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https://github.com/laulauthom/fiji-roiclicktools
Fiji Toolbar tool with Roi that perform measurements, are added to Manager and auto next slice
https://github.com/laulauthom/fiji-roiclicktools
clickable fiji ground-truth image-annotation imagej region-of-interest roi
Last synced: about 2 months ago
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Fiji Toolbar tool with Roi that perform measurements, are added to Manager and auto next slice
- Host: GitHub
- URL: https://github.com/laulauthom/fiji-roiclicktools
- Owner: LauLauThom
- License: bsd-2-clause
- Created: 2019-12-11T10:40:33.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2021-02-15T10:03:32.000Z (almost 4 years ago)
- Last Synced: 2023-10-25T22:21:35.426Z (about 1 year ago)
- Topics: clickable, fiji, ground-truth, image-annotation, imagej, region-of-interest, roi
- Homepage:
- Size: 2.31 MB
- Stars: 5
- Watchers: 3
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://saythanks.io/to/[email protected])
# ImageJ/Fiji Roi 1-Click Tool
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.
## Installation
In Fiji, simply activate the *ROI 1-click tools* update site.
See how to [activate an update site](https://imagej.net/How_to_follow_a_3rd_party_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.
## Configuration
Double-click on any of the ROI 1-click tool icon to configure the shape and options.
## Video tutorial
Playlist on [YouTube](https://www.youtube.com/playlist?list=PLbBgXlYof3_aEXBmXkkuLyQ78aVj_xdan)
[](https://www.youtube.com/watch?v=ZPS78T_-gUs)
## Examples
### - Circle tool
Using the 1-click circle tool, one can rapidly measure the average intensity for each dot in the sample image *Dot_Blot*.
### - Rectangle tool
Same for the quantification of bands in gels using the 1-click rectangle tool.
### Custom ROI 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.
### - Custom macro command
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 custom actions
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.
### - Keyboard shortcuts
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");
}
## Credits
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](https://doi.org/10.17912/micropub.biology.000215)*
Download the citation as a bib file from the journal website, [here](https://www.micropublication.org/citations?type=bibtex&id=8620)
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}
}
```