Tuesday, 19 August 2014

After busily deploying data loggers on white storks, what is happening to all that GPS location data?

Training the model with manually classified behaviours. The graphs on the left shows bird movement on 3 axes, plus speed, the graph on the right plots the track of GPS coordinates associated with the behaviour. In this sequence the bird is foraging. The head is going up and down (dark top line) as it walks along (denoted by the wavy movement in the bottom grey line). The speed line (circles and dashes) shows stop and start movement, and this is reflected in the change in position from the GPS coordinates.
Despite my resolve to write more frequent posts somehow months have slipped by!

All my fieldwork is finished and finally last week I finished my lab work in the stable isotope laboratory, both sad moments. With a complete data set now in front of me this means a serious switch to the next phase of my PhD: the data analysis and writing up (via preparing for oral presentations at 2 conferences coming up in September).

So after busily deploying all those data loggers on white storks, what is happening to that GPS location data?

Well, whilst plotting the GPS data to investigate landfill and non-landfill habitat use, home territories and preferred habitats, I am also investigating the behaviour of the birds during each GPS fix. Every transmission the loggers were also quietly collecting data about how the bird was moving, therefore what it was likely doing. From this I can tell for each location if the bird was head up or down, rolling movement from side to side, and also up and down through vertical space. Such amazing technology! Flicking through the graphs is like opening a window onto a secret world.
There are literally thousands of graphs for each bird so at the moment I am busy classifying behaviour by eye to train a model to classify the behaviours for me. I confess I am quite addicted to looking at the graphs so what sounds like a boring task really isn't. The photo above is a screen shot of this process.

These data will be presented at the 5th Bio-Logging Science Symposium in Strasbourg at the end of September (bls5.sciencesconf.org/).

Tuesday, 29 April 2014

The Belly of the Beast: Inside the Mass Spectrometer

As my lab work draws to a close I realise I have learned a surprising amount about running and fixing lab instruments, such as the Delta XP mass spectrometer (mainly when things go wrong as they often do with such high precision instruments). This post is more about the inner workings of the CosTech Elemental Analyser, used for analysing my stable isotopes of Carbon and Nitrogen from feathers.

The Delta XP in the foreground. The Costec furnace (with the blue stripe) for
Carbon/Nitrogen analysis and the tall red Vecstar furnace for Hydrogen in the

Inside the CosTec:

Not a tube of festive decorations, but a spent
reduction column filled with copper shot.

When new all the copper was grey, as in the
bottom of the column. 
A used and new combustion column with the 
handy ruler to guide column packing.
This is the column where the sample is burned.
Note the build up of ash from the tin capsules
in the used column.
    (QW= Quartz wool)

Inside the Mass Spectrometer:

The furnace has 2 reactor columns, 1 where the burning takes place (flash pyrolysis), the other is a reduction column that scrubs out unwanted compounds from the sample gas before it is carried by helium to the mass spectrometer which "counts" the number of isotopes of different weight in the gas. Simple!

Inside the Delta XP mass spectrometer

Even deeper inside the Delta XP. The Source  -if you see this then something has
gone very wrong and the mass spec has been opened up. It takes a few days for
it to return to vacuum and for atmospheric moisture to be removed.
So seeing the source means delays in lab work. Fixing it requires a steady hand,
tweezers and a tiny screw driver. 

I have only seen the ion source (known simply as The Source) 3 times during my 4 years of mass spectrometry as a Masters and PhD student. The ion source converts the sample in to charged particles (ions) which are then passed to the magnet. The magnetic field deflects the particles by differing amounts according to their mass:charge ratio. The detector then counts the relative abundance of the different ions based on their mass:charge ratio. I am measuring the ratios of 12C:13C and 14N:15N, the heavier form being rarer. 

Iberia is dominated by C3 photosynthetic pathway plants with an average 13C of -27 parts per thousand (per mil), where as in Africa in the savannas of Senegal, most plants are C4 pathway plants with an average of -13 per mil. All living things take up these isotopic ratios through diet and they become fixed in tissues like feathers. In this way if I select a Lesser Kestrel feather likely to have been moulted in Africa I can tell from the isotopic ratios whether an individual migrated to Africa or whether it wintered in Iberia. Really fascinating science!

Monday, 7 April 2014

Quadcopters -non avian flying things for a change!

I have submitted an application for funds to buy one of these Phantom quadcopters for White Stork research (fingers crossed), so I jumped at the chance to do a short course: Aerial Photography for Fieldwork using UAVs (Unmanned Aerial Vehicles). 
Also, it looked too much like pure good fun!

Meet the Phantom Quadcopter. With its glowing lights it is sometimes mistaken for an alien spacecraft!
Red is the front, green is the back -not so easy to see when it is a distant speck in the sky above you.

