Accidental anaglyphs
October 16, 2020
Everyone knows that the very first thing you should do to improve your specimen photography is to use a tripod: it eliminates hand-shake and gives you much crisper photos. In most respects, my photographs have got much, much better since I’ve been habitually using a tripod.
But it has meant I’ve not been able to benefit from happy accidents like the one that gave me this 3D anaglyph of the Archbishop‘s Cervical S in dorsal view:
(Do you have red-cyan glasses? Yes? Good! You will be able to appreciate all the delicious morphological information in this photo. No? Go and order some right now — they cost literally a dollar.)
The reason I was able to make this very useful image is because back in the old pre-tripod days I would sometimes accidentally move a little bit between taking two more-or-less identical photographs. Here are the two images that I was able to composite into the anaglyph above:
Each of them is pretty uninformative alone: who can tell one nondescript area of brown bone from another? But when combined, they are extraordinarily more informative. If you don’t have 3D glasses then (A) get some! and (B) you can get some idea of how helpful the 3D information is from the crude wigglegram below, which simply switches back and forth between the two images.
And I can’t overstate how enormously helpful I have found these accidentally sourced anaglyphs as I write the descriptive part of the Archbishop manuscript. Even at this level of crudity, they have shown me several important points of morphology that I would certainly have missed if I’d been working only from my orthogonal-view photos, and saved me from more than one misinterpretation.
The moral is twofold:
- When taking specimen photographs, use a tripod — but deliberately get some pairs of shots where the camera is moved to the side by about 7 cm (the distance between the pupils in an average human).
- If you don’t have any red-cyan glasses, get some!
Tutorial 17: preparing illustrations. Part 4: go big
December 30, 2017
Matt just commented to me: “One thing I am realizing is that I have loads(*) of cleaned-up, ready-to-post photos in old talks, that I’ve never posted.”
I too have that experience. The problem is, they tend to be sized for a 1280×960 projector screen, which is not really good enough for modern illustrations. A useful rule of thumb is that if you want to be able to print at 300 dpi across the active area of a sheet of A4 — (which is 8.27 inches minus 2-cm margins each side, for a usable width of 6.69 inches), you need horizontal resolution of at least 2007 pixels. But you really want to go much bigger than that, since online journals can provide much better resolution than even the best printed journals.
Now, whenever I create an image for a talk or poster, I consider up front if I will one day want to publish it. If so, I make it at full-size, and only shrink the render.
One of our problems in the sciences is that we work in five different media (at least, I do): in roughly ascending order of formality:
- Blogs
- Talks
- Posters
- Preprints
- Papers
Not everything moves well between those forms. We learned from experience that translating the text of even quite formal blog-posts into prose for a paper is a serious piece of work. The good news is that illustrations are largely identical between all these forms: the hard work of preparing clean multiviews from photos need be done only once, and the later more formal versions need only the additions of scalebars and suchlike.
The moral of this story is very simple: always prepare illustrations in the highest resolution you will ever need, and in full colour. You can reduce resolution later, or reduce to greyscale; but if you prepare at low resolution or in greyscale, you can’t increase resolution later or add colour.
(*) He actually said “assloads”, but I censored it for this blog.
Playing with Sauroposeidon photos
January 30, 2014
Following on from Matt’s post about the difficulty of photographing big specimens without distortion, I thought I’d have a play with our best Sauroposeidon C8 photo, which I think is this one:
(That’s been the basis for classic SV-POW! posts such as Your neck is pathetic and Darren’s new indeterminate Wealden maniraptoran is inadequate.)
I was motivated by Andy Farke’s comment:
Another–and perhaps more important–area where surface models excel is when you can remove colors on the original specimen that wash out relevant details…I bet this is probably the case for the example vertebra of Sauroposeidon. How many fossae and foramina just don’t show up well on the photos above?
Andy was talking about completely colourless 3d surface models, in which the 3d shape allows a render to make shadows that bring out the subtle shapes. But it made me wonder whether we could get anywhere just by washing out the most prevalent colour in the photo.
