From d281e984fda68528e7ba44168a84128d3130ce4c Mon Sep 17 00:00:00 2001 From: Marion LOUVEAUX <marion.louveaux@pasteur.fr> Date: Mon, 10 May 2021 13:09:19 +0000 Subject: [PATCH] Update README new-readme complete case when there is no README at all --- README.md | 67 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 66 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 280762b..c0c5ee7 100644 --- a/README.md +++ b/README.md @@ -1 +1,66 @@ -NA \ No newline at end of file +# Protocols + +<!-- badges: start --> +[](https://www.gnu.org/licenses/gpl-3.0) +[](https://twitter.com/Icy_BioImaging) +[](https://forum.image.sc/tag/icy) +<!-- badges: end --> + +This is the repository for the source code of *Protocols*, a plugin for the [bioimage analysis software Icy](http://icy.bioimageanalysis.org/), which was developed by members or former members of the [Biological Image Analysis unit at Institut Pasteur](https://research.pasteur.fr/en/team/bioimage-analysis/). This plugin is licensed under GPL3 license. +Icy is developed and maintained by [Biological Image Analysis unit at Institut Pasteur](https://research.pasteur.fr/en/team/bioimage-analysis/). The [source code of Icy](https://gitlab.pasteur.fr/bia/icy) is also licensed under a GPL3 license. + + + +## Plugin description + +<!-- Short description of goals of package, with descriptive links to the documentation website --> + +Design your own <strong>bioimage analysis workflow, graphically, </strong>and automate it on many images (<strong>batch processing</strong>).<strong> +</strong> + +No programming knowledge required! Protocols can be shared and re-used straight from the Icy website. + +Watch this 30 minutes<a href="https://www.youtube.com/watch?v=5SJqhKjCbMQ"> introduction to protocols</a> during the NEUBIAS Academy @home webinar (go directly to <a class="yt-simple-endpoint style-scope yt-formatted-string" dir="auto" spellcheck="false" href="https://www.youtube.com/watch?v=5SJqhKjCbMQ&t=1758s">29:18</a> to skip the general introduction to Icy) and see the corresponding slides (<a href="https://marionlouveaux.github.io/bioimage_analysis_with_icy/">whole webinar</a> or <a href="https://marionlouveaux.github.io/bioimage_analysis_with_icy/#23">protocol part only</a>). +A more detailed user documentation can be found on the Protocols documentation page on the Icy website: http://icy.bioimageanalysis.org/plugin/protocols/ + + +## Installation instructions + +For end-users, refer to the documentation on the Icy website on [how to install an Icy plugin](http://icy.bioimageanalysis.org/tutorial/how-to-install-an-icy-plugin/). + +For developers, see our [Contributing guidelines](https://gitlab.pasteur.fr/bia/icy/-/blob/master/CONTRIBUTING.md) and [Code of Conduct](https://gitlab.pasteur.fr/bia/icy/-/blob/master/CODE-OF-CONDUCT.md). + +<!-- Here we should have some explanations on how to fork this repo (for an example see https://gitlab.pasteur.fr/bia/wellPlateReader). Add any info related to Maven etc. How the project is build (for an example see https://gitlab.pasteur.fr/bia/wellPlateReader). Any additional setup required (authentication tokens, etc). --> + + +## Main functions and usage + +<!-- list main functions, explain architecture, classname, give info on how to get started with the plugin. If applicable, how the package compares to other similar packages and/or how it relates to other packages --> + +Classname: `plugins.adufour.protocols.Protocols` + + + +## Citation + +Please cite this plugins as follows: + + +Please also cite the Icy software and mention the version of Icy you used (bottom right corner of the GUI or first lines of the Output tab): +de Chaumont, F. et al. (2012) Icy: an open bioimage informatics platform for extended reproducible research, [Nature Methods](https://www.nature.com/articles/nmeth.2075), 9, pp. 690-696 +http://icy.bioimageanalysis.org + + + +## Author(s) + +Alexandre Dufour, Stephane Dallongeville + + +## Additional information + + + + + + -- GitLab