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:fig. 1 -- Sauropod neck gallery

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 er al. 2011a: fig. 4 -- Brontomerus caudal vertebra

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

Taylor, Michael P., Mathew J. Wedel and Darren Naish. 2009. Head and neck posture in sauropod dinosaurs inferred from extant animals. Acta Palaeontologica Polonica 54(2):213-230.

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

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9 Responses to “Tutorial 17: preparing illustrations. Part 1: use colour”

  1. BJ Nicholls Says:

    I’m a graphic designer and agree with you about the importance of working with, and preserving your color image material. I would add that you should avoid just converting color photo images to grayscale via a direct software conversion from three channel RGB to single channel grayscale. Since you have three channels of color information to work with, you can really get much better “black and white” images by using some of the many conversion tools that allow you considerable control over the results.

    Here’s a pdf overview of basic conversion concepts:

    http://www.adobe.com/digitalimag/pdfs/phs8bwconversion.pdf

    One of the easiest tools to work with include Photoshop CS’s Black and White adjustment layer. I recommend working with layered image files and, whenever possible, using adjustment layers that allow you to manage one image for many intended purposes. You can toggle adjustment layers on/off without directly manipulating the base color image, and you can modify those adjustment layers as needed (really valuable when you want to make a set of different images look consistent).

    There are many plugin software tools that help with visualizing and generating effective color conversions, but I do recommend a workflow that either works as a layer within a master file or that generates a separate image file.

    You do not need to convert to grayscale for most publishing output. In fact, it’s better to convert your color image to monochrome CMYK for offset print publishing. The reason why is that a single 8-bit channel grayscale image has relatively few gray levels, particularly in the light tones of an image. A monochrome CMYK image has four 8-bit channels that can be used by imasetting software to produce output with smoother tonal transitions. If the publisher requires only 8-bit grayscale images, it’s especially important to generate that file from a good monochrome color image. But as you suggest, the printer can usually do image conversion in the RIP (final conversion process for making press separations).

    If you want excellent “black and white” images, you don’t want to submit full color images and leave the conversion to automation. You’ll get much better results for important images if you create your own optimized conversions.

    Anyone preparing images for print should also learn how to apply sharpening for the intended output. For offset printing, an unsharp mask is an essential step to compensate for edge contrast loss when an image is printed as a halftone. A publisher could do this step, but they probably don’t.


  2. that’s some really useful advice – for me, the comment more than the post, because I’ve made all those experiences myself already. I just hope no newbie research has to go through them, too, after this post :)

  3. Stuart Pond Says:

    I would add a couple of points to this excellent post and comments:

    Never, ever, work on your originals. Ideally, you should have three copies of your work by the time you finish:

    original > unflattened working copy > various output versions

    Always back up.

    Did I say never work on your originals?

  4. Mike Taylor Says:

    Thanks to BJ and Stuart for important additions.

    I should have realised that the flatten-to-greyscale transformation is itself an artform. I’ve noted that the Colours -> Desaturate operation in GIMP offers three options — Lightness, Luminosity and Average — and seen that they give somewhat different results; but I don’t really understand the difference between lightness and luminosity (which I always though meant “lightness”, pretty much). It’s a bit shocking to find that greyscaling is so much more complex than that, even. Perhaps the moral is that I shouldn’t be writing tutorials on preparing illustrations!

    And yes, Stuart, absolutely — you never want to overwrite, or otherwise lose, your original photos. To ensure that’s the case, I always keep my specimen photos in a separate subdirectory from where I prepare the illustrations, and keep them in version-control too.

  5. David Marjanović Says:

    Many journals routinely let you have colour in the pdf for free even if you don’t pay to have colour in the dead-trees version.


  6. […] version free color figures are at the editors discretion.”  So it looks like Cary and Denver dropped the ball on […]


  7. […] This whole section, including the title, is mostly swiped from Mike’s Tutorial 17. […]


  8. […] be able to read the paper. The greyscaling of the figures is part of it — something that makes no sense at all in 2015. The small size and number of the illustrations is also a consequence of the limited page-count of […]


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