I started by doing a big, fat Gaussian blur on a duplicate layer — 500 pixels in each direction — and sampling the colour in the middle, to get a rough-and-ready average. (There may be a better way — please shout if you know one.) That average colour was#7e6b2f. I used it to run Colour To Alpha on another duplicate of the original layer, so that we’d be left with only residual colours. Here’s the result:
I’m in two minds about this. It may be informative, but it sure is ugly. To compromise, I reinstated the original layer underneath this mostly-transparent one, and turned its opacity down to 75%. Here’s the result — a nice compromise:
Of course, there are endless other approaches you can take — that’s the blessing and the curse of image-editing programs like GIMP. For example, here’s what I got doing a simple Colours → Auto → White Balance:
I’m not sure that isn’t the best of the bunch, in terms of informativeness.
—
I also tried something else — not amazingly successfully, but I think it’s worth seeing. Since the two photos that Matt showed in the previous post were evidently taken from somewhat different angles, I thought I’d have a go at compositing them into a red-cyan anaglyph. Because the variation in camera position is mostly dorsoventral rather than anteroposterior, the vert has to be pointed upwards for the two eyes to see the two versions from different horizontal points. Here’s the best I could do:
I would say this is of some value; but it’s nowhere near as good as, for example, the anaglyph of Cervical S of the Archbishop. I could sit and look at that one all day. The problems with this one arise for three reasons.
First, I had to reduce both parts of the Sauroposeidon anaglyph to monochrome (since one was already in that form), so all colour information was lost.
Second, I had to scale the high-resolution picture to the same size as the lower-resolution one, throwing away more detail.
Finally, and most important, the two photos were not taken with the intention that they should be used to make an anaglyph. To work well, this has to be done with the images taken under the same lighting conditions, at the same distance from the specimen, from perspectives differing by about the distance between the pupils of the viewer, and with the camera-position difference being perfectly in the plane of the specimen. Needless to say, none of these conditions was met in this case, so it’s actually quite impressive that it works as well as it does.
We have a lot of options for illustrating specimens these days. Postage-stamp-sized greyscale photos really don’t cut it any more.
In his post on Vicki’s new book Broken Bones, Matt told us his twelve-step process for producing stippled illustrations like this one of a crushed skull, which became the cover image of the book:
As soon as I saw that, I found myself thinking that it would look nice with some shading of the bone. Of course the existing stippling is a perfect guide to how dense the shading should be at each point, so I figured there had to be an easy way to do this automatically. There is, and this is what I whipped up in five minutes:
Here’s how I did it.
- I loaded Matt’s image into the GIMP, my image editor of choice.
- For some reason the crucial next step doesn’t work with greyscale images, so I converted it to RGB (Image → Mode → RGB)
- I removed the white background, leaving it transparent (Colours → Colour to Alpha… and click OK on the default colour, white)
- I added a new all-white background layer.
- I duplicated the skull layer, and named it “shading”
- I blurred the shading layer by 50 pixels (Filters → Blur → Gaussian Blur…, set the blur radius to 50 pixels and hit OK.) That gives you the shading you want, but it smudges out past the outline of the skull, hence the last two steps:
- I went back to the skull layer, and using the Fuzzy Select Tool (magic wand) selected the contiguous transparent area outside the skull parts.
- I went back to the shading layer and cut the selected area, leaving only that shading that’s inside the boundary of the skull.
As always with Gimp tutorials, it takes about ten times as long to explain as to actually do.
When I showed this to Matt, I rather immodestly said I was “super-happy with it”. Matt said he was “super-happy with the idea, but only regular happy with this specific execution”. He felt that the blurring was too strong, and that it should be backed off by 30-40%. So I made a new shading layer in the same way as above, but this time blurring by only 30 pixels. Here’s the resulting image:
It’s quite a subtle difference, but clear if you flip back and forth between the images (which you can most easily do by putting them in adjacent tabs of your browser). Personally, I think I prefer the 50-pixel version, since I think the shading clings rather too closely to the lines in this one, but YMMV.
