{"id":20373205,"url":"https://github.com/laulauthom/fiji-roiclicktools","last_synced_at":"2026-03-06T09:03:49.943Z","repository":{"id":201272856,"uuid":"227340924","full_name":"LauLauThom/Fiji-RoiClickTools","owner":"LauLauThom","description":"Fiji Toolbar tool with Roi that perform measurements, are added to Manager and auto next slice","archived":false,"fork":false,"pushed_at":"2021-02-15T10:03:32.000Z","size":2427,"stargazers_count":5,"open_issues_count":1,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-15T06:49:46.276Z","etag":null,"topics":["clickable","fiji","ground-truth","image-annotation","imagej","region-of-interest","roi"],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LauLauThom.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-12-11T10:40:33.000Z","updated_at":"2023-05-31T01:15:23.000Z","dependencies_parsed_at":null,"dependency_job_id":"44604804-9841-442a-ab54-5ef4bb3bd97d","html_url":"https://github.com/LauLauThom/Fiji-RoiClickTools","commit_stats":null,"previous_names":["laulauthom/fiji-roiclicktools"],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LauLauThom%2FFiji-RoiClickTools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LauLauThom%2FFiji-RoiClickTools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LauLauThom%2FFiji-RoiClickTools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LauLauThom%2FFiji-RoiClickTools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LauLauThom","download_url":"https://codeload.github.com/LauLauThom/Fiji-RoiClickTools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241921836,"owners_count":20042763,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["clickable","fiji","ground-truth","image-annotation","imagej","region-of-interest","roi"],"created_at":"2024-11-15T01:17:07.672Z","updated_at":"2025-12-02T09:03:13.486Z","avatar_url":"https://github.com/LauLauThom.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"![Twitter Follow](https://img.shields.io/twitter/follow/LauLauThom?style=social)\n[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/laurent132.thomas@laposte.net)\n# ImageJ/Fiji Roi 1-Click Tool\n\n\u003cimg src=\"https://github.com/LauLauThom/RoiClicTool/blob/master/Image/FijiMenu.JPG\" alt=\"MenuBar\" width=\"450\" height=\"80\"\u003e     \n\nToolset that offers additional toolbar ROI tools, with predefined custom ROI shapes.\n\nUsing the 1-Click ROI, clicking on an image generates a predefined ROI, centered on the clicked point.  \nIf 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.  \nWith 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.\n\n## Installation\nIn Fiji, simply activate the *ROI 1-click tools* update site.  \nSee how to [activate an update site](https://imagej.net/How_to_follow_a_3rd_party_update_site).  \n\nIn ImageJ, copy the file \"Roi 1-Click Tools.ijm\" to the folder *ImageJ\\macros\\toolsets*. \n\nTo display the toolbar, click the `\u003e\u003e` on the right side of the ImageJ toolbar, and select the ROI 1-click tools entry.  \n\n__N.B__: For optimal functioning, the macro toolset requires ImageJ \u003e= 1.52r.\n\n## Configuration\nDouble-click on any of the ROI 1-click tool icon to configure the shape and options.\n\n\u003cimg src=\"https://github.com/LauLauThom/RoiClicTool/blob/master/Image/Options.JPG\" alt=\"Options\" width=\"300\" height=\"250\"\u003e\n\n## Video tutorial  \nPlaylist on [YouTube](https://www.youtube.com/playlist?list=PLbBgXlYof3_aEXBmXkkuLyQ78aVj_xdan)  \n[![Tuto](https://img.youtube.com/vi/ZPS78T_-gUs/0.jpg)](https://www.youtube.com/watch?v=ZPS78T_-gUs) \n\n## Examples\n### - Circle tool\nUsing the 1-click circle tool, one can rapidly measure the average intensity for each dot in the sample image *Dot_Blot*.