Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Jun 6, 2025

Two-photon Calcium Imaging in Neuronal Dendrites in Brain Slices
10:35

Two-photon Calcium Imaging in Neuronal Dendrites in Brain Slices

Published on: March 15, 2018

10.7K

A preprocessing toolbox for 2-photon subcellular calcium imaging.

Anqi Jiang1, Chong Zhao2,3, Mark Sheffield1

  • 1Department of Neurobiology, Neuroscience Institute, University of Chicago.

Biorxiv : the Preprint Server for Biology
|November 28, 2024
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Malignant transformation risk and management dilemmas of atypical lobular endocervical glandular hyperplasia: A retrospective cohort study comparing Peutz-Jeghers syndrome versus sporadic cases.

Gynecologic oncology·2026
Same author

GTPBP4 promotes colorectal cancer cell proliferation by positively regulating MYC-driven glycolytic metabolism.

American journal of cancer research·2026
Same author

The MAPK Pathway Coordinates an Immunosuppressive Microenvironment in Colorectal Cancer: A Single-Cell Guided Prognostic Model.

Cancer informatics·2026
Same author

FKBP9 Enhances Colon Cancer Cell Proliferation by Inhibiting GPX4-Mediated Ferroptosis.

Cancer medicine·2026
Same author

Global burden, projections, and causal factors of maternal sepsis and other maternal infections: A comprehensive epidemiological and mendelian randomization study.

PLoS neglected tropical diseases·2026
Same author

Distinct CA3 inputs differentially shape the learning-dependent evolution of right CA1 spatial maps.

Nature communications·2026
Same journal

Layered social competition coordinates reproductive hierarchy formation in ants.

bioRxiv : the preprint server for biology·2026
Same journal

Combination epigenetic-targeted therapy increases the immunogenicity of poorly immunogenic sarcomas.

bioRxiv : the preprint server for biology·2026
Same journal

Loss of LanC-like proteins delays post-injury regeneration of aging skeletal muscles.

bioRxiv : the preprint server for biology·2026
Same journal

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets.

bioRxiv : the preprint server for biology·2026
Same journal

Confidence-supported label-free metabolic imaging with FPhaS phase autofluorescence microscopy.

bioRxiv : the preprint server for biology·2026
Same journal

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation.

bioRxiv : the preprint server for biology·2026
See all related articles

This study introduces a new computational pipeline to improve the analysis of two-photon calcium imaging data from neuronal subcellular compartments. The method enhances signal detection, removes motion artifacts, and groups regions of interest for more accurate neural activity recording during behavior.

Area of Science:

  • Neuroscience
  • Computational Biology
  • Biophysics

Background:

  • Two-photon calcium imaging allows recording neural activity from subcellular compartments like axons and dendrites.
  • Challenges include low signal-to-noise ratio, inaccurate region-of-interest (ROI) identification, movement artifacts, and difficulty grouping ROIs from the same neuron.

Purpose of the Study:

  • To develop a computationally efficient pre-processing pipeline for subcellular signal detection, movement artifact identification, and ROI grouping.
  • To standardize the extraction of physiological signals from subcellular compartments during behavior using two-photon calcium imaging.

Main Methods:

  • Subcellular signal detection using Fast Fourier Transform (FFT) and band-pass filtering (0.05-0.12 Hz) on calcium traces.
  • Movement artifact removal using Principal Component Analysis (PCA) and Bottom-Up Segmentation change-point detection.

More Related Videos

Imaging Local Ca2+ Signals in Cultured Mammalian Cells
09:30

Imaging Local Ca2+ Signals in Cultured Mammalian Cells

Published on: March 3, 2015

10.7K
Fluorescent Calcium Imaging and Subsequent In Situ Hybridization for Neuronal Precursor Characterization in Xenopus laevis
00:09

Fluorescent Calcium Imaging and Subsequent In Situ Hybridization for Neuronal Precursor Characterization in Xenopus laevis

Published on: February 18, 2020

7.9K

Related Experiment Videos

Last Updated: Jun 6, 2025

Two-photon Calcium Imaging in Neuronal Dendrites in Brain Slices
10:35

Two-photon Calcium Imaging in Neuronal Dendrites in Brain Slices

Published on: March 15, 2018

10.7K
Imaging Local Ca2+ Signals in Cultured Mammalian Cells
09:30

Imaging Local Ca2+ Signals in Cultured Mammalian Cells

Published on: March 3, 2015

10.7K
Fluorescent Calcium Imaging and Subsequent In Situ Hybridization for Neuronal Precursor Characterization in Xenopus laevis
00:09

Fluorescent Calcium Imaging and Subsequent In Situ Hybridization for Neuronal Precursor Characterization in Xenopus laevis

Published on: February 18, 2020

7.9K
  • Calcium transient identification by analyzing prominence and duration, followed by ROI grouping using hierarchical or k-means clustering.

    • Main Results:

    • The pipeline effectively detects subcellular signals and removes movement artifacts.
    • Clustering methods successfully grouped active ROIs, determining the optimal number of clusters.
    • Groupings correlated well with ground truth data for axon ROIs in the CA1 region.

    Conclusions:

    • The developed pipeline offers a standardized approach for analyzing subcellular neural activity from two-photon calcium imaging.
    • This method addresses key challenges in the field, improving data quality and interpretability.