Tips and tricks for shallow water surveys and processing?

[Xandian97]

Hi! I'm fairly new to drones, having recently gotten my hands on a Phantom 4. I'm hoping to use the multispec sensor to do some surveys of a coastal zone at low tide in order to map kelp. I've done a test survey, but Agisoft Metashape is really struggling to align photos covering shallow water - the submerged kelp forests are clearly visible, but the sun glint/glare is messing up alignment and masking them.

Does anyone have any tips and tricks for doing shallow water surveys? I've done some googling and am wondering about maybe using a polarising filter for future surveys, although I can't find any for the multispec sensor I use. Would appreciate any advice on processing/cleaning/filtering the imagery as well when trying to make an orthomosaic - at the moment mine is pretty much just the exposed intertidal zone, almost none of the water imagery has made it.

I've attached some example images of the kelp.

 

[Meta4]

Agisoft Metashape is really struggling to align photos covering shallow water - the submerged kelp forests are clearly visible, but the sun glint/glare is messing up alignment and masking them.

It's no wonder that Metashape is having trouble.
In the examples you posted, sun glare isn't the issue.
For Metashape to work, it needs to be able to find a large number of distinct identifiable points in each image and then to match pairs of points in adjacent images.
But the images have few if any, distinct points to be matched.
I doubt that you would be able to create an orthomosaic with any technique there.
You might need to consider a completely different method, like multi-beam sonar to achieve your desired outcome.

Does anyone have any tips and tricks for doing shallow water surveys? I've done some googling and am wondering about maybe using a polarising filter for future surveys, although I can't find any for the multispec sensor I use. Would appreciate any advice on processing/cleaning/filtering the imagery as well when trying to make an orthomosaic - at the moment mine is pretty much just the exposed intertidal zone, almost none of the water imagery has made it.

A polariser wouldn't help anyway (if glare was the problem).
It's not the magic solution to removing glare that some drone flyers imagine.
For it to work, the polariser has to be aligned relative to the sun angle for all shots.
Any time the drones changes direction, the polariser alignment will be incorrect.
I haven't tried it, but have read suggestions that it wouldn't work anyway for shooting downwards at -90°.