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+# Spot Detector
+
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+
+This is the repository for the source code of *Spot Detector*, 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 --> 
+
+Spot detector detects and counts spots.
+
+- Detects spots in noisy images 2D/3D.
+- Depending on objective, spots can be nuclei, nucleus or cell
+- Versatile input: sequence or batch of file.
+- Detects spot in specific band/channel.
+- Multi band labeling: automaticaly creates ROIs from one band and count in the same or an other band.
+- Filters detection by size.
+- Sort detection by ROIs
+- Output data in XLS Excel files: number of detection by ROIs, and each detection location and size.
+- Outputs withness image with ROIs and detection painted on it.
+- Outputs binary detection image.
+- Displays detections
+- Displays tags        
+A more detailed user documentation can be found on the Spot Detector documentation page on the Icy website: http://icy.bioimageanalysis.org/plugin/spot-detector/               
+
+
+## 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
+
+<!-- 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.fab.spotDetector.SpotDetector`
+
+
+
+## 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)      
+
+Fabrice de Chaumont
+
+
+## Additional information
+
+
+
+
+
+