New Site

After 5 years of blogging on the shag project I decided that since I am no longer studying shags, I should move to a new site that isn’t study system dependant.

I’ve been blogging on and off since near the start of my PhD. The blog started in the 2nd year of my PhD, though I do have a diary from the first year of fieldwork which I should archive somewhere. It’s quite nice to have a record of all the stuff I did, as my memory grows increasingly hazy. I therefore migrated all the posts to this new site, where I’ll continue my blog. Hopefully they all transferred correctly. I’ll try and spot any broken posts.

This gave me the excuse to trawl back through some of my old blog posts from my PhD. Here are a few of the things that stood out:



The post on telling the difference between a cormorant and a shag received perhaps the highest number of hits.








Living underground while doing fieldwork in the isles of Scilly










Actually seeing a shag chick hatch while doing seabird surveys















Giving a presentation whilst recovering from having my appendix out








Giving a less painful talk at Winter ASAB







Helping out at the Scilly swims








Racking up the miles handing in my thesis










And finally, finishing






So I’ve been playing with video tracking code in python for a while. In my first week as a post-doc I bashed together some code to automatically track chickadees doing captive trials. I’ve also tracked several crickets in various test arenas. These systems are steadily getting better, and now we’re hoping to ramp up the cricket work, both here and at Carleton University. Additionally, we’re hoping to potentially do something with tracking the chickadee captive trials..

Clearly at this stage, I can’t just send undergrads and volunteers my code. It’s too specialised for each particular problem and I can’t be everywhere at once. It therefore felt like it was time to perhaps starting sticking a graphical user interface on these things.

I had come up with a few quality of life improving pieces of code before. I’d written a script that automatically downloaded RFID data from an SD card, sorted it into it’s appropriate folder and then removed it from the SD card. That still looked like a command prompt though, even if all you had to do was hit enter.

I hadn’t really had any experience with coding user interfaces before, but TKinter seemed the way to go in terms of putting a friendly face on my python code. So I sat down and sketched out what I needed my software to do initially.

  • I needed it to be able to automatically load videos from a file structure, based on whatever variables the user had chosen.
  • I needed users to be able to refer it to a datafile containing data such as the time to start tracking, end tracking or find a clean background plate.
  • I needed users to be able to define areas of interest in the video such as maze arms or trees.
  • I needed a button to start tracking videos.

This seemed like a simple enough initial list. The first thing I decided was to have separate programs for doing the video tracking and defining the areas of interest, though they would share features. I decided to start with this “polygon clicker” as I referred to it. I had written some basic code to let me do this in the past, but it was set up to only work for a particular problem, and I wanted something far more generalised and user friendly.

I started pulling together a GUI, selecting a base folder, selecting variable names, automatically generating the required list of trials based on those variables, etc.

I quickly learnt that there were always more features to add. The first thing I bolted on was a config file so that I didn’t have to click through all the dialogues every time I wanted to test. This of course required a whole set of extra functions to save it and load it when the program was opened and closed.

Eventually I got to the stage where I could add the code to define polygons. This wasn’t without a few hiccups though.

Accidental modern art?

Finally I had the program in a form that I was happy with.

Now it’s time to work on the video tracker.

Once again I had some code ready, but there were always more features to add. What about cropping? What about the fact that our cricket videos had two trials going on in the same frame? What about the ability to copy and paste polygons? Or assign polygons based on a variable rather than on a trial by trial basis? What about making sure it works on a Mac?What about shiny progress bars?

I have to confess I like shiny progress bars:

Progress shall continue.

If this works well, I’ll hopefully make it public. I’m sure it might have some applications for other people!

Oh, in other news, it was my birthday!

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As I have advanced in years, I have been granted WISDOM by this bird. Admittedly it was mainly “CAWWW”, but every little helps..


MacGuyvering cameras

I wanted to do some cover analysis of the places my feeders were hanging, to see how “risky” birds might perceive them as.

One part of this that I decided to do was to use a camera with a wide angle lens to take a photo of the canopy above the feeder, a technique I’d read about in some papers looking at cover structure. The lab had a gopro that seemed perfect for the job. However, I soon discovered that a gopro does not easily fit on a normal tripod. Not without buying expensive accessories!

“Fine” I said, “I’ll kitbash something”

I took the “display tripod” the gopro had come on, a cheap plastic version of a gopro mount with a sticky base that is attached to the cardboard box which contains the manual and wires. I then attached this to one of our home made bird tables that attach to our tripods. However I quickly learned that attaching it in this fashion meant I couldn’t tilt the camera far enough backwards to get it pointing directly upwards. So I started adding layers of card under the sticky base to tilt THAT backwards. Eventually I ended up with this:

Hopefully I used enough duct tape

The orange box pictured here is also part of my cover analysis, in this case to help measure horizontal cover. I’m sure I’ll write more about this in the future.

