RTFP becomes RTFS – on mis-citations and mis-representations in scientific works

Here’s a topic that has started to peeve me a lot, lately. It is a spin-off, or rather a development out of, the old RTFP adage. RTFP means Read the …. paper (I’ll leave it to your imagination what the F means), and is sometimes used on mailing lists (such as the venerable Dinosaur Mailing List) and in internet fora and social media. Lately, it has been slowly falling out of favour, it seems, which may relate to the (relative) quiet of the Intelligent Design idiots. After all, it was often enough those morons who’d spout nonsense about a scientific topic, and get promptly hit with RTFP and a choice quote from the actual source showing them to be full of feces.

But, as I said, lately something has been bothering me a lot, something that has me writing RTFS a lot, instead of RTFP. ‘S’ is for source, in this case. Let me elaborate with three examples, the first of which is harmless and comical in a way, but the other two of which are worrisome.

Case 1) Recently, I received a manuscript for review that cited some of my work. And, it turns out that when I wrote my Plateosaurus range of motion paper, I made a mistake. A stupid but innocent one. I cited a previous work by the author of the manuscript whose new paper I was reviewing now, when in fact I had meant to cite someone else’s work. Seems I simply mis-clicked in my reference manager. Or I mis-remembered which paper dealt with what. Oops! The error was “believable”, because the paper I intended to chide for claiming nonsense dealt with the posture of the foot, the one I accidentally did cite with the posture of the hand of prosauropod dinosaurs. Thus, nobody noticed: not me, not the editor, not the reviewers, and as far as I know no readers – the wrongly cited author seems to be the first person who noticed.

Hilariously, in the paper I was reviewing that poor maligned author accidentally turned the tables on me: he cites two of my papers for (rather stupid) things I didn’t say! Neither of the two papers remotely deals with the topic of the paragraph in which they are cited! Obviously, I gleefully pointed this out in my review (and uses the chance to clear up my own mistake, and apologize for it).

Case 2) This year, a paper came out that had me scratching my head. There was some excellent new data in it, really cool stuff, and I immediately agreed with much of the conclusion based on it. But, it also cited some older works by others, and drew conclusion based on the combination of those older papers and the new data – conclusions that I simply couldn’t believe. In fact, I couldn’t believe the cited stuff from the old papers! Not that I am an expert in the field those papers all dealt with, and not that I could explain what was wrong, and why – thus, the term “believe” is the right choice here. It simply didn’t make sense to me, and although I am the first to say that data beats convictions, in this case I could not get rid of some nagging doubt.

Add to that the annoying turn of events that I was preparing a grant application, and the basis for the intended research was the very hypothesis that the new combo of old papers and new data cast doubt on. Application dead in the water right there! Gargh!

A few days ago I now received an email from an esteemed colleague asking me to translate an old German paper. A paper dealing with a highly similar topic. Well, turns out some of the stuff supposedly “novel” about last years surprise paper wasn’t novel, but could be found in the very old German manuscript. But that happens, especially with foreign languages. What’s important for the story here is that my esteemed colleague was as unbelieving as I was about the new claim, and that he knows about the subject and had gone to the bother of checking all the old cited papers in detail – and golly, they do not say what this year’s paper claims they say! In fact, this year’s paper makes a double misrepresentation: first, it implicitly claims the old works include test set-ups they didn’t, then it claims they conclude something they don’t. Together, these (accidental, I believe) errors stand the old work on its head, and result in the conclusion that makes no sense to me. If you correct the basis for the new conclusion, you have to revert it, and it all makes sense again.

The good thing is that my grant application can now be revived :D

Case 3) Another esteemed colleague complains that a recent paper grossly misrepresents his own work: where he used “likely” or “possibly”, the new work claims he made a statement of fact – essentially, his measured conclusions are being polarized by the new paper,a classic strawman argument version. I find such unnecessary antagonism or sloppiness (no idea which it is) un-collegial and annoying.

oh, now that I think of it, there was a Case 4, too: I wrote in a review last year: “I do not believe that this is actually what [ source ] claims! In fact, he seems to claim something quite a lot different.”

