Merge remote-tracking branch 'remotes/github/main' into HEAD

README.md

@@ -1,3 +1,39 @@
-# maizetrack
+## PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time
 
-tracking maize phenomenal outputs with sequence aligment algorithms
+This work is based on our biorxiv report (TODO), by Benoit Daviet, Romain Fernandez, Llorenc Cabrera-Bosquet, Christophe Pradal and Christian Fournier.
+PhenoTrack3D can be used to track leaf organs over time, in a time-series of 3D maize plant reconstructions. 
+Such 3D reconstructions can be obtained from sets of RGB images with the Phenomenal pipeline (https://github.com/openalea/phenomenal)
+
+### Maintainers
+
+* Daviet Benoit (benoit.daviet@inrae.fr)
+* Fournier Christian (christian.fournier@inrae.fr)
+* Pradal Christophe (christophe.pradal@cirad.fr)
+
+### License
+
+Our code is released under **Cecill-C** (https://cecill.info/licences/Licence_CeCILL_V1.1-US.txt) licence. 
+See LICENSE file for details.
+
+### References
+
+If you use PhenoTrack3D to your research, cite:
+
+Daviet, B., Fernandez, R., Cabrera-Bosquet, L. et al. PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time. Plant Methods 18, 130 (2022). https://doi.org/10.1186/s13007-022-00961-4
+
+```latex
+@article {daviet22,
+	author = {Daviet, Benoit and Fernandez, Romain and Cabrera-Bosquet, Lloren{\c c} and Pradal, Christophe and Fournier, Christian},
+	title = {PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time},
+	elocation-id = @article{daviet2022phenotrack3d,
+	title={PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time},
+	author={Daviet, Benoit and Fernandez, Romain and Cabrera-Bosquet, Lloren{\c{c}} and Pradal, Christophe and Fournier, Christian},
+	journal={Plant Methods},
+	volume={18},
+	number={1},
+	pages={1--14},
+	year={2022},
+	publisher={Springer}
+}
+
+```