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 Concept Videos

Imaging Biological Samples with Optical Microscopy01:18

Imaging Biological Samples with Optical Microscopy

12.3K
Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...
12.3K
Imaging Studies I: CT and MRI01:14

Imaging Studies I: CT and MRI

1.3K
Introduction: MRI and CT scans are crucial advancements in medical imaging techniques, playing a vital role in diagnosing conditions related to the gastrointestinal (GI) system. Each scan serves distinct purposes, targets specific areas, and requires unique nursing duties.
Description of the Procedures
Computed Tomography (CT) scan:
Computed Tomography (CT) scans use X-ray technology to generate detailed images of bones, organs, and tissues. During the scan, the patient lies on a moving table...
1.3K
Brain Imaging01:14

Brain Imaging

977
Brain imaging technologies provide critical insights into both the structure and function of the human brain, enabling medical professionals and researchers to diagnose, study, and treat neurological disorders or psychiatric disorders more effectively.
These technologies include computerized axial tomography (CAT or CT scans), positron-emission tomography (PET scans),  magnetic resonance imaging (MRI),  functional magnetic resonance imaging (fMRI), and Transcranial Magnetic...
977

You might also read

Related Articles

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

Sort by
Same author

A Case of Cecal Mixed Neuroendocrine-Non-Neuroendocrine Neoplasm Requiring Adjuvant Chemotherapy Based on Comprehensive Pathological Assessment.

Surgical case reports·2026
Same author

Conduit size and the risk of delayed gastric conduit emptying after esophagectomy.

Surgery today·2026
Same author

Saliva-Based Triple-Primed PCR as a Non-Invasive Tool for Detecting NOTCH2NLC GGC Repeat Expansions in NIID.

Clinical laboratory·2026
Same author

Clinical significance and predictive factors of delayed gastric conduit emptying after esophagectomy.

Surgery today·2026
Same author

Enhanced Ni Exsolution in High-Entropy Perovskite Oxides with Broadening of Migration-Reduction Energy Landscapes.

Nano letters·2026
Same author

Distinctive hydrocephalus-like phenotype in NOTCH2NLC-related neuronal intranuclear inclusion disease: clinicopathological features and therapeutic implications.

Acta neuropathologica communications·2026

Related Experiment Video

Updated: Apr 13, 2026

Identification of Disease-related Spatial Covariance Patterns using Neuroimaging Data
14:27

Identification of Disease-related Spatial Covariance Patterns using Neuroimaging Data

Published on: June 26, 2013

15.6K

Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis.

Yukako Yamane1, Yuzhe Li1, Keita Matsumoto2

  • 1Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.

Plos Computational Biology
|May 19, 2025
PubMed
Summary

Optical Neuroimage Studio (OptiNiSt) streamlines calcium data analysis for neuroscience. This framework simplifies pipeline creation, ensures reproducibility, and supports standard data formats for sharing optical neural recordings.

More Related Videos

Simultaneous Data Collection of fMRI and fNIRS Measurements Using a Whole-Head Optode Array and Short-Distance Channels
08:19

Simultaneous Data Collection of fMRI and fNIRS Measurements Using a Whole-Head Optode Array and Short-Distance Channels

Published on: October 20, 2023

969
Author Spotlight: Insights into Visual Cortex Research Through Wide-View fMRI Mapping
07:11

Author Spotlight: Insights into Visual Cortex Research Through Wide-View fMRI Mapping

Published on: December 8, 2023

1.3K

Related Experiment Videos

Last Updated: Apr 13, 2026

Identification of Disease-related Spatial Covariance Patterns using Neuroimaging Data
14:27

Identification of Disease-related Spatial Covariance Patterns using Neuroimaging Data

Published on: June 26, 2013

15.6K
Simultaneous Data Collection of fMRI and fNIRS Measurements Using a Whole-Head Optode Array and Short-Distance Channels
08:19

Simultaneous Data Collection of fMRI and fNIRS Measurements Using a Whole-Head Optode Array and Short-Distance Channels

Published on: October 20, 2023

969
Author Spotlight: Insights into Visual Cortex Research Through Wide-View fMRI Mapping
07:11

Author Spotlight: Insights into Visual Cortex Research Through Wide-View fMRI Mapping

Published on: December 8, 2023

1.3K

Area of Science:

  • Neuroscience
  • Optical Imaging
  • Data Analysis

Background:

  • Optical neural recording is increasingly common in neuroscience due to advancements in calcium indicators and imaging techniques.
  • Growing data volumes necessitate streamlined analysis pipelines for image preprocessing, signal extraction, and neural activity analysis.
  • Current challenges include ensuring data quality, selecting optimal algorithms, maintaining reproducibility, and adopting standard data formats.

Purpose of the Study:

  • To develop a scalable, extendable, and reproducible framework for creating calcium data analysis pipelines.
  • To address the challenges in optical neural data analysis, including data quality, algorithm selection, reproducibility, and data sharing.
  • To facilitate the standardization of optical neural data analysis protocols.

Main Methods:

  • Developed Optical Neuroimage Studio (OptiNiSt), a framework with a graphical user interface for creating analysis pipelines.
  • OptiNiSt allows users to select processing modules, tune parameters, and visualize results.
  • The framework supports adding new analysis algorithms, stores pipelines in YAML files for reproducibility, and integrates with high-performance computing clusters.
  • OptiNiSt reads various image formats and saves results in the Neurodata Without Borders (NWB) standard format.

Main Results:

  • OptiNiSt provides a user-friendly interface for building complex calcium data analysis workflows.
  • Pipelines created with OptiNiSt are reproducible and can be deployed on high-performance computing clusters.
  • The framework ensures compatibility with multiple data formats and promotes the use of the NWB standard for data sharing.

Conclusions:

  • Optical Neuroimage Studio (OptiNiSt) offers a robust solution for standardizing and simplifying optical neural data analysis.
  • The framework enhances reproducibility and data sharing in neuroscience research.
  • OptiNiSt is expected to significantly aid researchers in managing and analyzing large-scale optical neural recording datasets.