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MERIS MCI Processor
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MERIS MCI Processor
1/25/16 11:37 PM
I am (trying) to run the MCI processor on some MERIS reduced resolution level 1B data. For some reason every time I do so the generated values are very low (all well below zero). Does anyone have any idea why this may be happening? I realise this is a very vague question so if anyone thinks they may be able to help I can provide more detailed information!

For reference when I run the C2R processor on the same data it retrieves chlorophyll values for the area I am looking at of between 0 and 1.9 mg/m3.

Thanks!
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RE: MERIS MCI Processor
1/26/16 4:30 PM as a reply to Tom Pye.
Hi Tom,

the MCI is exploiting a peak in the spectrum at 700nm, or even larger wavelngth, which becomes measurable for (very) high chlorophyll-a concentrations. Red tides are mentions as examples in the algorithm documentation. Primarily this is a spectral feature which is most prominent at the water surface. When transported to top-of-atmosphere, the spectrum is modified by atmospheric effects which has as steadily decreasing slope. Finally, the MCI is applied at toa radiance (if I am not mistaken) and not toa reflectances, which introduces further a decreasing spectral slope. In total, the peak around 700nm is overlaid by a spectrally decreasing slope from short to longer wavelength. If the peak is not very pronounced at surface (i.e. comparably low chl concentrations) the corresponding toa-radiance at peak wavelength has vanished, i.e. the value is more or less at the level of the baseline and thus the MCI is very small or even negative (if the toa radiance at peak wavelength is below the baseline).

In summary, for small chlorophyll concentrations the spectrum around 700nm is not far away from a straight line because the atmosphere signal and the spectral slope of the sun irradiance dominate the spectral shape of the signal. Thus the MCI is close to zero and maybe even negative.

I hope this helps,
Carsten
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RE: MERIS MCI Processor
1/26/16 5:43 PM as a reply to Carsten Brockmann.
Hi Carsten,

This is really helpful thank you. This makes a lot of sense (as to why my values from MCI are negative), in light of the relatively low chlorophyll concentrations I have retrieved via the C2R processor. However I am still unsure about something - based upon your response I would expect the MCI signal to be broadly uniform (and low) across my area of interest, in that there is little chlorophyll present. However what is occuring is that the areas with the highest chlorophyll concentrations as identified by C2R (mostly coastal areas) are those with the lowest MCI signals. Which if nothing else would presumably be an unlikely conincidence. Is there any particular reason why there be such a discrepancy between the two processors? Or could it be indicative of something not being right about the way I am going about implementing them?

Thanks for your help thus far, if you could shed any light on the above it would be much appreciated!

Cheers, Tom.
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RE: MERIS MCI Processor
1/27/16 5:13 PM as a reply to Tom Pye.
Hi Tom,

could you let me know the product name (starting "MER_RR_*)? I would like to inspect it myself in order to understand what's happening.

Carsten
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RE: MERIS MCI Processor
1/27/16 10:21 PM as a reply to Carsten Brockmann.
Hi Carsten

the full product name is:

MER_RR__1PRBCM20120127_220841_000000563111_00101_51839_0002.N1

According to the file properties it is:

Envisat data product in N1 form

Let me know if you need any other info. And thank you for taking an interest!

Tom.
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RE: MERIS MCI Processor
1/28/16 3:16 PM as a reply to Tom Pye.
As an update, I have discovered that by changing the signal band from band 9 (709nm) and associated upper and lower bands to band 8 (683nm) and associated upper and lower bands the distribution of chlorophyll-a becomes much more similar to that identified by C2R. Is this an acceptable thing to do if stated in the methods?

Cheers,

Tom.
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RE: MERIS MCI Processor
1/31/16 1:34 PM as a reply to Tom Pye.
Hi Tom,

I attach here an image that shows a large part of the the full orbit product (left). You are working on a subset of this full product, New Zealand (right?), indicated by the red circle. On the right is an enlargement of that portion of the image. I show always the TOA RGB, and next to it the medium and high sun glint flags overlaid (taken from the MERIS Level 2 product). The full orbit shows the sun glint area which extends over a large part from north to south, and covers roughly half of the swath where it is at maximum, north of New Zealand. The east coast of New Zealand is still in the high sun glint are, with only some parts in medium glint.

The MCI algorithm works at the top-of-atmosphere signal, i.e. no correction for atmospheric effect and no correction of the sun reflection at the water surface (i.e. sun glint) is performed. The idea of the MCI is to be robust to the atmosphere signal. However, I don't think that there is yet an investigation on the robustness to sun glint. As first approximation sun glint is spectrally flat and an additive term to the water leaving reflectance, but of course transmitted through the atmosphere which has a strong spectral dependence. In any case, I think one should not use the MCI in high glint conditions (and better not using it in even medium glint) until a sensitivity analysis has been done to understand the relationship between sun glint and MCI.

Atmospheric correction algorithms remove the effects of the atmosphere as well as the specular reflection at the water surface (glint). The standard MERIS Level 2 product is able to cope with medium glint but not under high glint conditions. The C2R can work under much stronger glint conditions. That is the reason why apparently you get a reasonable Chl estimate from C2R (at least in some areas in the image, I haven't studied it).

Despite of the above, your observation makes sense that the MCI reveals more meaningful values when shifting the peak and baseline wavelengths a bit more to shorter wavelengths at the (rather low) Chl concentrations you found. The spectral location of the chlorophyll peak depends on the level of chlorophyll concentration, and it is shifting to higher wavelengths with increasing chlorophyll concentration. This red peak is actually a combined effect of the chl spectral absorption at 670nm, the chlorophyll fluorescence and pure water absorption. All these are spectrally fixed, but have different relative importance depending on the chlorophyll concentration and hence it seems as if the peak is spectrally shifting.

Carsten
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RE: MERIS MCI Processor
2/2/16 4:17 PM as a reply to Carsten Brockmann.
Hi Carsten,

Thank you very much for this response. As you confirmed, I identified that the values were more meaningful at lower wavelenghts. However I was unsure why this was the case and your response has proved invaluable in determining why this is. I cannot thank you enough for taking an interest in this issue!

Cheers, Tom.
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