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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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 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.
This project has been developed as a _Gradle_ project and can be opened with _Eclipse_ IDE.
### Available plugins
Available plugins
In danyfel.bigimage.io:
In danyfel.bigimage.io:
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This plugin reads the information of a well plate and then shows an interface with the available plates and their corresponding fields.
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:
In order to be able to work with this project you must have installed the following software:
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-**Eclipse**, version _Neon_ or above. Make sure to have the _Buildship_ plugin installed. ([Available here](http://www.eclipse.org/downloads/))
-**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.
-**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).
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._
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._
