Specimen photos with desaturated backgrounds
April 25, 2013
Generally when we present specimen photos in papers, we cut out the backgrounds so that only the bone is visible — as in this photo of dorsal vertebrae A and B of NHM R5937 “The Archbishop”, an as-yet indeterminate Tendaguru brachiosaur, in right lateral view:
But for some bones that can be rather misleading: they may be mounted in such a way that part of the bone is obscured by structure. For example — and this is a very minor case — the ventral margins of the centra in the photo above are probably slightly deeper than they appear, because the centra are slightly sunk within the plinth that holds the vertebrae upright.
So I’ve been toying with a different idea: instead of cutting the background out completely, leaving it in place but toning it down. Then the supporting structure is visible, but clearly distinct from the actual bone. (For a more extreme case, see the “Apatosaurus” minimus sacrum.)
Here’s how the image above looks if I desaturate the background:
I’m not sure what to make of this. It looks a bit strange to me, but that might only be the strangeness of unfamiliarity.
And it might not work so well (or indeed it might work better) for photos taken against a busier background.
What do you think?
And a happy Christmas from me, too!
December 23, 2011
Necks, I win; tails, Wedel loses –or– The SV-POW! Palaeo Paper Challenge
December 14, 2011
This year, I missed The Paleo Paper Challenge over on Archosaur Musings — it was one of hundreds of blog posts I missed while I was in Cancun with my day-job and then in Bonn for the 2nd International Workshop on Sauropod Biology and Gigantism. That means I missed out on my annual tradition of promising to get the looong-overdue Archbishop description done by the end of the year.
Brachiosauridae incertae sedis NMH R5937, "The Archbishop", dorsal neural spine C, probably from an anterior dorsal vertebra. Top row: dorsal view, anterior to top; middle row, left to right: anterior, left lateral, posterior, right lateral; bottom row: ventral view, anterior to bottom.
But this year, Matt and I are going to have our own private Palaeo Paper Challenge. And to make sure we heap on maximum pressure to get the work done, we’re announcing it here.
Here’s the deal. We have two manuscripts — one of them Taylor and Wedel, the other Wedel and Taylor — which have been sitting in limbo for a stupidly long time. Both are complete, and have in fact been submitted once and gone through review. We just need to get them sorted out, turned around, and resubmitted.
(The Taylor and Wedel one is on the anatomy of sauropod cervicals and the evolution of their long necks. It’s based on the last remaining unpublished chapter of my dissertation, and turned up in a modified form as my SVPCA 2010 talk, Why Giraffes Have Such Short Necks. The Wedel and Taylor one is on the occurrence and implications of intermittent pneumaticity in the tails of sauropods, and turned up as his SVPCA 2010 talk, Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus.)
We’re going to be realistic: we both have far too much going in (incuding, you know, families) to get these done by the end of 2011. But we have relatively clear Januaries, so our commitment is that we will submit by the end of January 2012. If either of us fails, you all have permission to be ruthlessly derisive of that person.
… and in other news …
Some time while we were all in Bonn, the SV-POW! hit-counter rolled over the One Million mark. Thanks to all of your for reading!
A lesson we don’t want to learn
August 6, 2011
Matt just wrote this, in an email exchange. It struck a chord in me, and I thought it deserved a wider audience:
I hate to admit it, but those two papers (i.e., Taylor et al. 2009 and 2011) that had particularly protracted gestations and lots of review time are among the ones I am most proud of. There might be a lesson there — but if so, I’d rather not learn it.
Rats.
Cervical vertebra V (from an unknown position in the anterior part of the neck) of the STILL undescribed Tendaguru brachiosaurid NHM R5937, "The Archbishop", in right lateral view. The posterior portion is missing in action.
The Archbishop in cake form
April 20, 2011
A few months ago, prosauropod supremo Adam Yates blogged about the Aardonyx cake that the BPI honours class baked in his honour. In the comments, I mentioned that my wife Fiona once made me a BMNH R5937:D9 cake (i.e. a cake in the form of the more posterior of the pair of nicely preserved dorsal vertebrae of The Archbishop, in right lateral view). At the time, I couldn’t find the photo that I knew had been taken, and Adam asked me to post it when it turned up.
