN or the eNeuro Editorial Board. Publication of an advertisement or other product mention in eNeuro should not be construed as an endorsement of the manufacturer’s claims. SfN does not assume any responsibility for any injury and/or damage to persons or property arising from or related to any use of any material contained in eNeuro.