Mittens

A ImageJ/Fiji plugin for generating aligned multichannel images in publishable style, now with time-lapse support.

Description

Mittens is a comprehensive plugin for ImageJ/Fiji that provides tools for advanced channel manipulation, alignment, and presentation of multichannel microscopy images. Perfect for creating publication-ready figure panels with consistent formatting and alignment. Version 2.0 adds full support for time-lapse data processing.

Features

Core Features

• Channel Processing: Duplicate, split, and invert channels from multichannel images
• Selective Merging: Create custom merged images using selected channels
• Image Alignment: Align multiple channels or merged images into horizontal montages
• Scale Bar Integration: Add calibrated scale bars while preserving pixel dimensions

New in Version 2.0

• Time Frame Support: Process entire time-lapse sequences with the "use frames" option
• Multi-dimensional Handling: Properly handles images with Z-stacks and T-frames
• Time Bar Integration: Add temporal annotations to time-lapse data
• Properties Access: Quick access to image metadata and properties
• Improved UI: Cleaner interface with better button organization
• Data Integrity: Preserves original pixel values without unwanted modifications

Installation

1. Download Mittens_2.0.js from this repository
2. Copy the file to your ImageJ/Fiji plugins folder
3. Restart ImageJ/Fiji
4. The plugin will appear under Plugins > Mittens

Usage

Basic Workflow

1. Open a multichannel image (with or without time frames) in ImageJ/Fiji
2. Launch Mittens from the Plugins menu
3. Use the interface to:
   • Adjust brightness/contrast
   • Duplicate and split channels (check "use frames" for time-lapse)
   • Select channels for merging
   • Align images for final presentation
   • Add scale bars and time bars

Time-Lapse Processing

1. Open a time-lapse multichannel image
2. Check the "use frames" checkbox next to the Dup/Split/Invert button
3. Process all time frames simultaneously
4. Create aligned montages that preserve temporal information
5. Add time bars for temporal annotation

Requirements

• ImageJ or Fiji
• Multichannel images (supports up to 4 channels)
• Optional: Time Bar plugin for temporal annotations

Version History

Version 2.0 (2025)

• Added time frame support for multi-dimensional images
• Integrated Time Bar plugin support
• Improved UI layout and organization
• Fixed data integrity issues
• Added proper hyperstack handling

Version 1.0 (2024)

• Initial release
• Basic channel processing and alignment features

Author

Tsung-Lin Tsai (TTL)

Version

2.0

License

MIT License - see LICENSE file for details