Voila!
And here, once more, is the real thing for comparison:
(Note that the topology of the lateral lamination is spot on, with a single infradiapophyseal lamina which forks into anterior and posterior branches only some way ventral to the diapophysis. That’s what you look for in a cake.)
Update (21 April)
Silly me, of course what I should have shown is the cake and the vertebra side by side. Here they are — together at last!
I do not dare behold it
January 14, 2011
By a curious coincidence, today’s Bob The Angry Flower cartoon is all about the Archbishop description.
But, hey, at least I got my confession in early — I was officially the first participant to fail the 2010 Paleo Project Challenge.
THIS year, for sure!
An open letter to Palaeontologia Electronica
November 23, 2010
For anyone who doesn’t already know, Palaeontologia Electronica is an on-line, open-access palaeontology journal — the only one in the world (unless you count Acta Pal Pol, which is freely available online and also published on paper.) PE is sponsored by the Palaeontological Association, the Paleontological Society and the Society of Vertebrtate Paleontology, the big three professional associations, so you can see that it’s a serious journal, not just some glorified blog. Among much else, it has published important sauropod papers such as Gomani (2005), Schwarz et al. (2005) and Rose (2007). PE is A Good Thing.
The new issue 13(3) of PE came out yesterday and was introduced by a post on the newish PE blog. In response I was moved to post a comment on that blog post. But because the blog is pretty new, it doesn’t seem to have attracted many readers yet, at least judging by the low number of comments, so I realised that what I’d said needed saying in a more widely read venue. Hence this SV-POW! article.
I am absolutely in awe of the Boltovskoy et al. World Atlas — my hat is off to everyone who worked on it, and it’s great that a reference work this comprehensive is freely available to the world.
But PE‘s tiny images are becoming more and more of an embarrassment: something has got to be done about this. It’s true that the maps in the PDFs are pretty high resolution (I can’t see exactly how high because my usual extract-images-from-PDF program isn’t working on these files for some reason). But the versions of the figures on the web-site are really inadequate — see for example Figure 6, which is a feeble 711×358 pixels — 1/4 Mp.
Compare that with, for example, Figure 10 (dorsal vertebrae) of the paper published in PLoS ONE today on new American iguanodonts. That image is 2067×2776 pixels — 5+3/4 Mp, or 22 times the size of the PE image.
Folks, I love PE and I really want it to succeed. But the PLoS journals, among others have raised the game. Hosting large images is so cheap now that it’s hard even to measure the cost: there is no excuse for PE to continue providing its figures only in what amounts to a thumbnail. Why shouldn’t the original image files submitted by the author be made available?
For me, and I am sure many other people, this is a deal-breaker. I simply can’t and won’t send any descriptive papers to PE, because when I prepare a 4100×3966 pixel figure like the one above [cervical rib "X1" of the Archbishop -- click through that images for the full-size version], I can’t tolerate having it shrunk to 711×688 to fit PE’s 711-pixel width limit — a 33-fold drop from 16 Mp to 1/2 Mp.
Please, PE. Fix this. Surely it can’t be hard?
References
- Gomani, Elizabeth M. 2005. Sauropod dinosaurs from the Early Cretaceous of Malawi, Africa. Palaeontologia Electronica 8(1):27A (37 pp.)
- Rose, Peter J. 2007. A new titanosauriform sauropod (Dinosauria: Saurischia) from the Early Cretaceous of central Texas and its phylogenetic relationships. Palaeontologia Electronica 10(2):8A (65 pp.)
- Schwarz, Daniela, Christian Meyer, Eberhard Lehmann, Peter Vontobel, and Georg Bongartz. 2005. Neutron tomography of internal structures of vertebrate remains: a comparison with x-ray computed tomography. Palaeontologia Electronica 8(2):30A (11 pp.)
