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Multi-Channel Nuclear Analysis v0.1.0 - Initial Release

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@ariel-waisman ariel-waisman released this 05 May 00:50
· 3 commits to main since this release
v0.1.0
9b2c3c1

Release Description

We are pleased to announce the first public release of Multi-Channel Nuclear Analysis, an ImageJ/FIJI plugin for automated nuclear segmentation and multi-channel fluorescence analysis.

What is Multi-Channel Nuclear Analysis?
This plugin combines StarDist's robust nuclear segmentation with versatile multi-channel analysis capabilities, providing researchers with a user-friendly tool for quantitative fluorescence microscopy. The plugin segments nuclei and measures various parameters across multiple fluorescence channels simultaneously.

Key Features:

  • Intuitive graphical user interface for parameter configuration
  • Automated nuclear segmentation using StarDist
  • Multi-channel fluorescence analysis with customizable settings
  • Batch processing capability for multiple images
  • Comprehensive data output in CSV format for downstream analysis
  • Automatic generation of visualization images

This Release Includes:

  • Main plugin (Multi_Channel_Nuclear_Analysis.ijm)
  • Plugin for Merging Channels into Multi-Channel TIF Files (Merge_multi_channel_tif.ijm)
  • Non-interactive script version (Script_manual_analysis.ijm)
  • Example image dataset for testing
  • Comprehensive documentation and link to video tutorial

Requirements:

  • FIJI/ImageJ (latest version recommended)
  • StarDist plugin
  • CSBDeep plugin
  • TensorFlow plugin

Getting Started:

  1. Install FIJI/ImageJ from https://fiji.sc/
  2. Install the required plugins via Help > Update > Manage Update Sites
  3. Follow the installation instructions in our documentation
  4. Watch our video tutorial for a complete walkthrough

Documentation:
Full documentation is available in the GitHub page

License:
This plugin is released under the MIT License.

Citation:
If you use this plugin in your research, please cite:
Waisman, A. (2025). Multi-Channel Nuclear Analysis: An ImageJ/FIJI Plugin for Automated Nuclear Segmentation and Multi-Channel Fluorescence Analysis. microPublication.

Acknowledgments:
We thank the developers of StarDist for creating a robust nuclear segmentation tool that forms a key component of our analysis pipeline.

This release has been tested on various operating systems and configurations. If you encounter any issues, please report them via GitHub Issues.

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