Using S2 MCI Processor

Dear Marco Peters:
I want to process Sentinel-2 A MSI data with "Optical/Thematic Water Processing/S2 MCI Processor’ menu, to retrieve chlorophyll information in a eutrophic lake in my province. But I don’t know how to
select the processing parameters. More specifically,the ‘Preset’ dropdown listbox only shows S2MSI l1b MCI,S2MSI l2 MCI.,does it mean I should use l1b or l2 S2 data products? But the data I downloaded from Sentinel Data Hub are
only l1c products. Should I first perform a sen2cor atmospheric correction and get the bottom of atmosphere reflectance (BOA) data product, and then set as the l2 S2 data input in S2 MCI processor?
Another puzzling question: the literature of J. F. R. GOWER 'Interpretation of the 685 nm peak in water-leaving radiance spectra in terms of fluorescence, absorption and scattering, and its observation by MERIS ’ (int. j. remote sensing, 1999, vol. 20, no. 9, 1771~ 1786) indicated the baseline calculator is based on water-leaving radiance, but the TOA or BOA S2 data products are reflectance., shall I convert the reflectance (either TOA or BOA) to radiance with ‘Optical/Thematic land processing/reflectance to radiance’ menu?
The Help of SNAP is not concurrent and up-to-date with the dialog of S2 MCI processor, your guidance is greatly appreciated.

Li Xuwen

The preset should have been named l1c, it is just a wrong name.
Regarding the help. It is true that the link from the processor menu is not working. Both things will be fixed with the next update of S2tbx.
But the content of help for the MCI processor is actually up-to-date. What are you missing?
If you type s2 mci in the little search box in the upper right and select the help entry, you get to the right documentation.

In general atmospherically corrected images will give the best results, but it also depends on how the AC performs over water.
Using TOA radiances or TOA reflectances should give more or less the same results. It depends on what you want to do with the results. If you want to compare it with other data you should use the same input data.
There is not yet so much practical experience with the algorithm. So your experience with it would be of value. Let us know what works best for you.

The MCI image compared to the band4®3(g)2(b) natural color composite of S2.

MCI shows the intensitiy of cyanobacteria blooms very clearly,and more interestingly, it is shown that the water bodies just close to the cyanobacteria blooms , shows very low MCI , maybe this is the build-up of nearby pyhtoplanktons to form the blooms.

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I am interested in using the MCI processor, but am considering using Google Earth Engine instead to reduce the amount of time I need to spend on downloading and pre-processing the images. I have a couple questions that I would be grateful if someone could provide insight on to help me figure out the best way to move forward:

  1. According to the MCI processor documentation, a modified equation with a correction factor for thin clouds, k, is used. Is this factor applied only to pixels where thin clouds are detected or is it applied to the entire image?
  2. My area of interest is in North America, where the L2 product is not available. When I download the L1C product, there is a different file for each band. Do I first need to stack the bands I want to use into an hdf, netcdf, or BEAM-DIMAP file format to use the processor?

It seems to me that it would be pretty straightforward to code the MCI equation into Earth Engine unless I am missing something ? Are there any behind-the-scene steps that are performed in SNAP?

Thanks for your help