My Geology Note-blog

A chronicle of my PhD journey and other geology writings

Month: August, 2016

XRM 2016 conference day 3: “Hay Jude” parody songs

“Day 3 in the XRM-house, the delegates are in Lecture room 1, singing.”

That is a thing that actually happened. In celebration of 3 of the founding members of the XRM conference who are also X-ray microscopy pioneers, Professors Schmal, Kirz and Burge, a lyric-swap of The Beatles No. 1 sing-a-long song was sung. Who say’s science conferences are dry affairs? (Granted, I think some people were a bit bemused and/or embarrassed by it but my time as a young worker has helped me embrace silliness such as that when I used to be among the embarrassed group).

Today was a half day but no less packed. Session one saw talks on studying art using microprobes; chemical mapping of low concentration elements in the tests of foraminiferas; and a talk on scanning theory and reconstruction that I would probably appreciated more had I had the right background in X-ray physics.

The second set of talks I attended discussed improvements to 4D tomography reconstruction (where the 4th dimension in this case is time). Once again freeware is on offer to try out the techniques back in the lab and I have been assured by the presenter that although the maths is complex (he showed us all the equations) it’s easier to use.

Today I presented my poster which is always heartening but quite tiring too. I like chatting over my work in that sort of situation because it gives me ideas that I wouldn’t have thought of before. It’s a bit of a problem in one sense though, I end up coming back with even more ideas that either would add directly to my work or would be really exciting to do.

In my free afternoon I mooched about, firstly, around a bookshop (they seem to call to me like a dog whistle). I always find that different cities have different types of things in their charity shops. Oxford, I predicted, would have a good selection of academic related texts (not necessarily textbooks, just notable works relevant to the field). To my delight I am now the proud owner of a very good condition copy of Flatland by Edwin A. Abbott. Another future blog post may be a review of said book. Books are one of the few things I have a genuine weakness for buying. Luckily charity shop books are always at a discount which is great for people who have to weight up buying food vs. books.

My second stop was the Oxford Natural History museum which I really enjoyed. I know I’ll have to go back again when I’m less brain dead from X-ray science as I didn’t do my usual amount of reading of signs. It’s a very beautiful building both inside and out, especially the stone pillars inside that are all made of different rocks from the British Isles complete with chiselled labels. Once again, photos will be forthcoming.

My only complaint is the frequent use of wet preserved specimens next to fossils in displays to show modern similar species. I’ve got better with spirit collections over the years (a biology classroom with a resident half-eviscerated rabbit in formaldehyde will do that) but most of them were invertebrates today and things like slugs and leaches make my skin crawl. The dinosaur skeletons are terrific and I really liked the “you can touch” style displays of rocks, fossils and even a stuffed black bear.

Notebook page count for today: 18

Time for bed, said Zebedee.


Day 2 at XRM 2016: Taiwan vs. Hamburg

Another packed day has been and gone at XRM 2016, so packed in fact I’m surprised that talks that happened only this morning weren’t actually from yesterday’s programme.

Update: I now know what ptychography is! But don’t ask me to explain it because I don’t understand it well enough to properly articulate it.

Today’s talk highlights included:
– imaging phase separation in Li Batteries
– 4D imaging of various stripes, 3D plus spectra and 3D plus time series, with the latter examples being Li Battery explosive failure and watching a match burn from inside it.
– Imaging and analysing the compound eyes of bees (including some seriously cool image segmentation methods) which I found particularly good.
– Lots of open source software

…….and the battle for the 2020 location of XRM, Taiwan vs Hamburg. Imagine the Olympic bidding only without the corruption and the presentations are more interesting. One of the fun things about the bid talks, and a lot of the other talks for that matter, has been finding out just how many X-ray and Synchrotron facilities are out there in the wide world. Voting closes later in the week so we’ll know then where the conference will be held in 4 years time. (In two years the conference will be in Saskatoon, Saskatchewan, Canada. And yes I did have to look up the spelling of ‘Saskatchewan’).

Today I did a lot more chatting to people. People who know me back in Swansea probably wonder if I ever shut up but I’m usually quite shy around new people so it helped that it was other people who instigated the conversations. In particular I ran into people who I’d met at the ToScA conference last year in Manchester. It’s always great to catch up and exchange lab stories.

People will often say that conferences are the best place to start collaborations. I never really understood how that actually happened but after the last 2 days I’ve realised that you don’t need to persuade a scientist to collaborate. It comes up so effortlessly; whether it’s an offer of an exchange of samples, machine time, software code or even just a lab visit. It really is heartening that although we can often feel like individual islands of research just a tiny bit of activation energy is enough to bring people together.


Pages of notes made today: 27

I’ve also been taking lots of pictures of the displays within the Institute including crochet hyperbolic planes, porcelain topographic sculptures and a modular origami bee hive with model bees. So there’s another blog topic for after the conference!

Tomorrow is a half day so I’ll be visiting some of Oxford’s sights and trying to bag a few more colleges to add to my list.

Analysis technique of the day: STXM (sticks-’em), scanning transmission X-ray microscopy
Best acronym of the day: MANTiS software (with a mantis shrimp as it’s logo), Multivariate ANalysis Tool for Spectromicroscopy




Ouch! My brain! XRM 2016 Day 1

If how well a conference is going were to be judged by the number of pages I’ve filled in the first day only XRM 2016 is doing rather well (18 pages!)

Got out of bed very much feeling like an undergrad in halls again, not least because I’m staying in a room in Keble College and had breakfast in their Great Hall (I think petite pans are the signature breakfast roll of academic institutions from one end of the country to the other). Bright sunshine and pretty architecture certainly make for a pleasant walk even when you know you’re going to be inside all day.

As a geologist and not an X-ray scientist by trade I feared that coming to a conference billed as “X-ray Microscopy” (of which X-ray tomography is only a tiny part of XRM) might leave me in over my head.

Well, yes and no.

Talks today ranged from overviews of several research facilities and new scanning components to direct applications. Talks on applications included an summary of an on going study hunting for why Alzheimer’s Disease develops and how; using sandpaper to enhance imaging (no really); and my personal favourite, a talk on what the structure of dinosaur teeth can tell us about their diet and evolutionary path (answer: a lot!)

But the title of this is “Ouch! My brain!” and for good reason. The science of X-ray microscopy, which seems to me to be three parts physics to one part algebra to two parts geometry, did go over my head at times so to dilute my shame here are the definitions of some words or vocabulary I had to look up later:

Microphages: In there more common recent usage, a microphage is a white blood cell in a vertebrate immune system.
Dark field X-ray: X-ray signals produced by scattering caused by porous structure within a material. These signals are dependant on the orientation of the sample in the case of materials showing anisotropy.
Spherical harmonics: mathematical functions applied to coordinates on a sphere surface. Handy for when you’re dealing with points on the surface of the Earth (which is more or less spherical in an oblate spheroid kind of a way).
Coloured X-rays: Bands of particular X-ray energies similar to how different colours of light are confined to certain wavelengths. Useful for detective chemical composition of a sample.
Ptychography: err… something about diffraction patterns and… yeah I’ve got no Earthly clue. Questions for someone tomorrow.

Despite attending the conference alone I did a surprisingly large amount of chatting to folks today, mainly because I set myself the goal that if I saw anything that a colleague might be interested in or relate to their work I should make enquiries.

I may submit something to the conference blog before the week’s out but for now, further updates will be here (including pictures hopefully when I work out how to get them off my phone).

Roll on Day 2… but right now I need sleep!