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

Main Features include:

• A Multi Tool to enhance mouse interactions with image windows in many ways
• Two plugins to control image contrast and LUTs (Look Up Tables)
• Utility macros :
  • A cool way to open images from thumbnail montages: Preview Opener
  • Fast basic multichannel montages: Split View
  • auto-generated scale bar
  • Auto-contrast macros
  • Save all opened images
  • A curtain tool to compare two versions of an image

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”
• All created palettes will be easilly accessible from the Channels and Contrast plugin!
  

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

Channels and Contrast

This plugin combines and enhance most 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
• Right click on the composite button to change projection mode : Sum, Max, Min and Invert
• Adjust all channels display range (contrast)
• Right click on a slider to set value manually
• Toggle visible channels in composite mode with the checkboxes
• Use two types of auto-contrast:
  • Auto: Uses imageJ “Enhance Contrast” command with a default of 0.1% saturated pixels (adjustable from “More” button). For stacks, contrast is based on displayed slice only
  • Min/Max: Resets the display range betwin the min and max values of the full channel stack. (this is why it can be a bit slow with huge images)
• 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
  

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
   NOW! With the Multi Tool, double click or middle-click on a thumbnail to open the corresponding image! So next time you search for a specific image on the folder, you will find it immediately

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 do nothing with a simple left click.
Howether it can do many actions based on the mouse button, modifier keys (shift, ctrl, alt) and context!

Windows

• Move Window:
  Left Click and Drag: Moves the image window position interactively.
• Reversible Full Screen:
  Double Left Click: Maximizes the image window, double click again to go back to previous size and position.

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 based on this 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 or double click on a thumbnail to open the corresponding file.
  If Caps Lock ON: Opens image as ‘virtual stack’.

Multi Tool Shortcuts Summary

Other Commands

A collection of utility macros:

Split View:

Quickly create clean multichannel montages for up to 5 channels :

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

Macro commands reproducing the Channels and Contrast buttons

Compare Tool

A macro tool you can find in the toolsets menu of ImageJ (the red double-greater-than >> “More Tools” button at the right end of the main toolbar.)
with it you can compare two versions of the same image. Double click on the source image and slide on the other image to compare with a curtain effect

Miscellaneous

• Apply first LUT Palette (to current image or all opened)
• Same contrast to all opened images
• Same composite mode to all images
• Save all opened images as

Installation

• in Fiji, add the Image Viewer Update Site. That’s it.
• For ImageJ, download this github repository
  Then 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.
However, The easiest way to access commands is from the toolbar menu you can find as Image_Viewer_Toolset under the red >> menu in the ImageJ window:

This will install a “View” menu in your Toolbar will all Image Viewer commands!

Macro snippets

If you like these tools so much you need to get them installed at every starts, just copy this macro code and past it at the end of your

• Fiji/macros/StartupMacros.fiji.ijm for Fiji
• ImageJ/macros/StartupMacros.txt for ImageJ :

var viewer_Menu = newMenu("Image Viewer Menu Tool",
	newArray( 
		"Channels and Contrast",
		"Multi Tool",
		"LUTs Manager",
		"Create Preview Opener",
		"-",
		"Apply first LUT Palette",
		"Split View (multi-channel montage)",
		"Auto scale bar",
		"-",
		"Auto contrast all images",
		"Reset min max all images",
		"Same contrast to all opened images",
		"Same composite mode to all images",
		"Save all opened images as",
		"-",
		"Image Viewer options",
		"Image Viewer online help"
	)
);

macro "Image Viewer Menu Tool - N20C000 T0c15v T8c10i  Tac10e Tfc10w" {
	command = getArgument(); 
	run(command); 
}

All commands are macro recordable so you can make your own keyboard shortcuts: in example:

macro "[1]"{ 
	run("Apply first LUT Palette", "active=[All opened images]");
}

macro "[S]"{ 
	run("Split View (multi-channel montage)", "channels=Grayscale montage=Linear border=5 labels=[No labels]");
}