Since I had both blur layers right there in the image, I thought it might be interesting to see how they look together. Here’s the result:
I’m actually rather fond of this version, but it’s a long way from the crisp, clinical feel of the original.
You can thicken up the shading by duplicating one or both of the shading layers as many times as you wish (or or course thin it out by sliding down the opacity level). Its also easy to make the shading coloured: just use Colours → Levels, select the individual colour channels, and bring up their bottom levels to taste.
Putting all that together, here’s one I made with very dense, yellowish (bone-coloured) shading. I did it starting with the 50-pixel shading layer, upping the red output level to 200 and the green to 150, then duplicating that layer, and reducing the 30-pixel shading layer to 50% opacity.
You can play for hours with all these sliders, tweaking as you wish, thanks to the magic of layers. It’s well worth investing a bit of time to learn some of the capabilities of a program like GIMP. Matt and I are very far from wizards, but we have at least got a bit past just using it to cut out backgrounds, and it opens up possibilities.
Vicki’s book, Broken Bones, is out!
December 18, 2013
When we last left my better half, Dr. Vicki Wedel, she was helping to identify a Jane Doe who had been dead for 37 years by counting growth rings in the woman’s teeth. That case nicely illustrated Vicki’s overriding interest: to advance forensic anthropology by developing new methods and refining existing ones. To that end, for the past few years she has been working with her PhD advisor, Dr. Alison Galloway at UC Santa Cruz, to revise and update Alison’s 1999 book, Broken Bones: Anthropological Analysis of Blunt Force Trauma. The revised and much expanded (504 pages vs 371) second edition, co-edited by Vicki and Alison, came out Monday (Amazon, Amazon.co.uk).
You can read the whole table of contents on Amazon (click to look INSIDE!), but the short short version is that the book has three major sections. The first covers the science and practice of trauma analysis (pp. 5-130), and the second classifies hundreds of common fractures throughout the skeleton, with illustrations (pp. 133-313). The chapters in these sections were all written by Vicki, Alison, and another of Alison’s former students, Dr. Lauren Zephro, solo and in varying combinations. Lauren, whom I always think of as “the Amazon cop”, is a 6-foot blackbelt forensic anthropologist for the Santa Cruz County Sheriff’s Office. If push came to shove I have no doubt that she could beat me to death with her bare hands and then produce a technical analysis of my corpse.
The final section (pp. 314-410) consists of nine case studies contributed by forensic anthropologists, pathologists, medical examiners, forensic and medical artists, and a DoD casualty analyst, based across the Anglophone world from Hawaii to Scotland. There’s some grim stuff in there: trauma to the homeless and elderly, from intimate partner violence, and from child abuse. It’s gut-churningly awful that the defenseless suffer from bone-breaking violence; it’s always been amazing to me that people like Vicki, Alison, Lauren, and the other contributors have both the courage to face these horrors and the technical chops to make the unspeakable solvable.
Beyond that unavoidable darkness, if you’re interested in the many, varied, and often just plain weird ways in which people die, the book is a treasure trove. There’s an elderly woman lying on her deathbed for six years, slowly turning into a natural mummy… (wait for it) …while her daughter went on living in the same house. There’s a classification of plane crashes with a description of what human remains will be found and over what area. There are people hit by trains; the funniest line in this very serious book is the deadpan and unsurprising, “The typical pedestrian hit by a train is male and often highly intoxicated.”
That’s from the top of page 122. At the bottom of the same page is my one contribution to the book, which also appears as the cover art (yeah, nepotism, whatcha gonna do). There’s a story behind this. This guy–yes, male, dunno if he was intoxicated–was hit by a train and his head was sheared in half, with the somewhat fractured but mostly intact facial skeleton separated by a lot of missing bone from the occipital region. With no way to obtain the deceased guy’s permission to use his mortal remains in the book, Alison and Vicki didn’t feel comfortable including their photos, so I spent a weekend bashing out a technical drawing for them to use instead. That reawakened my interest in pen-and-ink work and led to the dödö pöst.