In the last few years quadcopters have suddenly become easy enough to fly and cheap enough to be in the range of even the more humble research budgets. Whilst mostly used by snowboarders and skateboarders to film stunts (and most of the aerial footage in Top Gear is filmed with UAVs), they can also be used to help answer a whole variety of research questions.

Fitting the GoPro camera

This particular quadcopter is mainly used to map changes in mountain sides and valley floors before and after volcanic eruptions or erosion events in Ecuador, the Caribbean and other amazing places. The images can be overlaid on to terrain or elevation models to create amazing 3D images of changes over time. 

The Sainsbury's Centre, from the pilots view... 
...and what the quadcopter saw.
Structures from Motion. One of many hundreds of images that we will stitch
together to make a 3D model of the Sainsbury's Centre.
Mission complete. Good catch!
UAVs were all developed by the military so it is full of
military termimology. A flight is called a Mission -of course!

Investing in a quadcopter is much cheaper than purchasing a satellite image -and they are far more versatile and reusable! 

Uses include:
-Vegetation mapping
-Monitoring changes over time, eg slopes prone to rockfall or mudslides; or to detect patches of illegal logging in rainforests. 

-The camera can easily be modified to thermal or near-infra red imaging to look for nesting birds, or assess plant health (by detecting chlorophyll levels). In this way farmers could target fertilize crops rather than treating whole fields. 

-Fire fighters have used UAVs in controlled experiments to to assess how fire takes hold as it burns across a field, and to look for thermal heat patches that may signal fires in a building before any smoke is detected. 

-Or it could simply be used to view high or dangerous to reach places, like me checking number of eggs in inaccessible stork nests. 

The number of possible applications of UAVs in research will only increase as technology improves. I'm sure it wont be long before university degree courses feature modules in piloting UAVs and the post-processing of image data.
Quadcopter cam view from ground level.....
Mission: to map the UEA Broad. Lift off imminent with me at the controls.
Karen holds a GPS to log various control points round the broad.
After we have cropped and merged together a selection of images
into one photo this can then be geo-referenced and digitalised by
overlaying it on to a map layer in mapping software packages, such as GIS.

...and the Quadcopter's view of the UEA Broad.
You can just see a blue spec holding the white box -thats me
at the controls.

The Phantom flies in winds of over 30mph
and flies itself to some extent. It was amazing
to see it leaning against the wind to maintain
position as it hovered. 

Tuesday, 1 April 2014

Dont worry, nothing died: my favourite talk from the SPEA conference

It was a talk about how nothing died -quite rare for biologists because biological science is seemingly most interested in death and explaining why things died!

In an nutshell, Ricardo Tome and team are using radar and field observations to minimise collision deaths of soaring birds as they pass through wind farms -in fact they have done better than that, they have reduced the number of deaths to zero in their study site: a wind farm in south west Portugal.

I found myself sat opposite him and some of his colleagues over one of those long, tasty, boozy, cafe lunches during the SPEA conference (Birdlife partner for Portugal) that I was talked about in my last blog post. He was a very humourous and entertaining lunch companion as he explained his project in more detail.

As a flock approaches the wind farm, the radar and human observers (placed at some distance around the site), track the flock and decide if the huge sweeping blades of the wind turbines should be stopped. If the flock continue inbound, the turbines are briefly halted, just long enough for the flock to pass through safely. Stopping is near instantaneous and apparently it is quite something to see the wind farm suddenly shut down in unison.

During the whole study period no birds were killed by collisions with wind turbines and there was minimal impact on electricity generation. This seems like a win-win situation to me and captured my imagination, especially because I am an East Anglian lass living on the border of the North Sea in sight of many new off shore wind farms and important coastal areas of birds.

I encourage you all to follow this link and hit the "translate" button -if you dont speak Portuguese

Friday, 28 March 2014

Shes Back!

Apologies for the extremely long pause since I last posted. No excuses really, other than being very busy with data analysis. So what has been happening? 

Aldina and ringed neighbour on the same nests as last year
Goncalo -same nest as last year
 In the past few months over 30 storks have been caught on landfills and fitted with solar powered data loggers.

I visited quite a few of them recently in March by tracking them to their nests. They are being very well behaved this year! Unlike last year, some are in colonies and nests I am already following. Storks usually breeding in the same nest every year so this means I have previous years breeding history for them, which is fantastic news. Also unlike last year, this year many are in nests low enough to be reached with my camera pole. It was quite early in the season so most did not have eggs yet. However, some of the high quality breeding pairs already had a clutch of 5, including logged stork Alina. It will soon be possible to follow the new birds on the website of the BTO, I will let you know when.
I also visited some of the logged birds from last year. Although no longer transmitting they are back on the same nests and appear totally unaffected by carrying their loggers.

My application for funding for fieldwork this summer was successful!
Many thanks to the British Ornithologists' Union (BOU) for your support. Your money will be spent wisely!

A questions session, Congresso de SPEA
My first oral presentation at a conference: The VIII Congresso de Ornitologia da SPEA, Lisbon. 

