{"id":20566586,"url":"https://github.com/tferr/scripts","last_synced_at":"2025-04-14T15:53:01.719Z","repository":{"id":148950281,"uuid":"8709403","full_name":"tferr/Scripts","owner":"tferr","description":":microscope::cocktail: Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ","archived":false,"fork":false,"pushed_at":"2022-06-03T11:23:48.000Z","size":9948,"stargazers_count":24,"open_issues_count":3,"forks_count":18,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-03-28T04:41:43.918Z","etag":null,"topics":["beanshell","clojure","groovy","ijm","image-analysis","imagej","imagej2","java","jython","microscopy","python","ruby","scientific-workflows","scripts-collection"],"latest_commit_sha":null,"homepage":"https://imagej.net/BAR","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tferr.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2013-03-11T17:48:12.000Z","updated_at":"2024-05-31T01:53:46.000Z","dependencies_parsed_at":"2023-04-13T23:36:18.833Z","dependency_job_id":null,"html_url":"https://github.com/tferr/Scripts","commit_stats":null,"previous_names":[],"tags_count":22,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tferr%2FScripts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tferr%2FScripts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tferr%2FScripts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tferr%2FScripts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tferr","download_url":"https://codeload.github.com/tferr/Scripts/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248911223,"owners_count":21182058,"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":["beanshell","clojure","groovy","ijm","image-analysis","imagej","imagej2","java","jython","microscopy","python","ruby","scientific-workflows","scripts-collection"],"created_at":"2024-11-16T04:42:34.124Z","updated_at":"2025-04-14T15:53:01.694Z","avatar_url":"https://github.com/tferr.png","language":"Java","readme":"# IJ BAR\n\n[![DOI](https://zenodo.org/badge/8709403.svg)](https://zenodo.org/badge/latestdoi/8709403)\n[![Latest Release](https://img.shields.io/github/release/tferr/Scripts.svg?style=flat-square)](https://github.com/tferr/Scripts/releases)\n[![Issues](https://img.shields.io/github/issues/tferr/Scripts.svg?style=flat-square)](https://github.com/tferr/Scripts/issues)\n[![Travis](https://travis-ci.org/tferr/Scripts.svg?branch=master)](https://travis-ci.org/tferr/Scripts)\n[![GPL License](http://img.shields.io/badge/license-GPL-blue.svg?style=flat-square)](http://opensource.org/licenses/GPL-3.0)\n\nWelcome to the **IJ BAR**: A collection of \u003cb\u003eB\u003c/b\u003eroadly \u003cb\u003eA\u003c/b\u003epplicable \u003cb\u003eR\u003c/b\u003eoutines\nfor [ImageJ](http://imagej.net/), the de facto standard in scientific image processing in\nthe life sciences.\n\nTo install BAR you just need to subscribe to the\n[BAR update site](http://imagej.net/BAR#Installation). To know more about BAR, have a look\nat its [Wiki Page][Wiki]. Below is a lis of some of the BAR routines:\n\n\n## [Analysis]\nRoutines that complement built-in commands in the ImageJ `Analyze\u003e` menu.