Welcome to Sen2Extract!

Sen2Extract is a R Shiny web application allowing to extract time series of spectral indices (previously calculated from Sentinel-2 L2A satellite images) for the requested locations and dates. This can only extract values from images already available in the database.

This application was developed by UMR ESPACE-DEV (IRD, Univ Antilles, Univ Guyane, Univ Montpellier, Univ Réunion) at University of La Réunion – SEAS-OI Station, in the frame of the S2-Malaria Project. This project, funded by CNES (TOSCA 2017-2020), aims at using satellite data provided by Sentinel-2 for epidemiological surveillance (intially for malaria). The main objective is to guarantee quick and easy access to these images and the resulting indices.

How does the application work ?

MAP tab

The user indicates his sites of interest (points or polygons in shapefile format), the period and chooses the indices to be calculated. The application then executes this query on a server and sends the result in csv format directly by email. After receiving the email, the user will be able to open each csv produced to display the table in the Data tab or in graphical form in the Chart tab.

1- Import your zipped shapefile: Thanks to the upload button you can import your shapefile. It can contain points or polygons and must be zipped. When imported, it will automatically be reprojected in WGS84 (EPSG:4326). Only one zip file can be imported at a time.

2- Choose the desired index(s): Sen2Extract application proposes 4 spectral indices that can be selected separately or together.

-NDVI : vegetation index by standardized difference. This index is sensitive to the vigor and quantity of vegetation.

-NDWIGAO : Aimed at monitoring changes in leaf water content, using near-infrared (NIR) and short-wave infrared (SWIR) wavelengths, proposed by Gao in 1996.

-NDWIMCF : Aims to monitor changes in water content in water bodies, using green and near-infrared (NIR) wavelengths, defined by McFeeters in 1996.

-MNDWI: Modified Normalized Difference Water Index is an effective index to highlight the presence of water.

3- Select your period: a calendar allows you to choose your dates. You can easily switch from a weekly, monthly or yearly view by clicking on the date at the top of the calendar.

4- Enter your email address to receive the processed data

Depending on the size of your shapefile and / or the selected period, the processing time may be quite long. However, once the request is sent, you can quit the application. The csv will still be sent by email. If you do not receive an email, please, check the spam. Once the CSV is downloaded, you can go back to the application and use the Data tab to view it. Some software creates a subfolder when zipping.

DATA tab

Simply browse for your file and the table of values will be displayed directly


Browse for your file. By default, the application will choose the date field for the X-axis and the mean for the Y-axis. You can choose other fields and especially group the values according to the code of your entities for a better visualization.

Origin of Sentinel-2 L2A data

Sen2Extract does not allow to extract indices from any locality in the globe, but only on the Sentinel-2 L2A tiles available at SEAS-OI that have been produced in the framework of different projects.

Sentinel-2 images are provided freely by the Copernicus Programme developed and operated by the European Space Agency (ESA). These optical images are acquired by two polar-orbiting satellites : Sentinel-2A was launched on 23 June 2015 and Sentinel-2B on 7 March 2017. They have a high spatial resolution (10 m to 60 m) and high temporal repetitivity (every 5 days) over land and coastal waters. The indices provided by Sen2Extract are calculated from Sentinel-2 L2A images (i.e. after atmospheric, terrain and cirrus corrections). They were calculated at SEAS-OI Station using Sen2Chain, developed also by the S2-Malaria Project (CNES TOSCA 2017-2019) and by the Renovrisk-impact Project (INTERREG 2018-2020). Sen2Chain ( is a simple utility to download and process Sentinel-2 images. It uses the sentinelsat and peps_download packages to find and download data, and ESA's Sen2Cor processor to perform atmospheric, terrain and cirrus correction.