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Visualization Toolset

This macro Tool performs many actions in ImageJ based on the mouse click, modifier keys (shift, ctrl, alt) and context.

<aside> 💡 Notes : This Tool requires to activate the IBMP-CNRS and BioVoxxel Toolbox Update Sites and an ImageJ version ≥ 1.53t

ImageJ will ask once for beamshell installation, please accept and restart ImageJ / Fiji.

For macs ctrl key = cmd.

</aside>

With the Multi Tool selected, a left click on an image will trigger the Main Tool.

To change the main tool : Right click on an image and select “Set Main Tool” :

Also, a right click (or double click) on the icon opens an option dialog for the Scale bar and Wand Tools parameters :

• Table of contents

Main Tools :

Move Windows (default):

Easier way to move image windows

If you click on a selection : moves the selection.

default main tool.mp4

Scale Bar Tool :

Adjust the length and height by dragging the mouse on the image.

You can remove the text on the Multitool options

Scale Bar.mp4

Gamma on LUT :

Adjust the gamma of the current LUT, not the pixel values.

Gamma Lut .mp4

Magic Wand :

Detects local signal in a 5 pixel box to estimate the right Wand tolerance.

Drag mouse laterally to adjust tolerance if needed.

Click with the mouse wheel on a selection to add it to ROI Manager.

New Wand(1).mp4

Double click on Multi Tool to adjust Wand parameters:

Multichannel plot Tool :

Behaves like the built-in line Tool : draw, adjust and move line ROI

Then creates in live a Profile Plot of all active channels :

Multichannel Plot.mp4

Curtain Tool :

To compare two images : first set the “target image”

(the image you want to overlay) by a right click and “set target image”.

Or with a shortcut : the top number key 7.

Curtain Tool.mp4

Secondary Tools (with modifier keys) :

Composite / Color switch :

Without any modifier keys, middle mouse button switch the display

mode of multichannel hyperstacks between “composite” and “color” .

(Note : Middle click on a selection : adds the selection to the ROI Manager.)

middle click.mp4

Contrast Tool :

Hold Shift to adjust the contrast of the active channel :

Shift Contrast.mp4

Slice / Frame Tool :

Hold Alt key to navigate the Z dimension (slice or frame) from anywhere in the image :

alt slice.mp4

Local Auto Contrast :

Shift + Alt : local auto-contrast based on a box ROI (Region of Interest) around the click location.

local auto contrast.mp4

It resets the min and max contrast values of all channels, based on all slices and/or frames.

If the display mode is “color”, the auto-contrast is applied to the active channel only.

Rectangle Tool :

Hold ctrl to mimic the rectangle Tool :

to avoid back and forth between Multi Tool and Rectangle Tool

Ctrl Rectangle.mp4

Curtain Tool :

Ctrl + Alt : shortcut for Curtain Tool.

Note : to avoid the Error: "part" is not a valid choice : once activated, hold the mouse button but release the Ctrl and Alt keys…🤷‍♂️

Preview Opener :

If the middle mouse button is clicked on a Preview Opener montage : opens the selected image.