I should say two things right here: first, that yes, I am hijacking the rest of the post to talk about myself. (Is anyone really surprised? I thought not.) Second, that I have had no training and possibly my stippling violates Art Rules or best practice guidelines of which I am ignorant. But I hope it also illustrates what can be achieved in a couple of days, with about $15 worth of supplies, by a guy whose only rule is “möre döts”.
So anyway, if you’re curious, here’s the method I use for my pen-and-ink illustrations:
- Get a decent-sized photo of the object to be drawn. I usually roll with $2 8x10s from MalWart, in this case one for each half of the skull.
- Tape the photo down to your work surface. I have a large, incredibly hard, perfectly smooth cutting board that I use for this, but in a pinch you could use just about anything, including just a larger piece of paper. Cardboard off the backs of desk calendars is nice.
- Over the photo, tape down a piece of tracing paper.
- Lightly trace the outline of the photo and all the major details in pencil.
- Once you’ve gone as far as you can with that, peel up one side of the tracing paper, unstick the photo from the work surface, and remove it. Stick the tracing paper back down the work surface.
- Using the uncovered photo as a reference, pencil in any other salient details by eye. Also contour lines for shadows. All of the pencil lines are going to be erased later, so don’t be shy.
- Whenever you decide you’re done with the pencil, get a good pen and start tracing, directly over the pencil lines. I tend not to be too persnicketty about my tools but decent pens are a real help here. For these recent works, I picked up a three-pack of beige-tubed Micron pens for $7 (this set).
- In all of the following pen-related steps, be careful to keep your big stupid hand and arm off the wet ink you just laid down–one careless smear can ruin a few hours’ work. Having a work surface that you can rotate is nice, so your pen hand can approach the drawing from any angle. Anytime I have to lay my hand on the drawing, I put down a piece of clean scrap paper first. Even if the underlying ink is dry, it just feels like a smart precaution.
- Once the lines are on, add döts to taste. With a little experimentation, you can get patterns of dots to not only indicate light and dark but also suggest textures. Different pen tips and amounts of pressure will yield dots of different sizes, which can also be useful. Dense, overlapping dots can produce an effect similar to scratchboard. BTW, sometimes I do “gear down” and place each dot with thought and care, but in the dense sections I just rat-a-tat-tat like a Lilliputian jackhammer. Try different speeds and see what you can tolerate.
- When you’re done dötting, at least to a first approximation, and you’re dead certain the ink is all dry, get a decent eraser and erase all of the pencil lines. I used one of those clicky mechanical erasers because it was cheap and soft enough to not tear up the paper.
- Re-ink any lines lightened by the erasing. I find that the döts are usually unaffected, but lines are often knocked down a bit by the eraser work. I suppose it would be cleaner to just draw natively in pen, with no prior pencilling and therefore no erasing, but the few times I’ve tried it, it hasn’t gone well. YMMV. If you’re drawing a 3D solid, this is a good time to employ an old illustrator’s trick, which is to make the bottom outline heavier and darker than the rest, to subtly convey a sense of weight.
- Scan, touch up as needed in GIMP, post to blog, bask in self-admiration.
In this case I had a few more steps, which consisted of making variants of the drawing and test-driving them by Vicki and Alison so they could pick their favorites.
This is just embarrassing: after scanning the two drawings and doing a little touch-up, I just scooted them together until they looked like a skull. The problem is that the occiput is nowhere near anatomical position. See that flange of bone above the ear-hole, pointed down and right at a 45-degree angle? That’s the back end of the zygomatic arch, and it should be aimed at the forward stump of the arch, which is just down and back from the eye socket.
Here’s the B version, where I was working entirely off of the zygomatic arch ends, and trying to get the skull into anatomical position. Scientifically this is probably the best variant I produced (I’m not claiming it’s the best possible), but aesthetically it’s a little crowded.
I’ll spare you versions C-E, all of which just scooted the back end of the skull around in an attempt to find a balance between scientific and aesthetic concerns. Here’s the winning F version, which got used for the figure, and became the seed variant for the cover.
