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?
April 18, 2012
I’ve been thinking about Barosaurus lately.
<homer>Mmmm … Barosaurus …</homer>
The best (and only, really) good recent treatment of Barosaurus is in John McIntosh’s chapter of the 2005 IUP Thunder Lizards volume. The main weakness of that chapter is that, while a lot of material is illustrated, the figures are rather small and not particularly well reproduced — and, in the case of the two-page spread of dorsal vertebrae, monumentally confusing:
Quick! find the fourth dorsal in posterior view! [˙ʇɟǝן ɯoʇʇoq ʇɐ s,ʇı :ɹǝʍsuɐ]
To get a better sense of the variation along the column, I scanned the two pages, loaded them into GIMP, joined them together, cleaned up the “white” of the background while retaining all the contrast I could, then moved each of the 27 illustrations to its own layer. Then I was able to rearrange them to my liking, align them, and produce this modified version:
So here it is for anyone else who finds it useful.
(One character that varies sequentially is of course the degree of neural spine bifurcation. But we won’t be flogging that dead horse any more — we’re done blogging, and the paper is in prep.)
- McIntosh, J.S. 2005. The genus Barosaurus Marsh (Sauropoda, Diplodocidae); pp. 38-77 in Virginia Tidwell and Ken Carpenter (eds.), Thunder Lizards: the Sauropodomorph Dinosaurs. Indiana University Press, Bloomington, Indiana, 495 pp.
March 3, 2012
In among all the open-access discussion and ostrich-herding, we at SV-POW! Towers do still try to get some actual science done. As we all know all too well, the unit of scientific communication is the published paper, and getting a submission ready involves a lot more than just the research itself. One of the most important aspects is preparing the illustrations — indeed Matt once told me that he thinks one of the best ways to put a paper together is to start with the illustrations, then write the text around them.
[Illustrations are often referred to as "figures". I don't know how the tradition got started, but since that term also means numbers, I will try to avoid it. If I tell you "I am working on the figures for my diversity paper", you don't know if I am accumulating statistics or preparing illustrations.]
Done well, illustrations can be things of beauty as well as scientifically informative.
There are a few things to be said about preparing good illustrations, so we’re kicking off a short series on the subject. This is the first.
But the zeroth was published here a couple of years ago. Since the most important illustrations in many palaeontology papers are those of the specimens, the base you’re working from is your specimen photographs. So you might want to refresh your memory by reading Tutorial 8: how to photograph big bones before we proceed.
There are various steps in getting from a photo to a finished, publishable figure, and we’ll look at those along the way. But somewhere along the line, if you’re publishing in a conventional journal such as the Journal of Vertebrate Paleontology, you’re going to flatten your colour images down to greyscale. Postpone that step till the last possible moment.
That should be too obvious to need saying, but I’ve got it wrong myself. When I was preparing the specimen photographs for the Xenoposeidon paper, destined for Palaeontology, I flattened the images too early in the process, with the result that the greyscale versions of the figures that were included in the paper are the only versions in existence. The upshot is that if you look at the full-resolution illustrations in the unofficial supplementary information, you’ll see that the version of Figure 3 available there is greyscale, just like the one in the paper.
By the time the three of us did our neck-posture paper in Acta Palaeontologica Polonica, we weren’t quite so dumb. So although the illustrations in the published paper are all greyscale, the two that are based on specimen photographs, rather than assembled from previously published greyscale components, were prepared in full colour, then flattened as the very last process before submission. As a result, the full-resolution illustrations in the unofficial supplementary information have figures 1 and 2 in colour:
So we were pretty happy with that. But by the time we came to submit the Brontomerus description a couple of years later, we’d had a rather obvious (in retrospect) thought: just because we can’t have colour in the printed journal, does that mean we can’t have it in the PDF? We asked the good people at Acta Pal. Pol., and they agreed that we could submit colour illustrations, they’d use them in the PDF, and then flatten them to greyscale themselves for the printed edition.
