Add Image Viewer plugins documentation

This document provides an overview of the Image Viewer plugin, detailing its features, functionalities, and installation instructions for handling and visualizing microscopy images.

Author: kwolbachia

_pages/plugins/image-viewer.md

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+---
+title: Image Viewer
+description: utility plugins and macros to control images contast and LUTs
+categories: [Annotation, Interactive, Macro, Microscopy, Montage, Utilities, Visualization]
+---
+
+This Update Site provides utility plugins and macros to help with handling and visualizing microscopy images before any analysis.     
+Features include:
+
+- Plugins to control image contrast and LUTs  
+- A neutral Multi Tool for moving image windows and accessory functions  
+- Easy opening of images from thumbnail montages  
+- Utility macros for multichannel montages and auto-generated scale bars  
+
+Access commands and plugins via the **Plugins > Image Viewer** menu, or the toolbar menu (installable from Image_Viewer_Toolset under the red `>>` menu in the ImageJ window).
+
+---
+
+## Channels and Contrast
+
+This plugin combines "Brightness and Contrast" and "Channels Tool" functionalities to manage visualization of the active image.
+
+You can:
+- Adjust channel display range (contrast)
+- Change multi-channel display mode: composite, color, or grayscale
+- Set active channels
+- Use two auto-contrast modes:
+  - **Auto:** Uses "Enhance Contrast" with a default of 0.1% saturated pixels (adjustable via "More" button). For stacks, contrast is based on displayed slice only.
+  - **Min/Max:** Sets display range to the channel stack's min/max values.
+- Interface with **LUTs Manager** to set palettes or favorite LUTs.
+- Access more options and utilities for multi-channel images via the "More" button.
+
+shortcuts to "Brightness and Contrast" and "Channels Tool" is available for missing functionality.
+
+---
+
+## LUTs Manager
+
+### Multichannel Palettes
+- Create and edit LUT combinations
+- Add LUTs by drag-and-drop from **LUTs Finder**
+- Change LUT order with the mouse
+- Right-click palette to move or remove LUTs
+- Empty palette channels default to "Grays"
+
+### LUTs Finder
+Scans all LUTs in your ImageJ `luts` folder
+You can use the search bar and color buttons to filter the list.  
+The Favorite LUTs are stored for future sessions and accessible from the Channels and Contrast plugin.
+
+**Apply a LUT:**  
+- Double-click a LUT or press **Enter** to apply to your image
+
+**LUT preview bands:**  
+- Check for uniformity in color transitions for good contrast visibility.
+
+**LUT properties:**  
+Each LUT comes with an **estimated** description of its properties:
+
+- **Basic:** Identifies classic 'pure' LUTs (Red, Green, Blue, Cyan, etc.).
+- **Linear, Non-uniform:** Whether the perceptual brightness progression is linear.
+- **Diverging:** Transitions from one color through a neutral midpoint to another color.
+- **Isoluminant:** Changes in color but keeps the luminance consistent across the LUT.
+- **Cyclic:** If the first and last colors are the same.
+
+---
+
+## Multi Tool
+
+This Tool is a neutral tool but it can performs many actions in ImageJ based on the mouse click, modifier keys (shift, ctrl, alt) and context.
+Without any modifier keys: 
+- Left click on an image window will just move the window. But you keep the functionality to move and resize any ROI. 
+
+- **No modifier keys:** Left-click moves image window; Or move / resize any ROI.
+- **Middle mouse:** Switch multichannel display (composite/color)
+- **Ctrl:** Mimic rectangle tool
+- **Shift + Alt:** Local auto-contrast via box ROI around click
+- **Alt:** Navigate Z (slice/frame) anywhere in image
+- **Shift:** Adjust active channel contrast
+
+---
+
+## Preview Opener
+This command creates a montage of opened images and saves it in their directory.  
+With the **Multi Tool**, middle-click on a montage will open the image under the cursor—making it fast to find images within a folder.
+
+**How to use:**
+1. Open the images you want (virtual stacks supported)
+2. Adjust display settings.
+3. run the command `Create Preview Opener`
+
+**Notes:**
+- Montage title must include “Preview Opener” (can add text before/after)
+- Keep the Preview Opener file in the images folder
+
+---
+
+## Other Commands
+
+- **Split View:** Quickly create clean multichannel montages
+- **Auto Scale Bar:** Estimate and add scale bar. You can adjust the size and hide the text in options.
+- **Auto-Contrast** recordable macro commands similar to the Channels and Contrast buttons.
+
+---
+## Installation
+- in Fiji, add the Image Viewer [Update Site](https://imagej.net/update-sites/following)
+- For ImageJ, download this [repository](https://github.com/kwolbachia/Image_Viewer/tree/main) as .zip