For the cover, we tried a lot of things, including the white skull on a black background, and one that was simply inverted from the figure. By this point the publisher had sent Vicki some test versions of the cover, and I thought it would be cool if the drawing was in the same color as the cover text, so I sampled that color from the publisher’s sample cover image and applied it to all of the drawn bits. They knocked it down a few tones for the printed version, so happily it’s not this garish.
Incidentally, I had never tried to replace a bunch of discontinuous areas of the same color with another color in GIMP, so I had to look it up. The two key steps are Select > By color, with the threshold set to zero (or not, if you want to grab a bunch of related colors at once), and “Fill whole selection” in the Bucket tool. Hat tip to this dude and his commenters.
One last step: I thought the bare, unfilled yellow version looked too flat, so I tried different levels of fill to make the skull pop out from the background. I didn’t use bucket fill here–too fiddly with so many dots and edges. Instead I created a new layer of solid yellow and dropped the opacity to 17%. Then went to the drawing layer and used the magic wand tool to select the whole non-skull background. Then popped back to the yellow layer and cleared that selection, leaving yellow fill only in the boundaries of the skull outline. I also tried 10% and 25% opacity for the fill layer, but 10% was too subtle and 25% was starting to swamp some of the detail in the drawing. Between goofing around with colors and opacity levels we went through 10 versions at this stage, of which the one above is the ultimate champion.
So, that’s how the cover art came to be. Back to the book. There’s a bibliography with 1237 references (Vicki knows), and an index. The book is hardbound, with a printed cover and no dustjacket, and IMHO reasonably priced at $65, currently a few bucks less on Amazon. You probably already know whether you want a copy. If so, do the right thing–it’s not too late to get it by Christmas.
References
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?
Barosaurus lentus AMNH 6341 dorsal sequence
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:
Barosaurus lentus AMNH 6341 dorsal vertebrae 1 to 9 (A-I) in anterior, left side, and posterior views. From McIntosh (2005:fig. 2.5)
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:
Barosaurus lentus AMNH 6341 dorsal vertebrae 1 to 9 in anterior (top), left lateral (middle), and posterior (bottom) views. Modified from McIntosh (2005:fig. 2.5)
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.)
References
- 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.
Tutorial 17: preparing illustrations. Part 1: use colour
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.
Taylor et al. (2011b: figure 1). Sauropod necks, showing relationships for a selection of species, and the range of necks lengths and morphologies that they encompass. Phylogeny based on that of Upchurch et al. (2004: fig. 13.18). Mamenchisaurus hochuanensis (neck 9.5 m long) modified from Young & Zhao (1972: fig. 4); Dicraeosaurus hansemanni (2.7 m) modified from Janensch (1936: plate XVI); Diplodocus carnegii (6.5 m) modified from Hatcher (1903: plate VI); Apatosaurus louisae (6 m) modified from Lovelace, Hartman & Wahl (2008: fig. 7); Camarasaurus supremus (5.25 m) modified from Osborn & Mook (1921: plate 84); Giraffatitan brancai (8.75 m) modified from Janensch (1950: plate VIII); giraffe (1.8 m) modified from Lydekker (1894:332). Alternating grey and white vertical bars mark 1 m increments.
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:
Taylor et al. (2009: Figure 1). Cape hare Lepus capensis RAM R2 in right lateral view, illustrating maximally extended pose and ONP: skull, cervical vertebrae 1-7 and dorsal vertebrae 1-2. Note the very weak dorsal deflection of the base of the neck in ONP, contrasting with the much stronger deflection illustrated in a live rabbit by Vidal et al. (1986: fig. 4). Scale bar 5 cm.
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:
Taylor et al. (2011a: figure 4). Mid-caudal vertebra of the camarasauromorph sauropod Brontomerus mcintoshi from the Lower Cretaceous Cedar Mountain Formation of Utah, OMNH 61248 in dorsal (A), anterior (B), left lateral (C), posterior (D) and ventral (E) views.
(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.
References
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.
