C2RCC atmospheric correction for S2 MSI products returning high values

I have been using the C2RCC processor for S2 MSI LIC atmospheric correction after resampling products to 10 m. After pixel extraction, the Rrs band spectra look good, but appear on a larger y axis scale (0.295-0.325) with respect to every other paper or output values I’ve seen on the y axis which normally range around 0.000-0.006. Any idea what could be responsible for these strange values??

Could you check if you are looking at rtoa instead of rrs by mistake?

Definitely looking at rrs, thanks for the input though!

Attached is a screengrab of current spectra for reference, I suppose I should have mentioned I’m looking at Chlorophyll as an index for phytoplankton density which is why the spectra peak at band 3.


Have you checked the flags? It is an average, right? Could it be possible that you are including clouds or high glint values that should be masked and left out in your average?

It could be very possible, because I’m not entirely sure what you are referring to as flags. Forgive me, I’m very new to snap. Would you clarify what you mean by flags and how I can check them? Thank you so much!

I have the feeling that you made the average with rtoa (by mistake). I checked with one scene and even in the clouds the values are not so high as yours.

If you open the mask manager, you can see the flags that you should apply before calculating the average. By the way, how did you do it?

That makes sense, thank you. I am meeting with my research advisor shortly and will try the same technique. I resampled images and then just ran the atmospheric correction, without any steps in between, as my advisor instructed.