SPEA are the Birdlife Partners for Portugal. The White Stork is the SPEA bird of the year so it was very exciting to be making my oral presentation conference debut about them. I was quite nervous about it initially, but everyone was so friendly and interested in each others research that by the time the day of my talk arrived I was actually really looking forward to the opportunity to present my research. I presented the preliminary results of tracking my 15 adult storks from last year: how much they use the landfills, how it varies between winter and breeding season, and which non-landfill habitats they select. It lead to some very interesting discussions afterwards. A great opportunity to catch up with Portuguese colleagues and meet other researchers over many a long boozy Portuguese-style lunch!

Attempting to catch Sanderlings at high tide roosts in salt pans. 
With Jose Alves, Teresa Catry and team.  

Digging in the cannons  for a good firing angle.

A cannon. The charge is in the base and as it fires it carries
the net attached to the shackle at the other end

More on that another day... there is too much to say!

Literally in the news. 
As part of National Science Week team and as a STEM ambassador, I took my "Geology of Norfolk" work shop in to Great Yarmouth High School. It was run alongside 5 other hour long sessions run by UEA for the whole of year 10. The fossils mostly survived the occasion..... It made the local paper, though not as the headline piece:

Releasing a male adder

Spring has sprung, so it is survey season again at the consultancy branch of Norfolk Wildlife Trust
This will be my 3rd season as a Norfolk Wildlife Services (NWS) volunteer. Newts surveys are under way and I am also helping out with a series of adder hibernacula surveys too. This involves catching adders, photographing their heads to ID them, and GPSing their hibernaculum. It also involves gorgeous dawn walks on beautiful heaths!

Now you know why I have been a bit slack with the updates! A feast of news on all the above subjects and more to come more frequently from now on, I promise.

Saturday, 16 November 2013


Standby! Team Stork are waiting excitedly for news about funding...

Initial meetings have gone well and we should hear in a few weeks whether the funds will be released for us to attach more loggers to adult storks on Portuguese landfills this winter. I wont jinx it by saying any more about it now, just know that we are all very excited and have been tentatively getting ready to spring in to action the moment we get confirmation to go ahead.
Reading over wintering stork rings, Portimao landfill, 
on a gorgeous hot day in November. Chilly, damp UK
in November or Portuguese landfill in November? 
Its a no brainer!

This will sound very wrong to non birders (and some birders too) but I have been missing landfill! Not the stench, or the mud with the dubious bubbling black pools and the bits of unrecognisable floating stuff, but the ring reading. A whole day can fly in a flash by hunting back and forth through the ever changing sea of white stork legs hunting for those illusive colour rings!
Yum! A circuit board! 
One of these fellas is colour ringed but the legs 
closed over it by the time I got out my camera.

Here are some landfill photos to get you all excited with me!

The landfills are great for gull rings too. Peter Rock has been visiting landfills in Portugal to read gull rings almost since before I was born. Sadly this year we wont be meeting up to wash the unique landfill perfume from our throats over a few beers because he is already out there. All my gull ring sightings will be sent his way. All gull ring records are valuable -submit them to Peter Rock (pete.rock@blueyonder.co.uk)

Above: Beja Landfill, where storks almost outnumber bags 
of garbage. There is always a good haul of colour    
rings after a day here with a telescope.                      

Above: Taboueira landfill, Aveiro                                                       Above: Taveiro landfill, Coimbra

Due to EU directives, open landfills are closing. Aveiro and Coimbra have already closed and sealed -like the mound on the right in the Coimbra photo (above). Reading rings, both gulls and storks, will be a lot trickier in the future once scavenging on landfill is no longer possible and the birds disperse over the countryside.

All the gulls flush accompanied by the thunder of poo on plastic....
...far from shelter the only thing a ring reader can 
do is improvise cover and wait for the flock to pass 
over, hopefully without too many direct hits.            
   Daniel Cadwallader knows whats coming!                

Left: Preparing to catch storks. Ines Catry and Carlos Pacheco deploy the clap net at Alvito landfill, Right: a captured stork is hooded to prevent stress whilst the logger harness is fitted.

 Jose Alves, Phil Saunders and Daniel Cadwallader
 reading rings at Evora landfill whilst waiting for a 
stork to walk in to the traps.

 Letting you in to a secret here, if the funding doesn't come off I am thinking of taking some holiday and booking a long weekend in Portugal just to read rings on landfills!

Monday, 2 September 2013

Storks and Espionage!

 I never thought "Stork" and "Espionage" would appear in the same sentence! The bird is still in police custody so I really hope my storks do not get detained for questioning anywhere on their travels! Coincidentally, this avian James Bond has similar colour rings to my birds: white letters on a blue background! It is part of a tracking project by a french team.

Here is another link to the great work my co-supervisors the BTO are doing with loggers on cuckoos. No accusations of spying yet for these birds: http://www.bbc.co.uk/news/uk-england-23867438