\n\n1. (py) [LoG-DoG Spot Counter](./BAR/src/main/resources/scripts/BAR/Analysis#log-dog-spot-counter)\n1. (bsh) [Multichannel Plot Profile](./BAR/src/main/resources/scripts/BAR/Analysis#multichannel-plot-profile)\n1. (bsh) [Multichannel ZT-axis Profile](./BAR/src/main/resources/scripts/BAR/Analysis#multichannel-zt-axis-profile)\n1. (bsh) [Smoothed Plot Profile](./BAR/src/main/resources/scripts/BAR/Analysis#smoothed-plot-profile)\n1. (groovy) [Multi ROI Profiler](./BAR/src/main/resources/scripts/BAR/Analysis/Time_Series#multi-roi-profiler)\n1. (groovy) [Normalize Against F0](./BAR/src/main/resources/scripts/BAR/Analysis/Time_Series#normalize-against-f0)\n1. (groovy) [Register Against Average](./BAR/src/main/resources/scripts/BAR/Analysis/Time_Series#register-against-average)\n\n\n## [Data Analysis]\nOperations related to statistics, profiles, histograms and curve fitting.\n\n1. (bsh) [Create Boxplot](./BAR/src/main/resources/scripts/BAR/Data_Analysis#create-boxplot)\n1. (bsh) [Create Polar Plot](./BAR/src/main/resources/scripts/BAR/Data_Analysis#create-polar-plot)\n1. (ijm) [Distribution Plotter](./BAR/src/main/resources/scripts/BAR/Data_Analysis#distribution-plotter)\n1. (bsh) [Find Peaks](./BAR/src/main/resources/scripts/BAR/Data_Analysis#find-peaks)\n1. (bsh) [Fit Polynomial](./BAR/src/main/resources/scripts/BAR/Data_Analysis#fit-polynomial)\n1. (java) [Interactive Plotting](./BAR/src/main/resources/scripts/BAR/Data_Analysis#interactive-plotting)\n1. (py) [NN Distances](./BAR/src/main/resources/scripts/BAR/Data_Analysis#nn-distances)\n\n\n## [Image Annotation][Annotation]\nAiders for the annotation of scientific images.\n\n1. (ijm) [Combine Orthogonal Views](./BAR/src/main/resources/scripts/BAR/Annotation#combine-orthogonal-views)\n1. (bsh) [Cumulative Z-Project](./BAR/src/main/resources/scripts/BAR/Annotation#cumulative-z-project)\n1. (ijm) [ROI Color Coder](./BAR/src/main/resources/scripts/BAR/Annotation#roi-color-coder)\n1. (ijm) [ROI Magnifier Tool](./BAR/src/main/resources/scripts/BAR/Annotation#roi-magnifier-tool)\n\n\n## [Image Segmentation][Segmentation]\nRoutines for partitioning images into analyzable parts.\n\n1. (ijm) [Apply Threshold To ROI](./BAR/src/main/resources/scripts/BAR/Segmentation#apply-threshold-to-roi)\n1. (ijm) [Clear Thresholded Pixels](./BAR/src/main/resources/scripts/BAR/Segmentation#clear-thresholded-pixels)\n1. (bsh) [Remove Isolated Pixels](./BAR/src/main/resources/scripts/BAR/Segmentation#remove-isolated-pixels)\n1. (ijm) [Segment Profile Tool](./BAR/src/main/resources/scripts/BAR/Segmentation#segment-profile-tool)\n1. (java) [Shen-Castan Edge Detector](./BAR/src/main/resources/scripts/BAR/Segmentation#shen-castan-edge-detector)\n1. (ijm) [Threshold From Background](./BAR/src/main/resources/scripts/BAR/Segmentation#threshold-from-background)\n1. (ijm) [Wipe Background](./BAR/src/main/resources/scripts/BAR/Segmentation#wipe-background)\n\n\n## [Utilities]\nProductivity tools.\n\n1. (java) [Commander](./BAR/src/main/resources/scripts/BAR/Utilities#commander)\n1. (ijm) [Calibration Menu](./BAR/src/main/resources/scripts/BAR/Utilities#productivity-menus)\n1. (ijm) [List Folder Menu](./BAR/src/main/resources/scripts/BAR/Utilities#productivity-menus)\n1. (java) [New Snippet](./BAR/src/main/resources/scripts/BAR/Utilities#new-snippet)\n1. (ijm) [Shortcuts Menu](./BAR/src/main/resources/scripts/BAR/Utilities#productivity-menus)\n1. (ijm) [ROI Manager Tools](./BAR/src/main/resources/scripts/BAR/Utilities#roi-manager-tools)\n1. (ijm) [Toolset Creator](./BAR/src/main/resources/scripts/BAR/Utilities#create-toolset)\n\n\n## [My Routines]\nAn infrastructure to help users tinkering with ImageJ.