WinMan: Window Manager & Workflow Accelerator

The Ultimate Workspace Manager for Bioimage Analysis
Solve the "Desktop Explosion" problem with Smart Filtering, Batch Processing, and Memory Monitoring.

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(WinMan v1.0.0: Modern Flat UI with Compact Layout)

📖 Overview

WinMan (Window Manager) v1.0.0 is a lightweight yet powerful utility designed to streamline high-throughput microscopy workflows in ImageJ/Fiji.

Bioimage analysis often involves opening dozens of images, resulting tables, and plots, leading to a cluttered workspace and memory overflows. WinMan acts as your digital housekeeper, providing granular control over open windows and system resources with a modern, commercial-grade interface.

🚀 What's New in v1.0.0?

• Modern Flat Design: A clean, "Stick-supported" compact UI that minimizes screen real estate usage while maximizing usability.
• Smart "Invert" Logic: Not just closing windows—WinMan allows you to KEEP specific windows (e.g., "Keep only merged images") while clearing the rest.
• Workflow Acceleration: Batch tools to instantly Auto-Contrast or Reset Zoom for 50+ open images at once.
• System Health: An integrated Memory Bar that monitors RAM usage and performs Garbage Collection (GC) on click.

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✨ Key Features

1. Smart Filtering Engine

• Close Match: Instantly close all windows containing a specific keyword (e.g., remove all C1- channels).
• Keep Match (The Killer Feature): The inverse logic. Type result and click Keep Match to close everything except your final results.
• Safety First: The "Close ALL" button includes a confirmation dialog to prevent accidental data loss.

2. Image Tools (Batch Processing)

• Auto Contrast All: Applies an intelligent histogram stretch (Enhance Contrast, saturated=0.35) to ALL open images instantly. No more clicking Image > Adjust > Brightness twenty times.
• Reset Zoom All: Resets all windows to 100% zoom level for standardized viewing.

3. Layout & System Control

• Memory Monitor: A live progress bar at the bottom showing RAM usage (e.g., 2GB / 16GB).
  • Action: Click the bar to force Garbage Collection and free up memory immediately.
• Window Layout: Improved Tile and Cascade algorithms to neatly organize your workspace.

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📥 Installation

1. Download the latest WinMan-1.0.0.jar from the Releases Page.
2. Drag and drop the file into your Fiji/ImageJ plugins folder (or main window).
3. Restart Fiji.
4. Navigate to: Plugins > Biosensor Tool > WinMan Manager.

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🎮 Usage Guide

1. Filter Logic

Function	Input Example	Action	Use Case
Close Match	.csv	Closes any window with ".csv" in the title.	Cleaning up intermediate data tables.
Keep Match	Final	Closes everything EXCEPT windows with "Final" in title.	Isolating your processed results for export.
Close Match	C2-	Closes all Channel 2 images.	Removing reference channels after alignment.

2. Interface Guide

• Filter Selection: Input keywords here. Case-insensitive.
• Window Layout:
  • Tile: Arranges images in a grid without overlap.
  • Cascade: Stacks images diagonally with titles visible.
• Image Tools:
  • Auto Contrast: Fixes "black" 16-bit images instantly.
• Status Footer: Shows operation feedback (e.g., "Closed 12 windows") and Memory usage.

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📚 Technical Stack

WinMan is built with strict adherence to the CNS Lab Software Standards:

• Core: Java 8 / ImageJ 1.x API (ij.jar).
• UI Framework: Java Swing with custom FlatDesign implementation.
• Build System: Maven (SciJava architecture).
• Compatibility: Fully compatible with ImageJ and Fiji on Windows, macOS, and Linux.

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📚 Citation

If WinMan helps your daily workflow, please consider starring the repo or citing:

@software{wang_winman_2026,
  author = {Wang, Kui},
  title = {WinMan: A Modern Window Manager and Workflow Accelerator for ImageJ/Fiji},
  version = {v1.0.0},
  year = {2026},
  url = {[https://github.com/Epivitae/WinMan](https://github.com/kuiwang/WinMan)},
  doi = {10.5281/zenodo.18224551},
  organization = {Chinese Academy of Sciences}
}