The Archbishop … restored!
October 15, 2010
This post is nearly three weeks late — it’s based on a piece of artwork that appeared on 25 September, and which I wanted to write about immediately. But it got washed away in the flood of camel necks (which by the way is not over yet), and then in the festival of articular cartilage, then by the whole “Amphicoelias brontodiplodocus” thing and the subsequent discussion of amateurs in palaeo, and then by what was already an overdue announcement of my sauropod history paper and the attendant copyright nonsense. So it’s been a stupidly busy time here at SV-POW! Towers, but now the air has cleared a little, and it’s time to look at this beauty:
Life restoration of NHM R5937 "The Archbishop" (Brachiosauridae incertae sedis), by Nima.
This would be a beautiful piece of art by any standards — the world can always use brachiosaur art! — but what makes this extra special for me is that it is the first ever life restoration of my very own brachiosaur, BHM R5937, the Tendaguru specimen known as The Archbishop. It’s by SV-POW! regular Nima, and I am absolutely delighted to see it. It’s very Greg Paul-like, and I mean that in the most positive sense. (I may not be a fan of Greg’s taxonomic vicissitudes, but his art is just beautiful.)
Over on his blog, Nima has described in detail how he created this piece, and shows four progressively refined versions (of which the one above is the last) — I urge you to check it out if you’re interested in art, brachiosaurs or both.
Nima’s blog-post also includes a brief history of the Archbishop, mostly taken from my 2005 SVPCA talk. It’s a good summary, but I do have a few comments to make. (I typed a lot of this in as a comment to the original post, but Blogger ate my comments as usual.)
- The specimen is not known as M23, and has never been — that is in fact the designation of the Tendaguru quarry from which is was excavated. Paul (1988) mistakenly conflated the quarry name with a specimen number, and referred to this specimen as BMNH M23, and Glut’s (1977) encyclopaedia perpetuated the error, but it’s always been R5937.
- “The giant Brachiosaurus finds of the Germans” are now, of course, Giraffatitan.
- “Controversy lingered” — well, no, not really. The problem was worse than that: no-one paid a blind bit of notice to the specimen before 2004.
- “It turns out the double spine claim was totally bogus and unscientific” — well, we don’t really know that yet. It’s certainly true that none of the prepared vertebrae (five cervicals, two complete dorsals and an additional dorsal spine) have bifid spines; but Migeod reported these from the anterior dorsals, and it’s not clear that we have those. A fair bit of material remains in jackets, and more has probably been lost or destroyed. So it is possible, if unlikely, that one day we’ll open one of those jackets and find good evidence for bifid spines.
- “Close-up of the Archbishop vertebrae (doesn’t look much like the mitre of an archbishop to me, but who knows” — well, the name The Archbishop is not based on any resemblance of the bones to a mitre. (Nor is it based on anything else. It’s completely arbitrary.)
Last 0f all, what about the actual picture? Well, the long, thin, snakelike neck is beautiful art, but I don’t think it’s great science. The height of the cervicals that we have for this animal show that the neck would have had to be quite a bit dorsoventrally taller than shown here. And because there were only 13 cervical vertebrae — 12 if you omit the atlas, which is really a whole nother kettle of badgers, a neck bent into a strongly sigmoid pose like this would exhibit noticable kinks at some of the intervertebral joints — as you can see in giraffes when they twist their necks.
That aside, though, this is great. Again, I am really delighted that it’s out there. Congratulations to Nima!
Veronica the ostrich: right cervical rib #3
June 28, 2010
For reasons that seemed good to me at the time, I took my best shot at photographing the right cervical rib from cervical vertebra 3 of my ostrich, Veronica [see earlier Part A, Part B and Part C for context]. I thought you might like to see the result, so here it is:
Third right cervical rib of subadult female ostrich (Struthio camelus), total length 23 mm. (Total length of the rib, I mean, not total length of the ostrich.) Left column: anterior view; middle column, top to bottom: dorsal, medial, ventral and (inverted) lateral views; right column: posterior view.