\n\n1. [Multi-language libs](./BAR/src/main/resources/scripts/BAR/lib#lib):\n   User-defined libraries (BeanShell, Clojure, Groovy, IJ Macro, JavaScript, Python, Ruby)\n1. [Boilerplate Scripts](./BAR/src/main/resources/boilerplate/), multi-language skeletons\n   for new scripts that load lib files.\n1. [Script Templates](./BAR/src/main/resources/script_templates), multi-language snippets\n\n\n## [Java Classes]\nMaven project implementing the backbone of BAR, including several [IJ1 plugins and IJ2\ncommands](./BAR#commands-and-plugins), [External Ops](./BAR#external-ops),\nand the [BAR API](http://tferr.github.io/Scripts/apidocs/).\n\n\n## [Tutorials]\n1. [Introduction to Scripting](./BAR/src/main/resources/tutorials#tutorials):\n   101 of (IJ1) scripting using BeanShell and Python (Jython)\n\n1. [External Ops](./BAR#external-ops): Advanced tutorial exemplifying how to\n   provide [ImageJ Ops](http://imagej.net/ImageJ_Ops)\n\n\n# Help?\n * Want to Contribute to BAR?\n    * Thanks! Please, please do! See [here](https://guides.github.com/activities/contributing-to-open-source/)\n    and [here](https://help.github.com/articles/fork-a-repo) for details on how to\n    [fork](https://github.com/tferr/Scripts/fork) BAR or\n    [here](https://help.github.com/articles/using-pull-requests) on how to initiate a\n    [pull request](https://github.com/tferr/Scripts/pulls)\n    * Documentation updates are also welcome, so go ahead and improve the [BAR documentation page][Wiki]\n * Having problems? Found a bug? Need to ask a question?\n    * See the [BAR FAQs](http://imagej.net/BAR#FAQ), [IJ FAQs](http://imagej.net/Frequently_Asked_Questions)\n    and [Bug reporting best practices](http://imagej.net/Bug_reporting_best_practices). Then, you can either:\n      * [Open an issue](https://github.com/tferr/Scripts/issues) on this repository\n      * Report it on the [ImageJ forum](http://forum.imagej.net)\n\n\n# Citations\n\n* To cite BAR:\n\n[![DOI](https://zenodo.org/badge/8709403.svg)](https://zenodo.org/badge/latestdoi/8709403)\n\n* BAR scripts are known to have contributed to the following publications:\n\n  1. Parinejad et al. Disruption of an EAAT-Mediated Chloride Channel in a Drosophila Model of Ataxia (2016), 36(29):7640-7. [PMID 27445142](http://www.ncbi.nlm.nih.gov/pubmed/27445142)\n  1. Bouvier et al. High Resolution Dissection of Reactive Glial Nets in Alzheimer's Disease (2016), 19;6:24544. [PMID 27090093](http://www.ncbi.nlm.nih.gov/pubmed/27090093)\n  1. Ferreira et al. Neuronal morphometry directly from bitmap images. Nature Methods (2014), 11(10):982–984. [PMID 25264773](http://www.ncbi.nlm.nih.gov/pubmed/25264773)\n  1. Pope and Voigt. Peripheral glia have a pivotal role in the initial response to axon degeneration of peripheral sensory neurons in zebrafish. PLoS ONE (2014), 9(7):e103283. [PMID 25058656](http://www.ncbi.nlm.nih.gov/pubmed/25058656)\n  1. Medda et al. Investigation of early cell-surface interactions of human mesenchymal stem cells on nanopatterned β-type titanium-niobium alloy surfaces. Interface Focus (2014), 4(1):20130046. [PMID 24501674](http://www.ncbi.nlm.nih.gov/pubmed/24501674)\n  1. Ferreira et al. Dendrite architecture is organized by transcriptional control of F-actin nucleation. Development (2014), 141(3):650–60. [PMID 24449841](http://www.ncbi.nlm.nih.gov/pubmed/24449841)\n  1. Dobens and Dobens. FijiWings: an open source toolkit for semiautomated morphometric