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Revise Image Viewer documentation
Updated the Image Viewer documentation to improve clarity and organization. Added new features and installation instructions. first try at inluding media
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‎_pages/plugins/image-viewer.md‎

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@@ -3,105 +3,100 @@ title: Image Viewer
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description: utility plugins and macros to control images contast and LUTs
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categories: [Annotation, Interactive, Macro, Microscopy, Montage, Utilities, Visualization]
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---
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This Update Site provides utility plugins and macros to help with handling and visualization of microscopy images
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This Update Site provides utility plugins and macros to help with handling and visualizing microscopy images before any analysis.
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Features include:
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- Plugins to control image contrast and LUTs
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- A neutral Multi Tool for moving image windows and accessory functions
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- Easy opening of images from thumbnail montages
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- Utility macros for multichannel montages and auto-generated scale bars
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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).
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---
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## Channels and Contrast
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This plugin combines "Brightness and Contrast" and "Channels Tool" functionalities to manage visualization of the active image.
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- Two plugins to control image contrast and LUTs (Look Up Tables)
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- A pluginTool called Multi Tool to enhance mouse interactions with image windows
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- Utility macros :
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- basic multichannel montages (Split View)
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- auto-generated scale bar
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- A way to open images from thumbnail montages
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- Auto-contrast macros
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- Save all opened images
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# Installation
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- in Fiji, add the __Image Viewer__ [Update Site](https://imagej.net/update-sites/following)
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- For ImageJ, download this [github repository](https://github.com/kwolbachia/Image_Viewer/tree/main)
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In your imageJ app folder : place the **Image Viewer** folder on the ``plugins`` folder and the **Image_Viewer_Toolset.ijm** file on the ``macros /toolsets/`` folder
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All commands and plugins are located in the ``Plugins > Image Viewer`` menu
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But the easiest way is to install the toolbar menu from Image_Viewer_Toolset under the red `>>` menu in the ImageJ window
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![](https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-Toolset.png?raw=true)
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If you have a question, feedback or a bug to report, you can post it on the [Image.sc](https://forum.image.sc/t/looking-for-testers-channels-contrast-and-luts-manager-plugins/) Forum
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___
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### Channels and Contrast
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This plugin combines imageJ's "Brightness and Contrast" and "Channels Tool" functionalities to manage visualization of the active image
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![](https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-Channels-and-Contrast.png?raw=true)
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You can:
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- Adjust channel display range (contrast)
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- Change multi-channel display mode: composite, color, or grayscale
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- Set active channels
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- Use two auto-contrast modes:
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- **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.
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- **Min/Max:** Sets display range to the channel stack's min/max values.
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- Interface with **LUTs Manager** to set palettes or favorite LUTs.
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- Access more options and utilities for multi-channel images via the "More" button.
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shortcuts to "Brightness and Contrast" and "Channels Tool" is available for missing functionality.
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---
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## LUTs Manager
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### Multichannel Palettes
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- Create and edit LUT combinations
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- Adjust all channels display range (contrast)
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- Toggle visible channels in composite mode (checkboxes)
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- Use two types of auto-contrast:
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- **Auto:** Uses imageJ "Enhance Contrast" command with a default of 0.1% saturated pixels (adjustable via "More" button). For stacks, contrast is based on displayed slice only
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- **Min/Max:** Sets display range to the channel stack's min/max values
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- Interface with the **LUTs Manager** to apply LUT palettes or individual favorite LUTs
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You can change order of LUTs in a palette directly with the mouse from the palette menu
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![](https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-CC-palettes.png?raw=true)
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- Access more options and built-in utilities for multi-channel images via the "More" button
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![](https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-CC-More.png?raw=true)
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### LUTs Manager
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#### Multichannel Palettes
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- Create and edit LUT sets
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- Add LUTs by drag-and-drop from **LUTs Finder**
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- Change LUT order with the mouse
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- Right-click palette to move or remove LUTs
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- Empty palette channels default to "Grays"
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### LUTs Finder
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Scans all LUTs in your ImageJ `luts` folder
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You can use the search bar and color buttons to filter the list.
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The Favorite LUTs are stored for future sessions and accessible from the Channels and Contrast plugin.