For some reason, cervical ribs don’t seem to get a lot of love in the literature: the only paper I know that figures them in half-decent detail is Osborn and Mook’s classic (1921) monograph on Camarasaurus, and even there, the job is done in rather a half-hearted fashion. I’m planning to buck this trend by properly figuring the cervical ribs of the Archbishop when I finally get around to finishing that paper, and I included a sneak preview of the rib that I’ve arbitrarily designated X1 a while back. It’s instructive to compare that illustration with this one. In fact, here it is again:
Brachiosauridae incertae sedis NHM R5937, "The Archbishop", cervical rib X1. Preserved portion is 32 cm long. Top row: anterior view (dorsal to left); middle row, left to right: lateral, dorsal, medial and ventral views (all with anterior to top); bottom row: posterior (dorsal to left)
Enjoy!
Update (the next day)
It occurs to me that I should have composed the ostrich-cervical-rib illustration in the same orientation and order as the Archbishop one, for easier comparison. So that’s what I’ve done below. Since the Archbishop rib X1 is from the left side, I’ve also flipped the right-sided ostrich rib to match. Here it is:
Third right cervical rib of subadult female ostrich (Struthio camelus), reversed, total length 23 mm. Top row: anterior view (dorsal to left); middle row, left to right: lateral, dorsal, medial and ventral views (all with anterior to top); bottom row: posterior (dorsal to left)
Tutorial 8: how to photograph big bones
February 12, 2010
Since I started taking photographs of sauropod vertebrae back in 2004, I’ve got much, much better at it, and for the last few months I’ve been meaning to write an article about what I’ve learned along the way. A few weeks ago, fellow SV-POW!er Ranger Matt Wedel posted an article on his 10 Minute Astronomy blog on how to photograph the moon through binoculars, and that served as a prod to get back into blogging gear in the post-Christmas season.
Before I launch in, let me be really clear that I am not a proper photographer — not at all. I don’t even know what an F-stop is or what Single Lens Reflex means. Probably I should invest some time into learning some of this, since specimen photographs are so important in the world of sauropod vertebrae. (After all, the specimens are more than a little cumbersome to loan, so photos often have to stand as proxies for the actual specimens.) Nevertheless, what I’ve learned in the last five or six years has got me to the point where I am producing much, much better specimen photographs than when I started, and I hope at least some of you can benefit from what I’ve learned.
The very best (and still very bad) of the first batch of Archbishop photographs I took, back in July 2004. Note that it's not square on, doesn't fit in the frame, that it's over-exposed and (as you'll see if you click through to the full-sized version) both blurry and infested with artifacts. Compare with the recent photo at the end of this article. Copyright the NHM since it's their material.
Equipment
Camera
First up, get a decent camera. However skilled you are, you can’t take better photos than the hardware allows. Although I am to blame for the composition above and for some of blurriness, the over-exposure, poor definition and artifacts are the fault of the camera. I was using a truly horrible camera back then — some super-cheap list-of-features-on-a-discount-website piece of kit.
The good news is that a “decent” camera doesn’t need to break the bank: for our purposes you don’t need to spend a fortune on professional-photographer standard equipment. I am looking on ebay right now, and it seems you can get my model of camera for £100 in the UK or $150 in the US (second-hand of course) which is a level of investment we really should be prepared to put into one of the most important aspects of descriptive work.
What constitutes a decent camera? Mostly, optics. These days, every camera has more than enough megapixels for most purposes, so you can just forget about that statistic altogether. It’s about the quality of the lens and the size of the CCD — those are the factors that determine how much information the camera can capture, and if it puts out more bits than that, then all it’s doing is wasting disk-space and bandwidth.