analysis of insect wings. G3 (Bethesda) (2013), 3(8):1443-9. [PMID 23797110](http://www.ncbi.nlm.nih.gov/pubmed/23797110)\n  1. van der Meer et al. Three-dimensional co-cultures of human endothelial cells and embryonic stem cell-derived pericytes inside a microfluidic device. Lab Chip (2013), 13(18):3562-8. [PMID 23702711](http://www.ncbi.nlm.nih.gov/pubmed/23702711)\n  1. Soulet et al. Automated filtering of intrinsic movement artifacts during two-photon intravital microscopy. PLoS ONE (2013), 8(1):e53942. [PMID 23326545](http://www.ncbi.nlm.nih.gov/pubmed/23326545)\n  1. Paolicelli et al. Synaptic pruning by microglia is necessary for normal brain development. Science (2011), 9;333(6048):1456-8. [PMID 21778362](http://www.ncbi.nlm.nih.gov/pubmed/21778362)\n  1. Carnevalli et al. S6K1 plays a critical role in early adipocyte differentiation. Developmental Cell (2010), 18(5):763-74. [PMID 20493810](http://www.ncbi.nlm.nih.gov/pubmed/20493810)\n\n\n# License\nThis program is free software: you can redistribute them and/or modify them under the\nterms of the [GNU General Public License](http://www.gnu.org/licenses/gpl.txt) as\npublished bythe Free Software Foundation, either version 3 of the License, or (at your\noption) any later version.\n\n\n# Contributors\nBAR was created and is maintained by [Tiago Ferreira](http://imagej.net/User:Tiago)\nwith contributions from Maxime Pinchon, [Johannes Schindelin](https://github.com/dscho),\n[Wayne Rasband](http://imagej.nih.gov/ij/), [Mark Hiner](https://github.com/hinerm),\n[Jerome Mutterer](https://github.com/mutterer), [Kota Miura](https://github.com/cmci),\nNicolas Vanderesse, Peter J. Lee, [Jan Eglinger](https://github.com/imagejan) and\n[others](https://github.com/tferr/Scripts/graphs/contributors).\nBAR uses public domain [code](./BAR/src/main/java/bar/FileDrop.java) from Robert Harder\nand Nathan Blomquist. This project would not have been possible without the support of the\noutstanding [ImageJ community](http://imagej.net/Mailing_Lists).\n\n\n[Java Classes]: https://github.com/tferr/Scripts/tree/master/BAR\n[Tutorials]: https://github.com/tferr/Scripts/tree/master/BAR/src/main/resources/tutorials\n\n\n\n------\n| [Home] | [Analysis] | [Annotation] | [Data Analysis] | [lib] | [My Routines] | [Segmentation] | [Tools] | [Utilities] | [Wiki] |\n\n[Home]: https://github.com/tferr/Scripts\n[Analysis]: https://github.com/tferr/Scripts/tree/master/BAR/src/main/resources/scripts/BAR/Analysis\n[Annotation]: https://github.com/tferr/Scripts/tree/master/BAR/src/main/resources/scripts/BAR/Annotation\n[Data Analysis]: https://github.com/tferr/Scripts/tree/master/BAR/src/main/resources/scripts/BAR/Data_Analysis\n[lib]: https://github.com/tferr/Scripts/tree/master/BAR/src/main/resources/lib\n[My Routines]: https://github.com/tferr/Scripts/tree/master/BAR/src/main/resources/scripts/BAR/My_Routines\n[Segmentation]: https://github.com/tferr/Scripts/tree/master/BAR/src/main/resources/scripts/BAR/Segmentation\n[Tools]: https://github.com/tferr/Scripts/tree/master/BAR/src/main/resources/tools\n[Utilities]: https://github.com/tferr/Scripts/tree/master/BAR/src/main/resources/scripts/BAR/Utilities\n[Wiki]: https://imagej.net/BAR\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftferr%2Fscripts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftferr%2Fscripts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftferr%2Fscripts/lists"}