Hi,

I'm processing L1--> L2 MODIS images with seadas 6.1 and just noticed large sections of apparently cloud-free data missing in the L2 image.  These are highly turbid bloom conditions so perhaps its been masked as land? Can you advise on whether or not this data is retrievable (e.g. bloom in the north east of the lake: set to -32.77 @ nLw555) ?

Thanks!

Caren

Caren,

If you use the L2 Flags Display feature you can identify which flags are set for the area of interest.
This may help you understand what happened in the processing to prevent valid chl retrievals.
Land masking is not a possibility here.  Land is masked by geolocation - not reflectance.  However,
it is possible that high reflectance in the NIR could cause saturation - which would prevent the
atmoshperic correction algorithm from working - even in cloud-free scenes.

Regards,
Sean

Thanks Sean,

In the past I recompiled msl12 because of saturating nLw at 667 nm, would that be an option here? or perhaps a different atmospheric correction scheme?

ps - the link you provided for L2 flags doesnt appear to work.

Caren

Caren,

Before trying alternative atmospheric correction schemes, you'll want to know why the pixels are masked.
The link to the L2 flags option is fixed.

Sean

Thanks Sean.  The area is masked under flags 1, 16, 17, 18, and 20-29.

Flag 1 is 'ATMFAIL' which translates to atmospheric correction failure.
It is likely that one of the NIR bands saturated...

Sean

are these limits set in the L2 processing, in which case can I recompile? or any other way to get around it?

No, these are not limits in the code, rather a limitation of the data. 
There are ways to recover data in such cases, however.
You could  use non-saturating bands for the atmospheric correction.
Or you could use a fixed aerosol model.

Sean

thanks very much Sean, I'll explore those options.