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# wellPlateReader
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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
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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.

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 Available plugins
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In danyfel.bigimage.io:

- WellPlateImporter

  This plugin reads the information of a well plate and then shows an interface with the available plates and their corresponding fields.


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 Installation
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79
 Requirements
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In order to be able to work with this project you must have installed the following software:

- **Icy**, version 1.9.5.1 or above. ( [Available here](http://icy.bioimageanalysis.org) )
  - The following plugins should be already installed in order to execute BigImageTools:
    - EzPlug SDK
    - Protocols SDK
- **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.

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 Setup
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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._
3. Open Eclipse and select the menu *File > Import...* Then select *Gradle > Existing Gradle Project*. Click *Next* the project root directory is demanded select the folder **WellPlateReader** inside the folder you downloaded the at. Finally, click *Finish* to create the project in eclipse.

Eclipse will download the dependencies specified in the *gradle.build* file. When it finishes you should see the project without any problem on the project explorer of Eclipse. *If this is not the case, check that the environment variable ICY_HOME is correctly defined.*