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- Right-click on palette to move or remove LUTs
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- Empty palette channels default to "Grays"
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![](https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-LUTs-Manager.png?raw=true)
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#### LUTs Finder
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The plugin scans all LUTs in your ImageJ `luts` folder
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You can use the search bar and color buttons to filter the list
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The Favorite LUTs are stored and accessible from the Channels and Contrast plugin
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**Apply a LUT:**
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- Double-click a LUT or press **Enter** to apply to your image
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**LUT preview bands:**
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- Check for uniformity in color transitions for good contrast visibility.
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- Check for uniformity in color transitions for good contrast visibility
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**LUT properties:**
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Each LUT comes with an **estimated** description of its properties:
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- **Basic:** Identifies classic 'pure' LUTs (Red, Green, Blue, Cyan, etc.).
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- **Linear, Non-uniform:** Whether the perceptual brightness progression is linear.
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- **Diverging:** Transitions from one color through a neutral midpoint to another color.
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- **Isoluminant:** Changes in color but keeps the luminance consistent across the LUT.
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- **Cyclic:** If the first and last colors are the same.
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---
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## Multi Tool
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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.
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Without any modifier keys:
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- Left click on an image window will just move the window. But you keep the functionality to move and resize any ROI.
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- **No modifier keys:** Left-click moves image window; Or move / resize any ROI.
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- **Basic:** Identifies classic 'pure' LUTs (Red, Green, Blue, Cyan, etc.)
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- **Linear, Non-uniform:** Whether the perceptual brightness progression is linear
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- **Diverging:** Transitions from one color through a neutral midpoint to another color
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- **Isoluminant:** Changes in color but keeps the luminance consistent across the LUT
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- **Cyclic:** If the first and last colors are the same
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- **Luminance values:** Estimation of perceptual luminosity of the LUT min and max colors
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### Multi Tool
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This Tool is a neutral tool
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but it can perform many actions based on the mouse button, modifier keys (shift, ctrl, alt) and context:
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- **Without modifier keys:** Left-click moves image window; Or move / resize any ROI
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{% include video src="https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-Default-Main-Tool.mp4" %}
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- **Middle mouse:** Switch multichannel display (composite/color)
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- **Ctrl:** Mimic rectangle tool
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- **Shift + Alt:** Local auto-contrast via box ROI around click
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- **Alt:** Navigate Z (slice/frame) anywhere in image
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- **Shift:** Adjust active channel contrast
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---
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## Preview Opener
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- **Ctrl:** Mimic rectangle tool
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{% include video src="https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-Ctrl-Rectangle.mp4" %}
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- **Shift + Alt:** Local auto-contrast via box ROI around click
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{% include video src="https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-Local-Auto-Contrast.mp4" %}
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- **Alt:** Navigate Z (slice/frame) anywhere in image
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{% include video src="https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-Alt-Slice.mp4" %}
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- **Shift:** Adjust active channel contrast
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{% include video src="https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-Shift-Contrast.mp4" %}
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### Preview Opener
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This command creates a montage of opened images and saves it in their directory.
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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.
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**How to use:**
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1. Open the images you want (virtual stacks supported)
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2. Adjust display settings.
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2. Adjust display settings
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3. run the command `Create Preview Opener`
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{% include video src="https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-Preview-Opener-.mp4" %}
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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
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**Notes:**
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- Montage title must include “Preview Opener” (can add text before/after)
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- Montage title must include “Preview Opener” (you can add text before/after)
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- Keep the Preview Opener file in the images folder
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---
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## Other Commands
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### Other Commands
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A small collection of utility macros:
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- **Split View:** Quickly create clean multichannel montages
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- **Auto Scale Bar:** Estimate and add scale bar. You can adjust the size and hide the text in options.
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- **Auto-Contrast** recordable macro commands similar to the Channels and Contrast buttons.
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![](https://github.com/imagej/imagej.github.io/blob/main/media/Image-Viewer/Image-Viewer-SplitView.png?raw=true)
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---
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## Installation
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- in Fiji, add the Image Viewer [Update Site](https://imagej.net/update-sites/following)
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- For ImageJ, download this [repository](https://github.com/kwolbachia/Image_Viewer/tree/main) as .zip
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- **Auto Scale Bar:** Estimate and add scale bar. You can adjust the size and hide the text in options. This macro is adapted from [Aleš Kladnik](https://forum.image.sc/t/automatic-scale-bar-in-fiji-imagej/60774)
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- **Auto-Contrast** recordable macro commands similar to the Channels and Contrast buttons

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