Drones to data

I’ve posted a lot of really pretty drone pictures and video these last six months and I’m realizing that this drone is actually pretty exciting tool for science communication. A reporter the other day said that she’d watched my Redonda video as part of her background research and it really helped her get a feel for the island. The original intent for the drone though was to capture high-resolution aerial photos of study sites to try to capture data on important but hard to measure ecological characteristics like vegetation cover, habitat availability, and maybe even habitat structure.

It’s a rainy Saturday in Boston so I decided to go back and look at some pictures from sunny Greece and see if I could start working with the drone footage to get some data.

The first step is actually capturing the video, of course, and that happened in Greece. I flew at a constant height (40m) in a straight line along the long axis of the island with the drone camera pointing 90 degrees straight down.

Here’s what that video looks like (don’t forget to click HD):

Now, that’s really pretty but for analyses I want a single, static image of the whole island. One option would be to just fly really high so the entire island is in the field of view. Unfortunately, since this island is so long, that’d have put me way higher than I wanted (or was allowed) to fly. This would also cause the resolution to suffer – I want to be able to see individual plants pretty clearly. The other option is to decompose that video, frame by frame, into a series of still images that I can then stitch together into a panorama.

This is actually pretty straight forward in in photoshop:

File > Import > Video Frames to Layers…

In this dialog box you select the video you want to make into still images and how many frames you want to skip per layer (the default is one layer every 2 frames). I chose one layer per 30 frames or approximately 1 image per second of video. That’ll give me good overlap to stitch the panorama together but not so many images that my poor computer will have to jigsaw hundreds of pictures together. You can then save those layers as independent images.

The final step then is just stitching together the panorama! Again in photoshop:

File > Automate > Photomerge…

Default settings worked great for me and voila, a beautiful high-resolution aerial photograph of an island in Greece.

Agios Artemios

Click on the image for a high-res look at Agios Artemios

So what about the data? I used my Oru Kayak seat as a launching pad on each of these islands. You can see it as the bright orange oval in the bottom third of the island. That orange launch pad is 80 cm across. With that I can set a scale that’s consistent for the whole island. I also know that the kayak is 360 cm long, which means I can check my calibration to make sure I’m getting good estimates. After that, it’s time to measure. I’m running out of time today so I haven’t made measurements but I’ll be calculating the  area of the island, the area of the green space, maybe even some metrics of patchiness, stay tuned!

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Back from Greece!

Greece came and went this year faster than it ever has before. I think it had to do with the fact that it was the third of my field expeditions this spring. Maybe it had something to do with the only three days at home between returning from the Bahamas and leaving for Athens. Much of my time in Greece was spent breathless trying to get from island to island and now, in retrospect, the three weeks of fieldwork seem like a bit of a hazy dream.

Luckily I’ve got a big stack of data sheets to remember the lizards by.

The goal this year was to revisit the island introduction experiment I started in 2014. This is year three and the first year where all of the lizards we originally introduced to the island have likely died of old age. This means that most of the lizards we were catching were the grandkids of the original colonists and had never experienced any environment other than the little islands they were born on. This is terrific for our ability to start asking questions about evolution over the course of those three generations.

We revisited all five experimental islands and all of the lizard populations are still doing great!

Two of the islands now have well over 100 lizards on them. That’s starting from a seed population of just 20! The lizards are getting big too. It seems like they’re not having any trouble finding food on these little islands.

I’m putting together video from the trip now. I promise to show a bit more restraint in the aerial video than I did on Redonda. Here’s a short fly-over of one of the islands just to give you a look. (Don’t forget to play it on HD). This island was one of our most densely populated – well over 100 lizards on it!

For those of you with a particularly keen eye (and a very long memory on this blog) this is Galiatsos which used to have a fort on it. Here’s a map of the Bay of Naoussa from 1776. Galiatsos is the island with a “Batterie de 35 Canons.”

Big Map

From the flyby you can still see the raised embankments around Galiatsos that formed the foundations of that fort. Once upon a time, those canons were watching over one of the best-protected bays in the Cyclades. It’s fun to be on the island 250 years later and still be able to make out hints of its long history.

 

Flying on Redonda

(For email readers: make sure you come to the website so you can see the video. Also, for full screen – which I highly recommend – you might have to click the vimeo button in the lower right to watch it there.)

 

One of the pieces of equipment I was most eager to try on Redonda was the Mavic Pro drone that we’d brought along to survey vegetation and record a glimpse of just how it looked and felt to be on the island. That goal was very nearly foiled by the knock-you-over wind that never let up over much of the island, but luckily, the western cliff faces (picture below) were fairly protected from the prevailing easterly tradewinds.

Redonda from the air

But, I struggled to find a spot for taking off and landing. As you might guess there weren’t a whole lot of flat areas on this side of the island, and absolutely none of them were rock-free. By digging out rocks and wiping away loose dirt I was able to make this landing site below. Be sure to note, landing about 3 inches to the left, right, or front and those propellers are grinding on stone. Time to start sweating.

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Flyers among you might just have said, why not catch it in air? Well, the Mavic is “too smart” for that. With an array of sensors on its underside to avoid crashes, an extended hand and a projecting stone are avoided with equal enthusiasm. The first (and last) time I caught the little Mavic in the air the propellers did an emergency escape maneuver that was absolutely terrifying to behold. More sweating.

Then, there was the height. I’ll be honest, I’m a little squeamish about cliffs (Anthony and Geoff are going to chuckle at that understatement). Looking up while flying the drone wasn’t a problem. Even looking up at the drone and watching its view of me from a great height doesn’t make me woozy. But looking down at a drone and seeing its birds-eye view of a complete lack of immediately proximate terra firma had me quaking in my boots.  Buckets of sweat at this point.

But, it was worth it. I did two long evening flights and got 50 short clips of life on the western face of Redonda. I never flew quite close enough to the boulders to actually count lizards but hopefully by flying in similar areas year-to-year we’ll get a look at how this part of the island is changing. I hope you enjoy the video. Flying here does give a pretty remarkable view of just how rugged and beautiful Redonda is.

The Losos lab is taking to the sky

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I’m very excited to get some new tech out into the field asap! The Losos lab has decided to get a bird’s eye view of lizard habitat so we’ve just brought home this beautiful DJI Mavic Pro. It’s a little hard to tell from the photo but the drone folds up to be approximately the size of a Nalgene bottle! Our hope is to use it to survey lizard habitats from the sky and create high-resolution 3D maps of some of our field sites. As habitat structure is so important for lizard natural history, we’re thinking this is going to give us some cool new perspective on the habitats lizards are adapting to.

Look forward to many more posts with lots of video but for now the other postdoc, Anthony, and I are just trying to get a handle on flying toy drones…

I’m embarrassed to say this video was one of our most successful attempts… We’ve some more practicing to do before we get the big one out in the field!