An update on taking toepad pictures

This is an update from my previous blog post on Toepad pictures. 

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I’ve taken more than four hundred toepad pictures using the new macro photography technique I introduced  in an earlier post and I’ve learned a few tricks that I want to share in this update.

First and foremost, I highly recommend this approach. For those of you looking to capture a lot of toepad data, particularly in the field, this kit is way faster and more portable than using a flatbed scanner and the images I’m getting are at least as sharp.

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A few tips:

  • Petri dishes work great as a clear platform to place the lizard feet on. I found that the 60 mm diameter dishes were much easier to balance atop the lens (~40 mm in diameter) than the larger dishes I’d originally shown.
  • I cut and taped a scale bar to one edge of the petri dish so I wouldn’t have to worry about juggling a lizard and a tape measure.
  • Make sure you have several petri dishes – they scratch fast – and keep some ethanol and a kimwipe close at hand.

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  • The app that lets you remotely trigger your iPhone is absolutely maddening. Do not download it. I’m not even going to relink the name. Instead, I suggest a much more stable alternative: connect your phone to your computer with the USB cable, open QuickTime Player, select File > New Movie Recording and click the down arrow next to the record button. This will give you the option to select your attached iPhone as a recording device. This live-view is far more stable and less frustrating. *Windows and android users I’m afraid I haven’t had an opportunity to sort out a solution for those platforms. If you know of something that works, please include in the comments!

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Unfortunately, through the live view all you can see is whether the lizard is in position. You cannot remotely trigger the shutter this way. That means you’ll need a second pair of hands to help. I found it worked best when my partner was in charge of putting the ID tag in the frame after I’d placed the lizard foot and then pushing the volume button on the side of the phone to trigger the camera shutter.

  • Lighting is really important. I suggested a headlamp in the previous post providing an oblique light source through the diffuser around the lens. I tried using a microscope fiber optic light source but I was really unhappy with the “warmth” of the light. I found that the white-LEDs in my headlamp produced a much more realistic looking image (see above). Also, make sure you don’t have any light sources above/behind the subject. Backlighting confuses the camera’s auto-contrasting and results in dark and sometimes unfocused images.

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A new method for taking toepad pictures in the field!

This is a reblog of a post I wrote over on Anole Annals

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Getting good pictures of lizard toepads in the field can be tricky. Flatbed scanners are heavy and don’t take well to transit bumps and bruises, and getting a digital camera to focus on the toe, not the glass, requires surgical precision on the manual focus ring. I’ve just found a new solution for an iPhone (or GooglePixel, if that’s how you roll), and I’m eager to share.

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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!

How to put a lizard to sleep

Now, when I really want to put something (or somebody) to sleep, my dissertation prospectus is pretty much the first thing I grab. Reading that thing aloud… well, does the trick. Sometimes though, especially in the case of my little lizards, it’s handy to have a trick to get them to go to sleep just a little faster. Anthony Herrel was visiting last week to get a look at the system and taught me this little trick for putting a Podarcis out for the count. I have no idea why it works but it sure does! Check it out:

So there you have it. A few belly rubs and the lizard will happily stay there until disturbed. I haven’t tried for a time record yet… maybe I will and see just how long they’ll stay on their backs. So far it seems that I can easily count on 30 seconds! Go figure, but good to know!

Fishing for lizards

There are lots of ways to catch a lizard. The low-tech solution of course is the old ‘lift a rock and smash your hand down on anything that moves’ method. I tend to prefer more delicate techniques though, particularly in deference to the vipers that also make their homes under these rocks.

So if it’s to be tools, I’d suggest fishing. Luckily, when it comes to decision-making, these lizards tend to be guided by their stomach, not their brain. That means a nice, juicy, wriggling mealworm always seems like a good idea, regardless of whether it’s tied to a long pole and being bounced around by a human. Thus, often the easiest way to catch a lizard is to dangle a worm in front of its face, let it latch on (they often can’t bite through), and then just pick them right up off the ground and plop them into a bucket. Don’t believe me? Take a look here at this video I took:

Lizard sprint speed

As I’ve mentioned before, one of my primary research interests is how these lizards change in different contexts. So far I’ve measured a whole lot of morphological traits like limb length and head width on lizards from islands all over the cyclades. I’ve also measured a whole-organism performance trait, namely bite force, which relies on many of these head-related morphological traits working together in concert to see if that varied from one island to the next. Head measurements have differed significantly, as have bite force measurements. Now I want to determine whether the differing limb lengths also result in differences in performance, specifically sprint speed.

There are many ways in the literature to measure lizard sprint speed. The most common is to use a racetrack or small treadmill, set a lizard down and record how fast it runs across the surface. This works well, to a point, but I’ve never been entirely satisfied with papers discussing the implications of a lizard that runs 4% faster than another over a thick rubber mat. I wanted to test sprint speed in a more realistic context. My first thought was to build a fenced course out in the field, but I soon realized that wasn’t going to be feasible, so I set out to replicate field conditions in the lab.

The two populations I most wanted to test were both from Naxos. One lives in a highly developed valley full of rock walls and terraces and spends almost all of its time on and near the stones. The other lives in an area without any significant human land use – no grazing and certainly no walls, and so spends its time running across loose sand from bush to bush. These two substrates formed the basis of my question – because the lizards in the two areas have different limb lengths, does that mean they have different sprinting capacity over the substrate they’re most used to traversing?

