Commit 285e98cd authored by Marion  LOUVEAUX's avatar Marion LOUVEAUX
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Update README new-readme complete case when there is no README at all

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NA # Active Contour
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This is the repository for the source code of *Active Contour*, 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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Automatically segment the boundary of a nucleus or cell starting from an approximate ROI. It supports 2D and 3D processing and tracking of slowly moving cells. Ideal to study cell morphodynamics.
<a href="https://link.springer.com/chapter/10.1007%2F978-3-030-44826-4_25">This book chapter</a> proposes a <strong>step-by-step tutorial for the Active Contours plugin</strong> with <a href="https://link.springer.com/chapter/10.1007%2F978-3-030-44826-4_25#SupplementaryMaterial">video tutorials</a> (see tutorial 3 to 5). Images used in the tutorial are available on <a href="https://zenodo.org/record/3594363#.Xti6AsA6-Uk">this Zenodo repository</a>.
<strong>If you use this plugin in your work, please cite the following reference</strong>: "Dufour et al., IEEE Transactions on Image Processing, 2011". This reference describes the 3D version of the algorithm, but the 2D version works exactly the same.
A more detailed user documentation can be found on the Active Contour documentation page on the Icy website: http://icy.bioimageanalysis.org/plugin/active-contours/
## 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.adufour.activecontours.ActiveContours`
## 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, Daniel Felipe González Obando, Vannary Meas-Yedid, Stephane Dallongeville
## Additional information
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