So, it seems that currently, it is not the ignorant religious nutcases, the laypeople and the fanboys who are the problem, the people who haven’t read the paper they comment on, or at least have not read it thoroughly, but rather it is sloppy colleagues who commit the crime! Worse, they do not do so in emails or on the internet, they drag the misrepresentations into the scientific literature!

What can we do about this?

Firstly, as writers of publications we can double and triple check: does the paper I am about to cite really say what I seem to remember it says? RTFS again when you insert the citation!

Secondly, as reviewers, we must do more than a token effort to check the sources given in papers we review. RTFS for key claims in papers, and make sure that they say what the authors claim they do. And in your message to the editor, point out if previous works are misrepresented. Make clear that these errors MUST be fixed, or the paper rejected.

Lastly, as readers, we should RTFS before we believe a claim. And use any form of public commenting, including rebuttal papers and letters, to point out gross errors we find. Politely, but firmly.

I know it is a lot of work, but dammit, we’re not doing this for fun! We’re supposed to be professionals, and as professional we have an obligation to do our f-ing jobs!

Thus,

READ THE FUCKING SOURCE!

…..and by the way: happy holidays!

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(quidquid it est, timeo plateos et dona ferentis - link to wikipedia for explanation)

Posted in rants, WTF?

Photogrammetry tutorial 3: turntables

Previously, I said this series of posts wouldn’t be about the easy cases, the specimens you can photogrammetrize if you’ve got the brain of an amoeba an a cell phone camera from 1995. So remember: sometimes, much less effort is required than the description below seems to suggest. I still don’t intend to cover such easy cases, but there are helpful tools and tricks that can make harder tasks almost as easy.

Below is a protocol for photographing objects that fulfil the following criteria:

  • you’re allowed to handle them
  • they can be placed in a variety of positions, i.e. upside down
  • they are not over ~100 kg (varies, see below)
  • they are not shiny or translucent

These are the requirements for objects you can place on a turntable, the latter being on of the greatest time-savers for photogrammetry that exists. “Turntable” in the sense of “swivel” or “Lazy Susan”, by the way, not “record player”! It is nice to have a powered, computer controlled one if you want to use a laser scanner one, but for photogrammetry a hand-powered one is totally sufficient.

There are plenty of heavy-duty turntables our there, some of them quite expensive. In my experience, you better get a cheap one (or two or three), available via e.g. Amazon for less than $ 25. Toss them when there’s grit in the turning mechanism; it is cheaper and you can transport the light ones easier, too. Up to ~50 kg they can cost as little as $ 5, free shipping in the US. I paid € 11 for mine. Knowing I wouldn’t need very sturdy ones I bought plastic ones, but if you expect to put sharp-edged stuff on your, buy some with a sturdy cover. Usually, these are called “heavy-duty”.

Here’s a bone on a turntable, set up for photogrammetry:

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So, where’s the turntable? you ask. It is below the newspaper, and as for WHY it is below the newspaper – patience, young Padawan!

The next step, once you have your specimen on the turntable, is to set up the camera. On a tripod! Initially, you should set up the tripod so that the camera is slightly below the specimen and that the vertical extension at the top of the tripod is all the way down. If your tripod doesn’t have this feature, tough luck! It will later mean more tripod-handling than necessary.Here’s a photo of one of those easier cases, showing the tripod set-up. Instead of a turntable I simply used a sandbox, which I manually rotated, because the bones (oviraptor tail vertebrae) were so small that no turntable was necessary.

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Tail vertebra of Ingenia in sandbox, with camera set up for photogrammetry shoot. Photo taken in Mark Norell’s famous office in the AMNH. What’s that sheet of paper doing in there, Padawan?

An important step is now aligning the camera so that it points at the centre of the turntable, or at a spot vertically above it. Otherwise, the specimen will “wobble” in relation to the camera when you turn the table. Also, make sure your specimen is centred on the turntable, for the same reason. Now play with the distance of the camera from the specimen and the focal length of your lens. You should avoid extreme lengths; stay close to 50 mm if you can.

If you can’t ensure that the specimen and camera are well aligned, for example if you have a very long and narrow object, you are often better off using a far-away position of the tripod and playing with the focal length than moving the tripod between shots. Here, the rotatable screen on my camera comes in again, the one I keep harping on about. No need to crouch behind the camera so judge if the specimen fills the view nicely! You can simply twist the screen so that you can see well from a standing position, or even sitting down next to it. There’s an added advantage, too, to which I will come in a moment.

