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

You might also read

Related Articles

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

Sort by
Same author

From single cells to organotypic cultures: Measuring and analyzing keratinocyte migration.

The Journal of investigative dermatologyĀ·2026
Same author

Universal consensus 3D segmentation of cells from 2D segmented stacks.

Nature methodsĀ·2025
Same author

Shifts in keratin isoform expression activate motility signals during wound healing.

Developmental cellĀ·2024
Same author

Universal consensus 3D segmentation of cells from 2D segmented stacks.

bioRxiv : the preprint server for biologyĀ·2024
Same author

Keratin isoform shifts modulate motility signals during wound healing.

bioRxiv : the preprint server for biologyĀ·2023
Same author

Increasing the field-of-view in oblique plane microscopy via optical tiling.

Biomedical optics expressĀ·2023

Related Experiment Video

Updated: Mar 30, 2026

Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins
11:01

Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins

Published on: November 17, 2016

49.5K

Slide Set: Reproducible image analysis and batch processing with ImageJ.

Benjamin A Nanes1

  • 1Medical Scientist Training Program and Department of Cell Biology, Emory University School of Medicine, Atlanta, GA.

Biotechniques
|November 12, 2015
PubMed
Summary

The Slide Set plugin for ImageJ streamlines biological image analysis by automating repetitive tasks. This tool enhances reproducibility and transparency for small to medium datasets without complex programming.

Keywords:
automationimage analysisimage processingreproducibilitysoftware

More Related Videos

Fast Colony Forming Unit Counting in 96-Well Plate Format Applied to the Drosophila Microbiome
12:55

Fast Colony Forming Unit Counting in 96-Well Plate Format Applied to the Drosophila Microbiome

Published on: January 13, 2023

9.7K
Clock Scan Protocol for Image Analysis: ImageJ Plugins
07:19

Clock Scan Protocol for Image Analysis: ImageJ Plugins

Published on: June 19, 2017

18.1K

Related Experiment Videos

Last Updated: Mar 30, 2026

Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins
11:01

Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins

Published on: November 17, 2016

49.5K
Fast Colony Forming Unit Counting in 96-Well Plate Format Applied to the Drosophila Microbiome
12:55

Fast Colony Forming Unit Counting in 96-Well Plate Format Applied to the Drosophila Microbiome

Published on: January 13, 2023

9.7K
Clock Scan Protocol for Image Analysis: ImageJ Plugins
07:19

Clock Scan Protocol for Image Analysis: ImageJ Plugins

Published on: June 19, 2017

18.1K

Area of Science:

  • Biological sciences
  • Image analysis
  • Scientific imaging

Background:

  • Manual image analysis in biology is often repetitive, leading to errors and poor reproducibility.
  • Fully automated solutions are not always practical for small to medium biological datasets.

Purpose of the Study:

  • To introduce the Slide Set plugin for ImageJ, a tool designed for reproducible image analysis and batch processing.
  • To provide a framework that simplifies complex analysis tasks and improves data management.

Main Methods:

  • The Slide Set plugin organizes image data into tables, linking image files with regions of interest.
  • It automates the repetition of analysis commands across datasets and allows chaining of multiple commands.
  • Analysis parameters are automatically saved to ensure transparency and reproducibility.

Main Results:

  • The plugin facilitates batch processing of image analysis tasks, reducing manual effort.
  • It enhances the reproducibility and transparency of image analysis workflows.
  • The Slide Set plugin offers built-in commands and extensibility for other ImageJ plugins.

Conclusions:

  • The Slide Set plugin offers a practical solution for reproducible image analysis in biology.
  • It bridges the gap between manual analysis and fully automated solutions, especially for common dataset sizes.
  • This tool empowers researchers to perform complex analyses with reduced setup and programming effort.