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Working with Sentinel-2 Data

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Sentinel-2 is two identical satellites flying in a single orbit as Sentinel-2A and Sentinel-2B. It carries an optical-instrument payload that samples 13 spectral bands at various resolutions:

  • Four bands at 10 meter spatial resolution
  • Six bands at 20 meter spatial resolution
  • Three bands at 60 meter spatial resolution

There are various processing levels for Sentinel-2 data (Level 0, 1A, 1B, 1C and 2A). Level 1C is a widely available processing level. Level 1C products are created by using a digital elevation model (DEM) to project the image in cartographic coordinates. Level 1C processing includes radiometric and geometric corrections that include orthorectification and spatial registration according to a global reference system with subpixel accuracy. Geomatica ATCOR only supports level 1C Sentinel-2 data. Please note that Sentinel-2 ATCOR support was added in Geomatica 2017.

Level 2A processing consists of scene classification and atmospheric correction applied to Level-1C ortho-image products. Level-2A data is a bottom-of-atmosphere (BOA) reflectance ortho-image product. As this data is already atmospherically corrected, it is not supported in Geomatica ATCOR.

** Note: In December 2016 the Sentinel-2 file structure was changed. Any data with the shorter file structure (December 2016 and later) is only supported in Geomatica 2017 and later (not Geomatica 2016 or earlier).


Downloading Sentinel-2 Data

Sentinel-2 data is available for download from the Copernicus Services Data Hub:


Once you have registered and/or logged in you can search for the Sentinel-2 Data you require.

  1. Select your area of interest by drawing a polygon on the map.
  2. You can then filter the search to only look for Sentinel-2 data.
  • Click on the three lines beside the search bar to open the filter menu
  • Check off Mission: Sentinel-2
  • You can select additional search criteria as required.
  • Click the search button


  1. When the search has completed you can select the desired image.  View the image information by clicking on the eye symbol.


  1. Once you have found the image you would like to use, click the download button.


Opening Sentinel Data in Focus

Sentinel-2 data can be opened directly in Focus using the relevant XML (S2*.xml) or manifest.safe file.

  1. Open Focus from the Geomatica toolbar
  2. In Focus open the File Selector (File > Open) and navigate to your Sentinel-2 data
  3. To open the imagery select the manifest.safe file and click Open


  1. The band selector window will open. Sentinel-2 is delivered with three spatial resolution options. As per the ESA Sentinel-2 website the spatial resolution of Sentinel-2 is dependent on the particular spectral band: https://earth.esa.int/web/sentinel/user-guides/sentinel-2-msi/resolutions/spatial. For now choose the 10M option


*Note: If your imagery spans more than one UTM zone you may have 6 options in the band selector window; three for each UTM zone.

  1. Once the file is open in Focus you can switch to the Files tab to check which bands were loaded



Merge 10m and 20m bands

Level 1-C Sentinel-2 data includes the RBG-NIR as 10m bands and SWIR as 20m bands. You will need to upscale the RGB-NIR bands to 20m and merge them with the rest of the 20m bands. ATCOR makes use of RGB-NIR bands as well as SWIR bands. As ATCOR only accepts a single input MS image, these 20m and 10m bands need to be merged into one file. Since the imagery is quite large we will upscale the 10m to 20m to match with the SWIR bands. 

  1. In Focus open the Data Merge Tool (Tools > Data Merge)
  2. In the Data Merge tool click Browse and then navigate to the location of your Sentinel-2 imagery. Make sure that both the 10m and 20m bands are loaded.
  3. Select all of the bands and click Next


  1. In the Step 2 window click Browse and choose and Output File name.
  2. Under Geo-referencing Setup : Projection choose From File
  • Browse to the manifest.safe file and choose the 20m band option
  1. Under Resolution choose From File
  • Browse to the manifest.safe file and choose the 20m band option
  1. Click Next


  1. In the Step 3 window make sure that all of the required bands are listed.
  2. Click Finish



Atmospherically Correct Sentinel-2 Imagery

Now that you have the file that includes 20m bands for RGB-NIR and SWIR you can run ATCOR in Geomatica Focus. ATCOR will calculate the reflectance values at ground level to remove atmospheric effects in satellite imagery. Running ATCOR will prepare your imagery for analysis under different atmospheric conditions. The workflow generates a reflectance image at ground level, corrected by atmospheric (aerosol type and water vapor) and terrain effects.

Additional ATCOR information on the ATCOR workflow is available from the ATCOR Ground Reflectance tutorial and the Geomatica Help

  1. In Focus open the ATCOR – Ground Reflectance workflow


  1.  Sensor and Image Settings:
  • Use the merged Sentinel-2 20m file as the multispectral input
  • The ATCOR wizard will automatically read the metadata that is ingested when the image is imported into a PIX file. Where necessary, these values will be converted so that they can be used inside ATCOR.
  • Calibration coefficients (Gain/Offset) are automatically calculated and converted to ATCOR units. Each input band has been associated to their correct channel.
  • Set an output folder where all of the ATCOR outputs will be saved


  1. Haze and Cloud Masking:
  • Adjust the cloud, water and haze removal parameters as required for your dataset. More information is available from the Geomatica Help.


  1. Elevation Information Setup:
  • In this example the elevation will be set to a constant height. However, you can use a DEM file if you have one available. More information regarding the elevation and illumination parameters is available from the help.


  1. Visibility and Ground Reflectance:
  • You will likely need to adjust this panel depending on your specific image. These parameters are outlined in the ATCOR Ground Reflectance tutorial and the Geomatica Help


  1. Once you have set all of the parameters you can click Run.
  2. In your output folder there will be an atmospherically corrected image, haze, cloud, water and saturation masks. If you entered a DEM you will also see an illumination mask and terrain setup file.


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