Next, flip your specimen over! If you want to get a digital model that covers the whole surface, you need to capture that part currently in contact with the turntable as well. Also, there will be huge holes on the underside of the model, although you may well be able to see most of the surface. That’s because you can’t light these parts very well, and because you can only get photos of the underside at a very shallow angle. So test how it rests in various positions, then choose two (or three if you have to) that give you good access to all parts of the surface. Usually, it’s easy, but sauropod ulnae, for example, do not work both ways, but prefer to go three-ways ;) So you need to either be very careful how you place them, or take three sets of photos.

So, all set to take photos? No! Now you need to consider the lighting, too. In the example above I used a simple studio lamp, but you may need to find more elaborate means. So, let’s talk about lighting for a moment.

The ideal light for photogrammetry lights each and every piece of surface on your specimen completely equally. And brightly, but not so much that you get reflections, for example on somewhat shiny specimens that have been covered with lacquer. And that’s exactly what all collections rooms in museums world-wide will offer you – NOT! Usually, the biggest problem is not the light, but the lack of the same: collection rooms tend to be sufficiently lit to find specimens, but rarely to study them. That’s what the small lamps on the tables shoved into corners are for, on which you are allowed to work. And such lamps are usually not suitable for lighting specimens for photogrammetry.

On the other hand, sometimes conditions are a lot better than one may be inclined to think initially. Check out this photo of a typical collection room situation: cabinets and fluorescent lights.

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This is, in fact, not half bad! The white, smooth cabinets throw back a lot of light, which comes at a specimen placed between them at a shallower angle than the direct light from the light fixtures dangling from the ceiling. That means less shadowy undersides! And the fluorescent lights are decently long, so that they do not form a point source of light, but cover an arc. And if there are, as in the room the above photo was taken in, lights in rows, you get a fairly even lighting of a specimen you place smack in the middle. So do not be afraid to ask curators and collection managers for space where the light is best, but do expect the need to supplement them with additional light sources (a later post will have some info on how to do that). But remember: long exposure times, as enabled by the use of a tripod, can make up for darkness! They can not even out lighting very much! Thus, better darker and evenly lit, than having spotlights on parts of the specimen.

So, once you have the light you need, are you all set to shoot? Nope! You need to add something to the scene, or your model will be a limited usability. That something is a scale object. Something that will come out in the 3D model and has a feature of exactly known length, so that you can scale your model correctly. You can place a calliper on the turntable, a scale bar, you can add a business card, whatever! Ideally, you use something big, because there will be a measuring error. The larger the distance, the less the proportional influence of the error.

So, now finally ready to rock&roll? Theoretically, yes! But there is the issue looming over your work how you are going to combine the models you get from your several sets of photos into one 3D file! How can you register scans or photos sets?

There are basically three ways of registering scans:

  1. based on points found on the object itself,
  2. on points that you mark on the object, and
  3. on points on the background.

For 1., you can simply take your photos. When you throw them into your photogrammetry program, you can simply toss all photos into one batch. Now, you must mask the background, including the turntable, on all photos! Otherwise, points for alignment will be found there, and will turn out to be very powerful – after all, points on the background will be on ALL photos, because your camera doesn’t move versus the room. If you’re really lucky, the background will be so out of focus that masking is not necessary, thus it doesn’t hurt to run a very quick&dirty alignment to check. But that’s rare, so you should plan in some time for masking.

The advantage of this method is that it can be very quick and accurate. The downside is a high risk of failure (there may be too few points on the overlap), and the likely demand for time-consuming masking.

For 2., you will need to add at the very least three points. That means sticking tiny pieces of paper with an ‘x’ on them to the specimen, ideally with a number scribbled next to the mark. That way you can more easily identify the marks on your photos. More points mean you’re covering up more of the specimen, but it makes the registration easier and better. Also, you must make sure the marks do not shift, or fall off, when you move the specimen. And remember, they have to be visible is both sets of photos!

The advantage is a rather speedy alignment process, the downside that your model will have white spots, and that adding very many points for a very high accuracy alignment costs a lot of time.

