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

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
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hua-an Tseng
2Biomedical Engineering Department, Boston University, Boston, MA 02215
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kyle R. Hansen
2Biomedical Engineering Department, Boston University, Boston, MA 02215
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ruofan Wu
3School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Howard J. Gritton
2Biomedical Engineering Department, Boston University, Boston, MA 02215
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Howard J. Gritton
Jennie Si
3School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xue Han
2Biomedical Engineering Department, Boston University, Boston, MA 02215
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Article
  • Figures & Data
  • Info & Metrics
  • eLetters
  • PDF
Loading

Published eLetters

Guidelines

As a forum for professional feedback, submissions of letters are open to all. You do not need to be a subscriber. To avoid redundancy, we urge you to read other people's letters before submitting your own. Name, current appointment, place of work, and email address are required to send a letter, and will be published with your review. We also require that you declare any competing financial interests. Unprofessional submissions will not be considered or responded to.

Submit a Response to This Article
Compose eLetter

More information about text formats

Plain text

  • No HTML tags allowed.
  • Web page addresses and e-mail addresses turn into links automatically.
  • Lines and paragraphs break automatically.
Author Information
First or given name, e.g. 'Peter'.
Your last, or family, name, e.g. 'MacMoody'.
Your email address, e.g. higgs-boson@gmail.com
Your role and/or occupation, e.g. 'Orthopedic Surgeon'.
Your organization or institution (if applicable), e.g. 'Royal Free Hospital'.
Statement of Competing Interests
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
8 + 0 =
Solve this simple math problem and enter the result. E.g. for 1+3, enter 4.

Vertical Tabs

Jump to comment:

No eLetters have been published for this article.
Back to top

In this issue

eneuro: 5 (5)
eNeuro
Vol. 5, Issue 5
September/October 2018
  • Table of Contents
  • Index by author
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.
Automatic Cell Segmentation by Adaptive Thresholding (ACSAT) for Large-Scale Calcium Imaging Datasets
(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
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

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
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
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

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

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

  • Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain
  • A Toolbox of Criteria for Distinguishing Cajal–Retzius Cells from Other Neuronal Types in the Postnatal Mouse Hippocampus
  • 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

  • Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain
  • A Toolbox of Criteria for Distinguishing Cajal–Retzius Cells from Other Neuronal Types in the Postnatal Mouse Hippocampus
  • 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.