Genesis of an instant palaeo-art classic
March 3, 2011
After a couple of relatively hardcore posts on ilial osteology, we though it would be good to look at something lighter this time. If you’re interested in dinosaurs, or indeed alive, you will hardly have been able to avoid seeing Francisco Gascó’s glorious life restoration of Brontomerus. Here it is again, in case you’ve been in a coma:
As well as being Figure 12 of the paper (Taylor et al. 2011), it’s popped up absolutely everywhere in media coverage: among many others, it was used by the BBC, Guardian, Telegraph and Independent in the UK; by USA Today, Fox News and National Geographic in the USA; by Spiegel in Germany; and by SVT (the state-funded national TV station) in Sweden. There’s no question that this image contributed hugely to selling the paper to the secular media. It’s probably responsible for 80% of all the coverage our work got, and I’m confident that it’s going to quickly become one of those images that everyone recognises, like the tyrannosaur/styracosaur fight on the cover of The Dinosaur Heresies and indeed Charles Knight’s classic swamp-bound Brontosaurus.
So it was a huge win for us, and it’s worth looking at how it came about.
Back in 2004, Matt gave a talk at the SVP annual meeting, entitled Skeletal pneumaticity in saurischian dinosaurs and its implications for mass estimates. The material in this talk became a chapter in the Wilson and Curry Rogers edited volume of sauropod papers (Wedel 2005). Some time in 2006, Matt heard about the Paleonturology competition, which is all about making palaeontology accessible for teenagers, especially in Spain: anyone who’d had a paper published in 2005 was invited to submit it, and the judges would choose the one that seemed most amenable to being rewritten in a compelling way for non-specialists. Matt’s 2005 paper won the 2006 competition, and the rewritten version of that paper was translated into Spanish and published in a very nice booklet which I am pleased to have a copy of (Wedel 2007). In 2007, Matt was invited to the Fundación Dinópolis in Teruel, Spain, to receive his award, launch the booklet, and act as a judge for the 2007 competition.
The relevance of all this now finally becomes apparent: while in Teruel, Matt met Francisco “Paco” Gascó, and looked through some of his portfolio of palaeo-art — including, for example, this rearing Camarasaurus:
So Matt had Paco in mind as a promising palaeo-artist. Then towards the end of May 2008, when we were readying the Brontomerus paper for submission (not to Acta Palaontologica Polonica — to a different journal, which didn’t take it) I wrote to Matt saying:
I’m attaching a tentative skeletal reconstruction that I did. […] Now I’m thinking: should we approach a palaeoartist to see if we can get a life restoration done in time for the launch? The eponymous thunder thighs hardly make an impact in the skeleton, after all.
And Matt quickly replied suggesting that Paco could be the person to do it. He sent a few samples, including the Camarasaurus above, and I was sold. A couple of days later, Matt suggested the idea to Paco, he was up for it, and so we were all systems go.
At that time, Paco (who is now getting towards the back end of his Ph.D) was a humble recent graduate, which was great because it meant that Matt and I got to boss him about — something that he accepted with enormous good grace as we went through a sequence of some 44 images on the way to the pair that we ended up with.
By this time, Matt and I had already realised that we wanted the artwork to show kicking. So we started out by asking Paco to mock up three very rough sketches of how he thought a Brontomerus-kicking-a-predator scene might be composed. Here is one of the three — pretty representative:
Although this scenario is pretty sweet, it’s not really what we wanted as it shows Brontomerus kicking backwards like a horse, rather than forwards like a footballer. (That’s a soccer player, for those of you in the USA.) So Matt offered this concept sketch:
(It’s well worth clicking through and seeing the details.)
It’s interesting to see how much of the final image was already in place even in that very early sketch: the basic pose of the adult sauropod, the juvenile behind, the theropod getting its arse kicked — even if at this stage it was a juvenile Acrocanthosaurus rather than a mature Utahraptor.
