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Image Viewer

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