Fuzzy clustering for the within-season estimation of cotton phenology

PLoS One. 2023 Mar 8;18(3):e0282364. doi: 10.1371/journal.pone.0282364. eCollection 2023.


Crop phenology is crucial information for crop yield estimation and agricultural management. Traditionally, phenology has been observed from the ground; however Earth observation, weather and soil data have been used to capture the physiological growth of crops. In this work, we propose a new approach for the within-season phenology estimation for cotton at the field level. For this, we exploit a variety of Earth observation vegetation indices (derived from Sentinel-2) and numerical simulations of atmospheric and soil parameters. Our method is unsupervised to address the ever-present problem of sparse and scarce ground truth data that makes most supervised alternatives impractical in real-world scenarios. We applied fuzzy c-means clustering to identify the principal phenological stages of cotton and then used the cluster membership weights to further predict the transitional phases between adjacent stages. In order to evaluate our models, we collected 1,285 crop growth ground observations in Orchomenos, Greece. We introduced a new collection protocol, assigning up to two phenology labels that represent the primary and secondary growth stage in the field and thus indicate when stages are transitioning. Our model was tested against a baseline model that allowed to isolate the random agreement and evaluate its true competence. The results showed that our model considerably outperforms the baseline one, which is promising considering the unsupervised nature of the approach. The limitations and the relevant future work are thoroughly discussed. The ground observations are formatted in an ready-to-use dataset and will be available at https://github.com/Agri-Hub/cotton-phenology-dataset upon publication.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cluster Analysis
  • Gossypium*
  • Seasons
  • Soil
  • Weather*


  • Soil

Grants and funding

This work has been supported by the e-shape (https://e-shape.eu/) and CALLISTO (https://https://callisto-h2020.eu/) projects, which have been funded from the European Union’s Horizon 2020 research and innovation programme under grant agreement 820852 and 101004152, respectively. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.