I also played with video camera set ups:

I’ve been helping out with video tracking on some cricket projects. In this case, I wanted to mount cameras in such a way that they COULD NOT MOVE (this makes video tracking easier). My solution in this case was to get hold of a threaded rod of exactly the right diameter to fit into the hole a tripod screw normally goes in on the bottom of the camera. Then I drilled a hole in the beam above the test arenas. I’d like to see those cameras try to change their fields of view now!

Isometric birds

A thing I did in preparation for a presentation:

The first time in a while that I’ve fired up blender, I think they came out rather well. Isometric chickadees and an isometric feeder. I have some ideas for how I’m going to use them in a presentation I’m going to give in the summer, but there’s another conference coming up soon that I think they’d also be useful for..

When does Winter end?

I am never entirely sure when Winter properly ends in Canada. I know at some point we enter a time called “Spring”, which means that it might be burning hot on one day, then snow the next. In my book, this makes pinpointing the end of Winter hard.

This means there are melts, that then freeze again. This turns snow (which one can generally trudge through one way or another) into DEADLY SLIPPERY ICE.

It may be hard to tell but the ground is frozen solid

Even when the ice starts to melt, this means that ground that feels somewhat solid can give way, causing you to sink thigh deep in snow again.

We are currently attempting to do recaptures at various sites, so we can do repeat personality trials on individuals to see how consistent they are. I feel sometimes that Chickadees are unwilling to fall for being caught a second time. Still, it gets us out and about. We found this porcupine up a tree at one of our field sites:








Also, Canada has some insane woodpeckers who clearly just hate trees.

Our battle with squirrels continues. I can’t say who has won. I think it’s probably the squirrels. Even solid metal cannot stop them.

I also slightly crazily went tobogganing on the ice. I went back in January, when the snow was fresh and fluffy.

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This was a tobogganing trip back in January It was not as icy then.

This time the ice meant everything felt a little different. Firstly, you went insanely fast. Then if you fell off, there was a high probability of if hurting.

On the plus side, you could just slide down the hill with no sledge required.

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March Madness

The squirrels might be winning.

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Gaze into the cold dead eyes of a killer

I’ve been having a running battle with the squirrels since I started this years fieldwork. They love to chew EVERYTHING. Even if there is no food inside.


They just love to chew electronics. However, they will destroy anything they can get their teeth into. The first week we deployed our feeders, we used rubber lids. Tasty, tasty rubber lids.

So we replaced them with metal lids. Empty chopped tomato cans to be precise. This stopped them eating the lids. But the war was not over. Foiled in their attempts to chew the lids, the squirrels at one of our sites chewed the ropes the feeders hung from instead. So we replaced the ropes with plastic covered wire. Surely this would stop them.

We were wrong. Nothing stops a squirrel.

Hopefully this picture gives some idea of how thick the plastic is that they managed to chew through.

In other news, I’ve tried another quintessential Canadian activity. I went curling!








Curling was harder work than I anticipated! I did manage not to fall over, but I was surprised at how little effort it took to make the stone slide all the way to the target.. and keep going!

I also went and watched Crashed Ice.. which is… which is.. well, somewhat insane:













I think it could be described as downhill skating, I’m not sure the photos convey how fast these guys flung themselves down this course. It was certainly worth the many hours we spent slowly freezing our toes off waiting for the event to begin.

Finally, right at the beginning of March I imported some Welsh culture to Canada. Almost every year since the first year of my PhD I’ve had a St. David’s day party. I make Cawl and picau ar y maen. This year I got the help of some Canadians to make caws pobi too.











Then everyone falls asleep because they have eaten/drunk too much. This is the sign of a successful St. David’s day party.

The snow is getting deeper..

So last time I wrote about fieldwork, the snows had just arrived and we were still catching. Well now, we’ve moved from catching to feeder maintenance. Refilling feeders, moving feeders, changing the batteries and SD cards on feeders.

The snow is starting to make that work a lot harder. Now as we tramp through the woods, we’ll suddenly find ourselves up to our waists in snow. It’s time to bring out the snow shoes.

My first time wearing snow shoes in the office

The snow shoes helped enormously. I’d never worn them before, but was amazed at how much easier it made hiking about the field, even if it did take some getting used to tripping over them.

Did I mention we also do all of this at night?

My field assistant Nicolas removing lid of a feeder

The snow makes it eerily quiet. However it is quite handy, in that we can navigate using our own footprints. More reliable than the GPS unit in these woods!