Earth Observation for high impact multi-hazards science (EO4Multihazards)
Published September 14, 2025 | Version v2
Dataset Restricted

HDBSCAN Clusters Rice Crop Stress - Senegal River Delta, 2019-2020

Creators

  • 1. ROR icon University of Twente
  • 2. ROR icon University of Plymouth

Description

Demonstration Case Name 

Multi-hazards in Senegal (transferability case)

Dataset Name/Title 

HDBSCAN Clusters Rice Crop Stress - Senegal River Delta, 2019-2020

Dataset Description 

The dataset contains HDBSCAN (Hierarchical Density-Based Spatial Clustering of Applications with Noise) clusters based on a synthetic stress indicator obtained through a PCA (Principal Component Analysis) on NDVI (Normalized Difference Vegetation Index) and NDMI (Normalized Difference Moisture Index) Sentinel-2 based indices. The dataset contains identified vegetation stress clusters on the following dates: wet year: '2019-06-02', '2019-06-07', '2019-06-17', '2019-06-22', '2019-06-27', dry year: '2020-05-27', '2020-06-11', '2020-06-21', '2020-06-26',  '2020-07-01' , covering the end portion of the rice cropping season in the area. All observations are located in a plain area that relies on the SenegalRiver for cropland irrigation. For each row, the dataset contains the following columns: 

  • date: date of the clustering, in YYYY-mm-dd format

  • cluster: cluster number, -1 identifies the noise (unclassified) cluster

  • ndvi_mean: mean NDVI across field polygon

  • ndmi_mean: mean NDMI across field polygon

  • bsi_mean: mean BSI across field polygon

  • distance_t: average distance (m) of a rice field from the closest irrigation channel

  • geometry: polygon geometry of the cluster in EPSG:32628

Key Methodologies 

Sentinel-2 Level-2 NDVI, NDMI and BSI were computed, averaged per field and exported for 2019-2020. The rice growing period is April to July; the end of season is May-June.  Bare fields were filtered out by BSI >= 0.08. For the remaining fields, NDVI and NDMI  were combined in a principal component (PC) that underwent HDBSCAN clustering. Clusters with average NDVI < 0.45 and NDMI < 0.15 were considered stressed crops.

Temporal Domain 

5 days in 2019, 5 days in 2020

Spatial Domain 

Senegal River Delta, West Africa, EPSG:32628 (UTM Zone 28N)

Key Variables/Indicators 

HDBSCAN clusters

Data Format 

ESRI Shapefile

Source Data 

Sentinel-2 Level-2

Accessibility 

Zenodo, https://doi.org/10.5281/zenodo.17116834

Stakeholder Relevance 

The dataset provides valuable post-disaster information on crop vegetation dynamics during hot and dry events.

Limitations/Assumptions 

The HDBSCAN algorithm was not optimized for the dataset; a fixed version of hyperparameters was directly taken from https://doi.org/10.5281/zenodo.15301314 

Additional Outputs/information

The dataset access is currently restricted due to pending related publication.

Contact Information 

Egor Prikaziuk (UT-ITC, Faculty of Geo-Information Science and Earth Observation, ITC, University of Twente, the Netherlands)

Files

Restricted

The record is publicly accessible, but files are restricted to users with access.

Additional details

Funding

European Space Research Institute
EO4Multihazards (Earth Observation for High-Impact Multi-Hazards Science), funded by the European Space Agency and launched as part of the joint ESA-European Commission Earth System Science Initiative