MicroCT and visualisation

Fancied getting my current plans out somewhere other than my notebook, hopefully sharing some useful resources I’ve been working with and keeping this blog up to date with my activities.

At the end of this month I’m going to be scanning some lizard specimens from the Cambridge Zoology Museum and the Natural History Museum assuming all arrangements go to plan.

I’ll be using micro computer topography, which essentially fires thousands of high intensity X-rays through the specimen, taking many thin slice pictures, which can then be stitched together to make a single 3D representation of the specimen. You can see individual slices in the top left and bottom left and right tiles below, with the overall model shown top right!

Working view of 3DSlicer, showing a scan of the Dwarf crocodile, Osteolaemus tetraspis. White areas indicate high density (bone/metal) and green areas show where I’ve highlighted particular bone, in this case in the limbs.

After a little bit of computer wizardry within a free program called 3DSlicer, you can generate fantastic 3D visualisations of the scanned specimens. For an example of this, see the limbs of O. tetraspis below.

Limbs of Osteolaemus tetraspis, complete with some of my working measurements.

These images can be created by anyone at home using 3DSlicer, open-source crocodile CT scan data from CrocBase and a handy guide by paleontologist Peter Falkingham. I’m using them to build up a comparative database of limb bone morphology across a range of quadrupedal and bipedal species to investigate whether things such as limb length ratio can contribute to facultative bipedality (the ability to rise up on two legs from four and move around). Currently, I’m working through some data from CrocBase and Digimorph (both free resources) before collecting primary data at the end of the month.

Hopefully this has given you a little insight into what I’m currently working on. Watch this space for more details about how scanning goes (and hopefully some fancy pictures) next month.

Any scans of any species of lizard or bird are gratefully accepted should you have any available! Limbs are of particular importance. 


Cambridge PhD: a six month reflection

So, I’ve made it 6 months into my PhD at the University of Cambridge.


Today we’re going to reflect on what it’s like here, both in terms of my work and the general atmosphere of being in Cambridge. I realise when beginning my own PhD I hadn’t got the foggiest idea what to expect, so maybe this gives someone else insight into what your experience may be like. A lot of this is unstructured rambling, and is more life based then science-y.


Academic life


Going to start with how “work” is. I’m based in the Earth Science department here, which is largely a geology/climatology department, with a smattering of palaeontologists hidden in the woodwork. Of these, most study shelly fossils and early invertebrates, but there are a few vertebrate people, of which I’m one. Which is kind of a falsehood, since I won’t be doing any real paleo work for a year or so, so I’m still really a biologist in the earth science department.


To begin with, this was tough. Listening to conversations in the common room was alien and daunting. Having little to no geology knowledge, I’d be left wondering exactly what these different rocks even were, or why certain magmatic systems (that’s volcanos) are more interesting than others. As time has progressed, I’ve picked up enough to understand the projects of my peers, so the alienation is gone. Additionally, I realized that my lack of understanding but desire to learn was shared. A hard-core earth scientist (that’s a geology joke in case you missed it…) doesn’t necessarily understand the musculoskeletal system at first, but that doesn’t mean they’re uninterested. Everyone listens to and learns from each other, so the department is very inclusive and open, which is great.


I get a desk in a shared office, with internet access and IT support should it be needed. So work space is provided, then there are also college and university-shared working spaces should you fancy a change of scenery. I do this often, finding that it’s really draining to write at my office desk but far easier to analyse data there than anywhere else. So that is also great.


Sometimes it can be a little weird trying to understand how Cambridge works, which systems to follow for different things, but these become clear soon enough.


I also managed to secure space in a different department for dissection work when I start that this summer, which was an achievement since Cambridge departments can allegedly be notoriously uncooperative (though this was not my experience).


I spent a couple of weeks this term “demonstrating”, which is essentially supervising practical lab sessions for undergraduate students answering questions and the such. This was good fun, and something I’m looking forward to doing again next term and each year leading forward. Oh, and you get paid at a decent rate too which is nice.


College life


This will vary greatly based on your college, but I can attest to the Darwin experience.


People: Good. Everyone I’ve met here seems a genuinely nice person, and the few college friends I have are great to spend time with. My college social circle is perhaps smaller than many people due to the amount of time I spend in the department, but this doesn’t bother me, and in fact makes managing college friendships a little easier.


Accommodation: Decent – but doesn’t promote socialising itself. The kitchen area is standard student accommodation, but lacks a “social” are such as a common room. As such, it highly promotes going to the college bar, but I find this is often annoying since I tend to get home from work, chill for a while, eat dinner and then not particularly want to drag myself back out to go to college, even if it is just a couple minute walk. But, as I said, that’s a shortcoming of living offsite. Living in house may be very different, as the bar then serves as the onsite “common room” function. High speed internet is good and I’ve got around 3m of desk space to fill with tech which is much welcome. Oh, we got freezers recently, so I can batch cook a meal without eating the same food for 5 days straight, so life in halls has improved dramatically since October, and I’d definitely consider living in college accommodation again, should the opportunity arise.


Social: Great – provided you put yourself out there. Darwin is regarded to have one of the best college bars in town, the legendary DarBar, I don’t go as often as I’d like, but it’s something I constantly am trying to improve. Without being an extrovert it can be tough to meet people at first, but I’ve managed it so most people would be fine! Also, a double rum for £3.50 is not to be missed out on.


Other factors


You may have heard of PhD students, and Cambridge students generally, often having a tough time dealing with the mental pressures associated with studying here. It’s something I’m likely going to address in detail in the future, but worth touching on here for reasons of comprehension.


It’s stressful. Some days you feel like you get nothing done – that’s stressful. Some days you feel like you did a lot but it wasn’t enough – that’s stressful. Some days everything goes right and you’re happy with how things went – thankfully not stressful. The pressure is indeed high to get work done, but it is by no means (at my stage at least) and unmanageable workload. I tend to manage the stress by making sure I never work late and by eating copious amounts of chocolate digestives. It’s working so far.


In any event that the stress does get too high or you fall prey to other pressures, Cambridge has A TON of pastoral care, from college tutors and councillors to departmental help and even more. That’s something I haven’t heard of being available in such abundance at other institutions.


So there you have a snapshot of what my first six months have shown me. There’s more I could talk about, but I think this covers all the main points. Rereading my last post, I said I’d keep this blog updated more. That’s gone really well this past six months, maybe I’ll manage two posts by next October.