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!


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.


And some high-speed videos

Yesterday’s post was a bit of teaser for the setup of the high-speed video. Now let’s see a couple of examples! (For full effect, I’d recommend playing this on full volume in the background. Rest assured, once we have a highlight reel of lizard runs we’ll definitely be creating a montage of our own)

There’s all sorts of cool stuff going on in this video I had never seen before. For example, notice as the fellow is running into the frame at full tilt he does a little hop and lands with all four feet planted and comes to an almost immediate halt. He then looks left to right to survey his surroundings, and as my big scary hand approaches, turns, pushes off with forelimbs and then generates speed with some big back-leg strides that cause his back to twist with the momentum. He navigates the corners cleanly, but slowly, pausing to look around the corner. Remember though, all of this happens within the span of about a second and a half in real-time.

Now look at this enthusiastic fellow:

He comes barreling in and can’t stop to notice the impending wall. His first crash just turns his head but he sure doesn’t look like he’s attempting to negotiate the turn. At the second crash he crumples and decides a different tact might be best; perhaps climbing the wall and getting out (though it looks more like he’s tap dancing). Again, all of this is happening faster than the eye can really register but at 500 frames per second we’re given a new perspective on these two very different runs.

So now comes the analysis, and this is going to be tricky. Menelia recorded 885 videos and each averages about 2.5 seconds in length. At 500 frames per second that works out to some 1.1 million frames of video to process… Know any good books on tape?

High-speed Sprint Speed

I’ve posted in the past about the lizard sprint speed studies I’ve tried over the years on erhardii. Each of those experiments have come with the caveat that without a high-speed camera (shooting around 500 frames per second and costing the down-payment for a house) we can’t detect more subtle differences between lizard populations. Well, this year Menelia brought a beautiful high-speed camera from her home institution in Antwerp and we had fun finally getting a good look at these lizards on the run.

IMG_3501First steps, warm up the lizards. We used individual socks this year – a major innovation that made it a lot easier to be sure each lizard did their trial run before the next, and sped the process up without having to chase the lizard around the bin.

IMG_3512Then the white dots. These dots show up nice and clear in the video camera and help track the back of the head, the midpoint between shoulders and hips, and the middle of the back. Hopefully these will make processing the video a lot easier.

IMG_3515Here’s our setup. Note the two rainbow kiddie pools (hard not to notice them). This was a major improvement! The lizards would come rocketing out of the sprint speed track and land on the nice inflated pool floor, ready for us to scoop them up back into their sock.

Notice too that the sprint speed track has a couple of right-angle turns in it. One of Menelia’s questions deals with maneuverability and so we were anxious to see how well the lizards negotiated both the first, and second turns in the course.


Here’s the camera’s eye view. Beautiful! Time to run the lizards.

It’s Working!

I’m about to fall into bed after and before another big day of lizard catching tomorrow but just a quick update because I’m really excited. The island manipulation experiment is working! We’ve revisited two of the islands so far – actually the two least productive I think – and the lizards have made it. What’s more, several of last year’s individuals sporting flashy PIT tags (read more and watch a video about that from last year) have survived. It’s such a delightful feeling catching a lizard, seeing that little bump, bagging it, and then waving a little magic wand over the bag to figure out who the lizard was. In fact, it’s such a terrific feeling I’ve video recorded it and uploaded a video so you can experience it as well. Enjoy!

More from the field soon but I’ve put a bet down that we’re going to catch 50 lizards on Agios Artemios so I’m going to get some sleep! Kali Nichta!

PIT Tagging Lizards

A critical component of this study is being able to keep track of who is who, every single year. There are a lot of tried and true methods for doing so, including the low-tech of removing the last joint of different combinations of toes. There’s the mid-tech: injecting multi-colored liquid plastic that congeals just under the skin to give a unique marker. Finally, the high-tech (and my favorite): PIT tags. PIT stands for “Passive Integrated Transponder” which means little tiny circuit that, when activated with an electrical current, replies with a unique identification code.

While toe clipping is a very common means of keeping track of individuals, it suffers from problems because lizards lose toes all the time in fights. To our knowledge though there are not yet PIT tag parlours on any of these islands (though I think the lizards think they’re really cool) so we can be very sure that we’re getting exactly the individuals we want.

The process of implanting a PIT tag is remarkably straight forward. Here’s a video:

As you can see, the PIT tag is tiny – it doesn’t seem to affect the lizard’s movement or behavior at all. Next year, we’ll be able to know exactly who is who!

A look at the islands

So here’s just a bit of background to get you caught up before we dive into the new stuff. I’ve several posts from last May and June about the island introduction experiment (you can get to them from the archives) but I’ll give you the broad overview just so we’re on the same page.

Islands are unique and fascinating laboratories for studying what makes a species “tick.” The limited food, shelter, access to mates, and good nesting sites, makes islands challenging places for lizards. Nonetheless, numerous species do great on small islands in the Mediterranean – indeed all over the world. To do so, small-island lizard populations often adopt a suite of physical, behavioral and/or physiological adaptations.

In P. erhardii, I’ve found a lot of interesting differences between lizards living on Naxos (a very large island) and on the near-by small islets. Small-island lizards are larger, have proportionally larger heads, and a proportionally stronger bite force. The manuscript detailing these results is currently in review, so I can’t elaborate here just yet, but suffice it to say, small-island P. erhardii look and behave differently than their large island kin.

The process by which this transpires, the order and drivers of of these adaptations, and the consequences for the ecological community are largely unknown. That is the question I set out to test, but that’s quite a handful. It’s large-scale and long-term, and necessitates fundamentally changing the ecology of five small islands that don’t currently have lizards on them. After a great deal of scouting, (again see the archives) I found 10 small islets that don’t have Podarcis. After an even greater amount of outreach and discussion, my team gained permission from local stakeholders, and just about every Greek Ministry, to choose five islands for introduction.


Here’s Kambana with a beautiful little church on it. This is a lovely little island – great for lizards.PetalidaHere’s a picture of Petalida all in spring bloom. Petalida is the Greek word for “limpet,” and indeed, the island looks just like a limpet shell rising out of the sea.

Mavronissi SouthHere’s Mavronissi – much rockier with interspersed shrubs. It means the “Black” island. In the background there you can just make out the town of Naoussa, our home base on Paros.

Agios Artemios

Here’s a picture of Agios Artemios – our big producer this year! This island’s huge advantage is seabird nests bringing lots of marine nutrients to bolster the plant and insect community on the island. So much delicious lizard food!


Finally, Galiatsos. This island is flat as a pancake, and frankly was my chief concern for the lizards. Those little lizards pulled through though, even here!

So, after extensive baseline quantification of everything we could count, measure, or photograph, 20 marked lizards were released. Here’s the video from Kambana:

In total, I put 20 lizards on each island: 12 females (8 of whom were gravid) and 8 males. All of the lizards originated from the same large-island population on Naxos. After that, it was a nail-biting 10 months to return and find who had made it. Stay tuned!

*A note to those of you reading these updates on email: these videos don’t come through so check out the website to watch the video footage.