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# Well Plate Reader - Read well plates on Icy
# wellPlateReader
## Description
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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
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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).
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## Main functions and usage
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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._
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