Toolset that offers additional toolbar ROI tools, with predefined custom ROI shapes.
Using the 1-Click ROI, clicking on an image generates a predefined ROI, centered on the clicked point.
If the option are selected, the generated ROI is added to the Roi Manager, the command run Measure is run for the selected region and if a stack is used, the next image is displayed.
With the latest version, maintaining the left click pressed allows to preview the roi and to move it around. The roi is "validated" once the click released.
In Fiji, simply activate the ROI 1-click tools update site.
See how to activate an update site.
In ImageJ, copy the file "Roi 1-Click Tools.ijm" to the folder ImageJ\macros\toolsets.
To display the toolbar, click the >> on the right side of the ImageJ toolbar, and select the ROI 1-click tools entry.
N.B: For optimal functioning, the macro toolset requires ImageJ >= 1.52r.
Double-click on any of the ROI 1-click tool icon to configure the shape and options.
Playlist on YouTube
Using the 1-click circle tool, one can rapidly measure the average intensity for each dot in the sample image Dot_Blot.
Same for the quantification of bands in gels using the 1-click rectangle tool.
Instead of defining the dimensions, the custom ROI tool allows to generate ROI from an existing model ROI.
This is particularly convenient for freehand and polygon ROI.
To define the model ROI, draw a ROI, then click the Update custom ROI tool button.
Then select the custom ROI tool, and use it like the others 1-clik tools to generate new ROI based on this model.
Using the "custom macro command" field, any additional action can be executed upon click.
Below an example where the clicked region is cropped to a new image using the "duplicate" commands.
Multiple commands can be entered inline in the one-line field by separating them with ;
More complex operations to be executed on click can be implemented by adding a few lines in the source code.
Edit the file Roi 1-click Tools.ijm in Fiji.app/macros/toolsets.
Then look for the paragraph
* MORE CUSTOM COMMANDS (executed even if the tick box is not ticked)
* Examples (remove the //, save the file and relaunch fiji to test it)
*/
//run("Duplicate...", " ");
//run("Invert", "slice");
You can add some commands of your choice below the examples.
Installing the ROI 1-click tools, also installs some default keyboard shortcuts.
-
0-9 of the numerical keypad (right side, not top row of keyboard) will set the current roi group to the key pressed.
-
1 of the top row triggers the custom shortcut, currently making a montage of opened images.
Additional shortcuts (letters also possible) can be added by modifying the source code.
The key and the set of commands can be edited at the beginning of the source code in the macro "Custom shortcut"
macro "Custom shortcut [1]" {
// ADD CUSTOM COMMANDS HERE
run("Images to Stack", "name=Stack title=[] use");
run("Make Montage...", "columns=5 rows=1 scale=1");
}
If you use those tools please cite
Thomas, LSV; Gehrig, J (2020)
ImageJ/Fiji ROI 1-click tools for rapid manual image annotations and measurements
microPublication Biology.
DOI: 10.17912/micropub.biology.000215
Download the citation as a bib file from the journal website, here
or copy/paste this to a .bib file
@misc{https://doi.org/10.17912/micropub.biology.000215,
doi = {10.17912/micropub.biology.000215},
url = {https://www.micropublication.org/journals/biology/micropub-biology-000215/},
author = {Thomas, Laurent SV and Gehrig, Jochen},
title = {ImageJ/Fiji ROI 1-click tools for rapid manual image annotations and measurements},
journal = {microPublication Biology},
year = {2020}
}