With this reference in the back of his mind, Paco started work on a 3D model of the sauropod that would be the core of the composition. He was quickly able to show us a first draft that had all the pieces in place to look convincing at least as a generalised sauropod:
Already at this stage, I was pushing for the uniquely Brontomerus-like aspects of the anatomy to be made more apparent, so I sent back this modified and uglified version of the image to give a sense of where we wanted to be heading:
(You might want to open this image and the previous one in two tabs and switch back and forth between them.)
The purpose of the modified version, of course, was to show how high the ilium would sit on the torso and how it brings forward the anterior margin of the leg muscles. We wanted the thigh to be much more thundrous! This was part of a merciless campaign of anatomical criticism of many, many aspects of the in-progress restoration — for example, the cross-sectional shape of the neck, which at this point had a crest on top and flat sides. (You’ll notice that in the final version, the neck has the distinctive subtriangular cross-section that is produced by the ventrolateral excursion of the cervical ribs in sauropods.)
While that stream of refinement was going on, Paca was starting to skin the model. Here’s the first version we saw that had skin texture:
Seeing this was an exciting moment in the progress of the project. It was the first time that the artwork started to look like actual art, and the sauropod to look like an actual sauropod. We knew then that we were on the way to somewhere good.
That feeling intensified the first time Paco showed us the complete cast of our little drama: mother, baby, and evil raptor, all skinned and showing rather fetching stripes which survived in more or less this form through to the final version:
By this stage, most of the anatomical problems are getting ironed out: the flat-sided shape of the neck has gone, replaced by a broader and wrinklier ventral aspect; and the ilium was higher on the torso, with the shape of the dorsal margin more closely reflecting that of the Brontomerus holotype ilium.
Note the care that Paco took with the juvenile: it’s not just a scaled-down copy of the adult, but proportioned subtly differently in a way that reflects what we know of sauropod ontogeny: the limbs grow isometrically, but the neck is positively allometric, so that Baby Bronto’s neck is noticably shorter in proportion. At this stage, the baby is too big — more than half Mama’s size, whereas the sizes of the elements from the Hotel Mesa quarry suggested that he should be closer to a third of her size.
At the same time that Paco was working on the details of the models, we were all still batting around composition ideas, trying to find the best way to put our three actors together. This version of Paco’s was similar in concept to Matt’s earlier sketch, but different in a lot of details: the baby is running away rather than sheltering, the theropod is rather bigger than before, and has morphed from an acrocanthosaur to a raptor; and it’s upside-down in an attempt to show that it’s not in control of the situation:
I wasn’t convinced by this version, because the theropod seems to have been spun 180 degrees on the spot as well as kicked upside-down: I felt that he needed to be in a posture that more naturally emerges from having been facing Mama when he was kicked, so I ‘shopped Paco’s sketch into this version:
As well as turning the baby around (something that didn’t really help). I flipped the raptor and tried, clumsily, to convey that Mama had broken its neck. Of course, that didn’t really work, because the extension at the base of the neck is habitual for most tetrapods anyway, but it at least gave us a sense of the direction we wanted to go in.
OK, so back to the model. Paco had sent us a simple lateral-view render of Mama alone, as well as the group shown above, so that we could more easily critique its anatomy in isolation. Here is that simple render, followed by the vandalism I did on it to show changes that we still wanted. (See what I mean about Paco being patient?)
As you can see (and as you’ll see more clearly if you flip back and forth between the two images), I was asking for two changes. The simpler was that I wanted to see the distinctive profile of the Brontomerus scapula showing through the skin. The more interesting is in the profile of the tail. It’s been shown in many sauropods that there is a distinctive upwards kink at the base of the tail, so that the dorsal profile of the body does not progress smoothly from hips to tail, and I wanted to see that in Brontomerus. At the same time, the tail needed to have more flesh on it and the ischium should have been producing a visible bulge in the ventral margin behind the hips.
The next version addressed these points (though the scapula outline was not yet right):
But picky as I am I still wasn’t satisfied…
I made a few changes here — again, in a hacky way using the GIMP, with the result not in any way intended as in improvement in itself, but as a sketch of how the model could be improved. I shifted the tail up a little, smoothed the dorsal profile so that there was no longer a sort of dip at the base of the tail, and smoothed out the rear margin of the top of the thigh, so that there was no longer a “buttock”, but a hint of caudofemoralis musculature connecting the tail-base with the thigh.