\n\u003cimg src=\"https://github.com/LauLauThom/RoiClicTool/blob/master/Image/DotBlot.png\" alt=\"DotBlot\" width=\"600\" height=\"250\"\u003e\n\n### - Rectangle tool\nSame for the quantification of bands in gels using the 1-click rectangle tool.\n\u003cimg src=\"https://github.com/LauLauThom/RoiClicTool/blob/master/Image/Gel.png\" alt=\"Gel\" width=\"650\" height=\"350\"\u003e\n\n### Custom ROI tool\nInstead of defining the dimensions, the custom ROI tool allows to generate ROI from an existing model ROI.  \nThis is particularly convenient for freehand and polygon ROI.  \nTo define the model ROI, draw a ROI, then click the `Update custom ROI tool` button.  \nThen select the custom ROI tool, and use it like the others 1-clik tools to generate new ROI based on this model.   \n\u003cimg src=\"https://github.com/LauLauThom/RoiClicTool/blob/master/Image/customRoi.gif\" width=\"400\" height=\"400\"\u003e\n\n\n\n### - Custom macro command\nUsing the \"custom macro command\" field, any additional action can be executed upon click.  \nBelow an example where the clicked region is cropped to a new image using the \"duplicate\" commands.  \nMultiple commands can be entered inline in the one-line field by separating them with ;\n\u003cimg src=\"https://github.com/LauLauThom/RoiClicTool/blob/master/Image/customMacro.png\" alt=\"customMacro\" width=\"900\" height=\"320\"\u003e\n\n### - More complex custom actions\nMore complex operations to be executed on click can be implemented by adding a few lines in the source code.  \nEdit the file `Roi 1-click Tools.ijm` in `Fiji.app/macros/toolsets`. \nThen look for the paragraph\n\n\t* MORE CUSTOM COMMANDS (executed even if the tick box is not ticked)\n\t* Examples (remove the //, save the file and relaunch fiji to test it)\n\t*/\n\t//run(\"Duplicate...\", \" \");\n\t//run(\"Invert\", \"slice\");\n\nYou can add some commands of your choice below the examples.\n\n### - Keyboard shortcuts\nInstalling the ROI 1-click tools, also installs some default keyboard shortcuts.\n- 0-9 of the numerical keypad (right side, not top row of keyboard) will set the current roi group to the key pressed.\n\n- 1 of the top row triggers the custom shortcut, currently making a montage of opened images.  \n\nAdditional shortcuts (letters also possible) can be added by modifying the source code.  \nThe key and the set of commands can be edited at the beginning of the source code in the macro \"Custom shortcut\"\n\n\tmacro \"Custom shortcut [1]\" {\n\t\t// ADD CUSTOM COMMANDS HERE\n\t\trun(\"Images to Stack\", \"name=Stack title=[] use\");\n\t\trun(\"Make Montage...\", \"columns=5 rows=1 scale=1\");\n\t}\n\n## Credits\nIf you use those tools please cite  \n\n*Thomas, LSV; Gehrig, J (2020)  \nImageJ/Fiji ROI 1-click tools for rapid manual image annotations and measurements  \nmicroPublication Biology. \nDOI: [10.17912/micropub.biology.000215](https://doi.org/10.17912/micropub.biology.000215)*\n\nDownload the citation as a bib file from the journal website, [here](https://www.micropublication.org/citations?type=bibtex\u0026id=8620)  \nor copy/paste this to a .bib file\n\n```\n@misc{https://doi.org/10.17912/micropub.biology.000215,\n  doi = {10.17912/micropub.biology.000215},\n  url = {https://www.micropublication.org/journals/biology/micropub-biology-000215/},\n  author = {Thomas, Laurent SV and Gehrig, Jochen},\n  title = {ImageJ/Fiji ROI 1-click tools for rapid manual image annotations and measurements},\n  journal = {microPublication Biology},\n  year = {2020}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flaulauthom%2Ffiji-roiclicktools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flaulauthom%2Ffiji-roiclicktools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flaulauthom%2Ffiji-roiclicktools/lists"}