diff --git a/_pages/plugins/image-viewer.md b/_pages/plugins/image-viewer.md new file mode 100644 index 000000000..364551932 --- /dev/null +++ b/_pages/plugins/image-viewer.md @@ -0,0 +1,107 @@ +--- +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