diff --git a/README.md b/README.md index 219b4669debe71e64e207787bfae1da19f16542b..df09c0ffa7a68b141341aa44e84257d4d6777dce 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,71 @@ -# Well Plate Reader - Read well plates on Icy +# wellPlateReader -## Description +<!-- 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 *wellPlateReader*, 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 --> + +Well plate support for Icy, with an interactive well plate viewer and batch processing capabilities within Protocols +A more detailed user documentation can be found on the wellPlateReader documentation page on the Icy website: http://icy.bioimageanalysis.org/plugin/well-plates/ + + +## 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.hcs.WellPlateImporter` + + + +## 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, Vannary Meas-Yedid, Daniel Felipe González Obando + + +## Additional information + + + + + + + Description This project contains the code necessary to import and show well plates from Opera machines. This project has been developed as a _Gradle_ project and can be opened with _Eclipse_ IDE. -### Available plugins + Available plugins In danyfel.bigimage.io: @@ -15,9 +74,9 @@ In danyfel.bigimage.io: This plugin reads the information of a well plate and then shows an interface with the available plates and their corresponding fields. -## Installation + Installation -### Requirements + Requirements In order to be able to work with this project you must have installed the following software: @@ -28,7 +87,7 @@ In order to be able to work with this project you must have installed the follow - **Eclipse**, version _Neon_ or above. Make sure to have the _Buildship_ plugin installed. ([Available here](http://www.eclipse.org/downloads/)) - **Icy4Eclipse** plugin for Eclipse, the latest version available. Follow [these](http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy) instructions. -### Setup + Setup 1. Use your *Git* repository manager of preference to download this repository (you can use Eclipse Git perspective to do this). The repository URL is [https://gitlab.pasteur.fr/bia/wellPlateReader.git](https://gitlab.pasteur.fr/bia/wellPlateReader.git). 2. Make sure the environment variable **ICY_HOME** is set to the location of your Icy installation. _**Note**: This could be tricky on Mac so make sure to follow [these](https://stackoverflow.com/questions/829749/launch-mac-eclipse-with-environment-variables-set) instructions._