Multi-Channel Nuclear Analysis: An ImageJ/FIJI Plugin for Automated Nuclear Segmentation and Multi-Channel...

Area of Science:

• Cell biology
• Biophysics
• Microscopy

Background:

• Quantitative analysis of fluorescence microscopy is crucial for understanding protein expression, localization, and interactions.
• Existing automated tools often lack user-friendliness, customization, or multi-channel capabilities with nuclear segmentation.

Purpose of the Study:

• To develop an open-source ImageJ/FIJI plugin for user-friendly, customizable quantitative analysis of multi-channel fluorescence images.
• To integrate robust nuclear segmentation with versatile multi-channel analysis features.

Main Methods:

• Developed the Multi-Channel Nuclear Analysis plugin for ImageJ/FIJI, incorporating StarDist for nuclear segmentation.
• Implemented a graphical user interface for parameter configuration and batch processing.
• Created a companion tool for merging separate fluorescence channel files into multi-channel images.

Main Results:

• The plugin enables comprehensive quantitative analysis of nuclear-centered multi-channel fluorescence images.
• It generates both individual and consolidated measurement tables for streamlined downstream analysis.
• The tool supports diverse microscopy systems through its file merging capability.

Conclusions:

• The Multi-Channel Nuclear Analysis plugin provides an accessible solution for researchers lacking extensive programming experience.
• It facilitates detailed quantitative studies of protein expression and localization within cell nuclei.
• This open-source tool enhances the capabilities of fluorescence microscopy image analysis.