This Update Site provides utility plugins and macros to help with handling and visualization of microscopy images
If you have a question, feedback or a bug to report, you can post it on the Image.sc Forum

Features include:

• Two plugins to control image contrast and LUTs (Look Up Tables)
• A pluginTool called Multi Tool to enhance mouse interactions with image windows
• Utility macros :
  • basic multichannel montages (Split View)
  • auto-generated scale bar
  • A way to open images from thumbnail montages
  • Auto-contrast macros
  • Save all opened images

Installation

• in Fiji, add the Image Viewer Update Site
• For ImageJ, download this github repository
  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

All commands and plugins are located in the Plugins > Image Viewer menu
But the easiest way is to install the toolbar menu from Image_Viewer_Toolset under the red >> menu in the ImageJ window

Channels and Contrast

This plugin combines imageJ’s “Brightness and Contrast” and “Channels Tool” functionalities to manage visualization of the active image

You can:

• Change multi-channel display mode: composite, color, or grayscale
• Adjust all channels display range (contrast)
• Toggle visible channels in composite mode (checkboxes)
• Use two types of auto-contrast:
  • 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
  • Min/Max: Sets display range to the channel stack’s min/max values
• Interface with the LUTs Manager to apply LUT palettes or individual favorite LUTs
  You can change order of LUTs in a palette directly with the mouse from the palette menu
  
• Access more options and built-in utilities for multi-channel images via the “More” button
  

LUTs Manager

Multichannel Palettes:

• Create and edit LUT sets
• Add LUTs by drag-and-drop from LUTs Finder
• Change LUT order with the mouse
• Right-click on palette to move or remove LUTs
• Empty palette channels default to “Grays”
  

LUTs Finder

All LUTs in your ImageJ luts folder are scanned
You can use the search bar and color buttons to filter the list
Favorite LUTs are stored 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
• Luminance values: Estimation of perceptual luminosity of the LUT min and max colors

Preview Opener

This command creates a thumbnail montage of opened images and saves it in their directory
Then the Multi Tool can interact with this montage to open the selected image

How to use:

1. Open the images you want (virtual stacks supported) from a single folder
2. Adjust display settings
3. run the command Create Preview Opener
   The generated montage will auto-save in the images folder
   With the Multi Tool, middle-click on a montage to open the image under the cursor
   

Notes:

• Keep the Preview Opener file in the images folder
• Montage title must include “Preview Opener” (you can add text before/after)

Multi Tool

This Tool is a neutral tool :

Windows

• Move Window:
  Left Click and Drag (outside ROI): Moves the image window position interactively.
• Reversible Full Screen:
  Double Left Click: Maximizes the image window, reversible to original size.
  But it can perform many actions based on the mouse button, modifier keys (shift, ctrl, alt) and context:

  Composite Display Switch

• Switch Composite Display:
  Middle Click on composite image: Toggle display mode between Composite and Color.

  ROI

• Create Rectangular ROI:
  Ctrl + Left Mouse Drag: creates a rectangular selection.
• Handle Polygon/Point ROI:
  Drag ROI handles using Left Mouse and modify selected selection / points.
• Remove ROI:
  Ctrl + Click outside the ROI removes the current ROI.

  Contrast

• Local Box Auto-Contrast:
  Shift + Alt + Left Click (on non-RGB images): Creates a fixed-size box ROI and auto-adjusts contrast in its area.
  
• Live Contrast Adjustment:
  Shift + Left Mouse Drag (non-RGB images): Drag pointer in the image to interactively adjust contrast.
  

  Stack Browsing

• Live Scroll through Slices/Frames:
  Alt + Left Mouse Drag (on stack/multi-frame images): Drag horizontally to scroll through slices or frames.

  Preview Opener interaction

• Open Image from Preview Opener:
  Mouse Over thumbnails will update top left label showing the file name of the selected image.
  Middle Click on a thumbnail to open the corresponding file.
  If Caps Lock ON: Opens image as ‘virtual stack’.

Multi Tool Shortcuts Summary

Mouse & Keys	Action
Left Drag (no ROI)	Move image window
Double Left Click	Maximize/minimize image window
Middle Click	Composite display toggle / Preview opener open
Ctrl + Left Drag	Create rectangle ROI
Ctrl + Click out of ROI	Remove current ROI
Shift + Alt + Left Click	Box auto-contrast
Shift + Left Drag	Live contrast adjustment
Alt + Left Drag	Stack/frame scroll

Other Commands

A collection of utility macros:

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. This macro is adapted from Aleš Kladnik

Auto-Contrast

Recordable macro commands reproducing the Channels and Contrast buttons