Since about fifty times as many people see the PDF as see the printed journal [yes, I just made than number up out of my head], that solution suited us very well. The outcome was the the PDF has gorgeous figures like this one:
(I’m slightly sorry to be displaying all our own illustrations here, but they do make the point and frankly I like looking at them. Especially that beautiful caudal vertebra.)
Why am I making such a big deal about colour? Because colour is information, and as scientists we love information. When you flatten a colour image to greyscale, you lose information, and that should never be done without regret. It’s perfectly possible that adjacent regions of a fossil will be a different hue but the same brightness: flatten the image and the two colours look the same, but in the original you can see a distinction. That’s valuable.
So in this day and age, The Right Thing is:
- Prepare your figures in colour
- Submit them in colour
- If the journal has a printed edition (and charges extra for colour printing, as most do), tell them to flatten to greyscale.
On the other hand, if you’re submitting to an open-access journal — and you should be, if you want to be widely read — there’s a good chance that it’s online-only (as with PLoS ONE and Palaeontologia Electronica), in which case the use of colour is a complete non-issue. The only reason to prepare monochrome figures then is (as with the Taylor et al. 2011b sauropod-neck bestiary above) when you’re constructing them from pre-existing greyscale images.
Taylor, Michael P., Mathew J. Wedel and Richard L. Cifelli. 2011a. A new sauropod dinosaur from the Lower Cretaceous Cedar Mountain Formation, Utah, USA. Acta Palaeontologica Polonica 56(1):75-98. doi: 10.4202/app.2010.0073
Taylor, Michael P., David W. E. Hone, Mathew J. Wedel and Darren Naish. 2011b. The long necks of sauropods did not evolve primarily through sexual selection. Journal of Zoology 285:150-161. doi: 10.1111/j.1469-7998.2011.00824.x
If you’re a scientist, then one of the things you need to do is prepare high-quality images for your papers. And, especially if you’re a palaeontologist, or in some other science that involves specimens, that’s often going to mean manipulating photographs. So image editing has become one of those “grey skills”, like word processing and phylogenetic analysis, that you need to have a little of, even if you’re not specialising in that direction.
Here at SV-POW!, none of us is anything remotely approaching wizardly when it comes to image-editing. But we’ve done enough of it that we have a few tips to pass on, so this is the first in an occasional series that will offer some random but relevant hints. (Matt and I both use GIMP, a free image-editing program, but I’m sure PhotoShop has the all the same facilities and more.)
Today: thirty-second colour-balancing. It’s a technique that comes in handy every now and then, especially if you take a lot of specimen photographs in poorly lit basements that make everything look greenish. It came up because in the previous post Matt included this photo of a partially dissected turkey neck:
All the orange made my eyeballs hurt.
So you can spend hours on colour-balancing a photo carefully, and that can be appropriate if you’re preparing a figure for publication. But to fix a photo like this one in thirty seconds, here’s what I do.
Load the image.
Bring up the Layers window and use it to duplicate the layer:
With the top layer selected, choose Colours -> Auto -> Equalize. (There is also a Colours -> Auto -> White Balance option, but I never find that it gives good results.)
Equalize will make the top layer look truly horrible:
Now go back to the Layers window, and play with the top layer’s opacity, so that you get a blend of the original and equalised images:
In this case, I found that 50% opacity looked about the best:
(While it’s still no oil-painting, it’s much better than the all-orange-all-the-time original.)
With the top layer still selected, choose Layers -> Merge Down to make the layers into one, and save the result.
It really does take about thirty seconds total, including the time to start up and shut down the image editor. (Yes, GIMP starts up more quickly than PhotoShop!)
Update (11 April 2012)
If you’re wondering why this is “part 0″, it’s because it was originally posted as a stand-alone article, and we only realised much later that it fits into the tutorial sequence — in particular, the planned multi-part tutorial on preparing illustrations.