Once Paco had made the necessary changes to the model, the next render looked superb — and very recognisable as the basis of the now-ubiquitous final version:
At this point, work on the main model was essentially complete, and Matt and I were both really happy with the result. For people who’ve spent as much time gazing at the Brontomerus ilium and scapula as we have, this is very obviously Brontomerus and not just a generic sauropod. Now it was time to put the model together with the composition ideas we’d been playing with:
We went through several versions of this, mostly varying in the posture of the theropod, but this is the one that led to the final piece. For the first time, we were all happy with Baby Bronto in this one, too: he’s about the right size, and has a sort of skittering look to him, as though he wants to be elsewhere but doesn’t want to leave Mama. (Am I anthopomorphising? Very well; I contain multitudes.) It’s a bit too close to the adult, though, so we can’t quite see its shape. This was fixed in the next version, which also contained a backdrop for the first time:
Now we’re really getting somewhere. You’ll notice that the raptor’s head is bent further back this time, hopefully conveying that its neck is broken. But because I was really keen on getting it across that the raptor is DOWN and it’s NOT getting up again, I once again vandalised Paco’s work, this time with buckets of blood:
What I wanted to convey was: if this raptor wasn’t already secondarily flightless, it is now. Still, I admit that the amount of blood, and the vividness of its colour, are a little over the top. So in the final version, Paco took some of the blood back out, and toned it down to a more realistic colour. The other important difference is that the raptor was moved a bit closer to the sauropod — not because that’s necessarily a better composition, but because we expected newspapers and other media outlets to crop the image mercilessly, and we wanted to give them best chance of keeping all the key element in frame when they did.
And so we arrive at the final version, as it appeared in the paper:
The very last thing we did was ask Paco for a second render of the same scene, so that media outlets would have a choice of artwork and wouldn’t all need to use the exact same image. That was doable because all three dinosaurs, with their skin-textures, were built as a 3D model, which can be viewed from any angle. But producing a finished artwork from this is not trivial: once an angle is chosen and the animals rendered, there is still a lot of post-production work to be done in putting in the background, the blood, the dust and so on. So we didn’t ask for a complete array of 128 of these — just the one addition. After reviewing a few candidate exported renders, we settled on one from a more anterolateral perspective, and Paco worked his magic to yield this alternative take:
I hardly have words to tell you how much I love this. Several times, looking at it, I’ve found myself laughing out loud at how comprehensively the theropod is getting owned. It’s OVER for that would-be predator. It’s DONE. The only question is whether Mama is going to put it out of its misery by stomping it flat, or whether it’ll be left to bleed out. Either way, it picked on the wrong victim for dinner.
Part of what I love so much about this is that Brontomerus looks like an animal, not like a monster. It works anatomically, feels like something that lives and breathes … and, indeed, kicks.
Let me close by clearly stating that 99% of all the Awesome here is the work of Paco — a talented and hardworking guy, who made Matt’s vision come to life. My own input was basically restricted to whining. I hope we’ll be seeing this image for many years to come, and that plenty more of Paco’s pieces make it out into the wide world where they belong.
For more of Paco’s stuff, please see his blog, El Pakozoico (TARDIS alert!), and his deviantART page.
References
- Taylor, Michael P., Mathew J. Wedel and Richard L. Cifelli. 2011. 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
- Wedel, M.J. 2005. Postcranial skeletal pneumaticity in sauropods and its implications for mass estimates; pp. 201-228 in Wilson, J.A., and Curry-Rogers, K. (eds.), The Sauropods: Evolution and Paleobiology. University of California Press, Berkeley.
- Wedel, M.J. 2007b. Aligerando a los gigantes (Lightening the giants). ¡Fundamental! 12:1-84. [in Spanish, with English translation]
Sauropod Vertebra Picture of the Week 