So, I built a 3 meter long plastic-lined chute in the lab. I covered the bottom with sand, set up my video camera, and started recording lizards from both populations running across it. Things got really interesting when, after I absconded with about 15 large stones from an old rock pile, I built a mini rock wall in the chute. I then re-ran all of the lizards across the stones to see if some managed better than others. I now have a few hours of video to go through, frame by frame to calculate the sprint speeds of each individual, but fingers crossed something interesting comes of it! Here are a few pictures of the set up.Sprint Speed SetupSprint Speed Rocks Sprint Speed Sand

Harnessing Social Media For Science: Part 2: Collaboration and Education

My more candid readers have pointed out that I promised to convince you that scientists should be on social networks and my first post in this series managed only to demonstrate that social networks are big. I didn’t want to belabor the point but hopefully I also partially convinced you that people are making big gains (in cash or publicity) from their social media presence. Now it’s time to elaborate a bit on why I think scientists should join these networks.

First, and most obviously, social networks are a great way for scientists to… network. We all know that networking is important, that’s part of the reason we go to conferences. Twitter connects scientists from all over the world instantly. If you want to find people with similar interests, brainstorm with someone in a totally different field or just get a sense of what others are talking about, spend a day on twitter following some of the scientists in your field. Real, valuable, scientific conversations are happening daily online. Twitter has a reputation for inanity, after all how much can we say of worth in 140 characters? The answer is a lot, and distilling conversations and points to just a couple of short sentences is itself a valuable skill. Twitter is intimidating to the uninitiated (I’m thinking about ways around that) but I’d strongly encourage scientists at any level in their career to create an account and give it a try.

There are quite a few other social networks springing up specifically for scientists to network, collaborate and brainstorm. If you’re interested here are a few that I’ve looked into from time to time: mendeley.com, f1000.com, academia.edu. These social web portals are a great way for scientists to meet, discuss and share ideas but I think they miss the great potential of social networks: reaching outside the scientific bubble.

There is an epidemic of science illiteracy plaguing the United States. 72% of Americans can’t pass a basic science literacy test (1). This test covers basic information assumed in order to understand the NYTimes Science section or a NOVA program on TV. The test questions include “Did modern humans live alongside dinosaurs?” and “Does the Earth revolve around the sun?” Participants only need to answer 20 of the 30 questions in order to be considered science literate and almost three quarters of Americans can’t cross that threshold! Furthermore, two thirds of Americans can’t name a living scientist (2). These two findings, in my mind, are a tragedy.

I think that science illiteracy takes two critical forms. The first is a lack of knowledge about the facts scientists do agree upon (I’m thinking evolution and climate change here). The second is a basic lack of understanding about science itself as a discipline, as a process. Scientists on social networks have a chance to change this.

According to the most recent survey I can find, put out by the Pew Center, some forty million Americans rely on the internet as their primary source of news and information about science (3). Now this survey was conducted in 2006. As a sense of scale, Facebook was 5 orders of magnitude smaller back then. I’m sure this number has increased in the intervening years. If tens of millions of Americans (lets ignore the rest of the world for now) are looking online for science information but very few scientists have a significant online presence, where are they getting that science information?

Well, this begs the question, who do scientists rely on to publicize their findings? The answer, largely, is journalists. This is a problem because for every conscientious, well-informed journalist there are many more who don’t fully understand the research they’re reporting on or who intentionally highlight (dare I say misrepresent?) components of research in order to grab headlines. (See here for a diagrammatic representation of the science news cycle) And these are just the journalists. The story gets much scarier when you realize that many people think they’re getting science information when in fact they’re being fed information from interest groups with an agenda capitalizing on the title “science” to gain credibility.

So what’s to be done? In my opinion, the best way to make sure your research is being presented accurately to the world is to communicate it yourself, online, in ways that are searchable and easily approachable. The ideal format for this is a blog. Of course you’re reading a blog now, and while mine by no means represents the gold standard of science communication, this post itself illustrates some of the strengths that I think make blogs a valuable tool for scientists.

First, it’s littered with links, so if something I write strikes your interest you have an opportunity to immediately follow up and continue learning. This is an exciting idea making blogs a powerful tool for education; following link after link around the world wide web can quickly and engagingly give someone a deeper understanding of a topic. Second, it’s permanent. This blog post will be archived both on this site but also on the web at large so if someone wants to revisit it in a year or in ten, they’ll be able to. That leads to a third strength: it’s searchable. The content of a blog is easily searched for on the web which means that people who are interested can get directed to your site quickly and easily. Fourth, it’s international. Remember I said that more than 40 million Americans are online looking for science information? Expand that number to the rest of the world which is increasingly being connected to the web. While there are significant language barriers to contend with, the potential reach of a single blog post is outstanding (For example, my blog has been read by people in 58 countries).  Finally, blogs lend themselves to less formal writing, meaning that, as Christie Wilcox, a blogger for Scientific American said, “jargon-walls” (4) can come down and non-scientists can begin approaching cutting-edge science research.

So what’s in it for you, the scientists? Well, networking has myriad obvious payoffs and Twitter is arguably an even better way of networking than exchanging business cards over cocktail hour at a conference. Blogging is a bigger time commitment though and the returns are a bit less obvious. For myself, I am passionate about science education, and so I am motivated by my desire to get people excited about science. Enlightened self-interest should also sway some to want to communicate more with the public: elected officials affect science directly through NSF budgets or legislated research restrictions and our daily lives through, for example, environmental policy. I want the electorate to know as much as possible about the issues and I think we have valuable information to share. If that’s not enough, there’s some cool evidence that published papers that are blogged about are cited more frequently (5) – see if you can’t boost your impact factor.

If you’re still not convinced, stay tuned for my next post where I’ll talk about using social networks to facilitate research projects that otherwise couldn’t happen.