Can I justify the claim that all modern cameras have enough megapixels? I think so. Suppose you’re preparing a full-page plate for the Journal of Vertebrate Paleontology. In practice, plates are nearly always composites of several photos, but suppose you want a single shot filling the whole plate. The printable area of a JVP page is 182 x 233 mm, which is 7.2 x 9.2 inches. At 300 dpi, that’s 2161 x 2752 pixels, which is 5947072, or a slice under 6 megapixels. So 6 Mp is enough for a full-page plate. (For what it’s worth, my camera does 2272 x 1704 = 3.8 megapixels, and I have never found myself feeling a need for more resolution.)
For the same reason, you definitely want optical zoom rather than digital zoom, which really amounts to just blowing up the image.
Accessories
Another big win: get a spare battery, so that one can be recharging while you’re using the other. If you don’t do that, your camera is out of commission half the time.
And get a big enough memory card. What’s “big enough”? For me, that means enough space to hold a whole day’s images so I can do a single dump onto the laptop in the evening, rather than having to keep stopping to transfer. I can take maybe a maximum of 300 photos a day. With 1 Mb images, that means I need a 300 Mb card, which is chickenfeed. You literally can’t buy cards that small any more, so this is not really a factor these days and I might just as well not have mentioned it. (The reason I did mention it is that my camera originally came with a 16 Mb card or something similarly stupid, which meant ten minutes or so of photography before downloading.)
Horrible photograph of a Brachiosaurus altithorax dorsal (holotype specimen FMNH P25105, natch), showing how NOT to compose a picture.
Composition
Get the specimen in frame
Shoot from cardinal directions
Don’t put anything in front of the specimen
Use a plain background when possible.
But the good news is that all these problems can be ameliorated if you follow the last and most important rule in this section which is:
Take many shots and keep only the good ones
I remember reading once, long ago, that the single biggest factor in the difference of quality between a professional photographer’s work and an amateur’s is that the pro takes ten times as many shots and throws 90% of them away. In these days of digital cameras with huge memory cards, we can all make like professionals now. When Matt and I were at the Field Museum in Chicago, we took 168 photos of those Brachiosaurus dorsals alone. Of those, maybe a dozen or so are really worth keeping. But at least I have those dozen.
In general, I take every photograph twice. As I’ve got better at taking the photos, I am increasingly finding that both come out well and it’s a toss-up which to keep, but maybe one time in ten or twenty, one of them just doesn’t come out right — something is wrong with the focus, or the camera shakes, or something — and that’s when I’m glad I have the spare.
Another terrible photo, this time with the flash washing out all the detail of the neural spine of Giraffatitan brancai lectotype HMN SII, 8th cervical, in left lateral view.
Lighting
Flash
On the other hand, my camera’s built-in flash is pretty lame. Expensive flash units might do much better.
Other lights
As with flash, it seems that the only thing to do is try photos with and without external lights, and with the lights in various different positions, and see what comes out best.
Giraffatitan brancai paralectotype HMN SI, cervical vertebra 6 in right anterolateral view. Not a bad photo -- click through to the full-sized version to appreciate the awesome.
Stability
So what can you do? Well, there are several levels of compensation.
Simply being aware of remaining still
When I have to hold the camera in my hands and I know it’s going to be a long exposure I find myself going into a sort of zen state — I become aware of my heartbeat and try to time the shutter release so that the camera doesn’t get moved by my pulse. It’s error-prone, but at least being aware of it can help.
Brace against a door-frame or similar
Tripods
Shutter delay
The combination of tripod mounting and shutter delay means that you can get good exposure in almost any light.
The Archbishop in all its glory, with everything working right. The much-loved dorsals 8 and 9 in right lateral view. Click through to see the detail. Compare with the horrible photo of the same bones at the top of this article. Copyright the NHM since it's their material.
Summary
… And finally …
From: Carol Brown<bcarol83@gmail.com>
Hi Michael,
We just posted an article, “100 Best (Free) Science Documentaries Online” (http://www.onlineuniversities.com/blog/2010/01/100-best-free-science-documentaries-online/). I thought I’d drop a quick line and let you know in case you thought it was something you’re audience would be interested in reading. Thanks
Enjoy!