Lastly, for method 3., you’re limited to points on that part of the background that moves WITH the specimen. Essentially, stuff that’s also on the turntable. That stuff will also help with aligning the photos of each set to each other, increasing the quality of each batch or chunk, so this approach sounds like a good idea. As you can see in the photos above, I used printed paper as a background even with a turntable. However, the enormous drawback is that you must ensure that the points move with the specimen when you flip it over! Ouch! This essentially limits the method to small specimens that you can fixate in some way to a scaffolding that also carries the points for alignment. Doing this without hiding some part of the specimen is near-impossible, so it is a last resort. I cropped these parts of the photos out for my two cases shown above, and opted for method 2!

So, NOW you can take your photos! But how?

First, raise the camera so that it looks at the specimen side-on, or slightly higher. Then, take a photo, turn the turntable 5 or 10°, take the next photo. If you have a camera with a touch screen or a remote-control release, use it! Touch screen release means you can easily control which point the camera should focus on, and jiggles the cam a lot less than the manual shutter release. A remote is nice, too, because it avoids jiggling, but you still have to adjust the focus point (if necessary) manually.

Once you’ve gone all around the specimen, raise the camera so that it points down at the specimen at a ~30° angle. Now, take another round of photos.

Next, decide: is the specimen rather flat and you have already captured the entire surface well? Then you may already be done. If not, raise the camera further and take another set of photos.

Here’s a screenshot of little 3D CAD model I made to illustrate the process:

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A question I get asked regularly in this context is: “Why do you not need to take photos from the top down?” The answer is fairly simple. Your object will typically rest well on a turntable with its flatter sides down (and up). Therefore, two or three sets of photos at shallow to intermediate angles will suffice to cover the top. Only if there are deep recesses on top will you need to take top-down photos – and then one or two will suffice! The key to good photogrammetry is to MOVE the camera between photos, and “move” in this context means a 2D or 3D-displacement, not just a rotation around the long axis of the lens.

Afterwards, there are still things to do right away, before you can throw your photos into the photogrammetry software of your choosing. Mainly, checking photos – did they come out ok? Did you follow the protocol, or did you mess up? I didn’t check my AMNH photos in time, and now have photo sets of two verts only from one side each. oops!

Also, you will need to sort your photos: which photos show which specimen from which side? There are two tricks for making this task easier. First, you can start each series of a specimen with a photograph of the specimen label. In between the first and second series (i.e. when I flip the specimen over) I always take a photo of “nothing” – my hand, or I tilt the tripod and photograph the ceiling. When you now look at the photos in the explorer view, using medium-sides thumbnails, the start of each specimen will stand out optically (label photo), as will the break between the series.

Lastly, even though I said above that you should add at least one scaling object, it is also advisable to measure at least one characteristic dimension of the specimen itself, if you can. Think of it as insurance ;)

Posted in Digitizing, photogrammetry

Dinosaur mounts at the NHM L.A.: Triceratops

In the previous post on the L.A. NHM I gave a quick all-around introduction. Now, it is time to take a closer look at some of the mounted skeletons, and talk a bit about how they are set up in relation to each other and the room.

Let me start with Triceratops prorsus again, as it will usually be the first dinosaur mount you see when walking through the museum. It is, as you can see in the photo in the introductory post, set up on a quite high pedestal. That is always a mixed blessing, as you can, on one hand, see the feet very well and look up under the dinosaur’s skirt (so to speak)….

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which can be quite an educational perspective. You can simply see a lot of bone and bone-bone contacts that are less easily visible if the skeleton is mounted at ground level. And it shifts the feet more into focus, a much more interesting part of an animal that the stupid ribcage and dorsal spines. On the other hand, you end up looking up at the animal, which makes it larger-than-life. For a similar reason, zoos have long ago abandoned enclosures where people are higher up than the animals, because the animals then look smaller-than-life – in both cases, you get a wrong impression of size and shape. In museums, high pedestals also play a role in the decision on how many railings you need to keep people from touching and breaking the bones. Here, there is a glass wall along the left side, and because of the high pedestal it reaches up only about the knees of the dinosaur.

The mount is a composite, consisting of parts from four different animals and quite some cast material (left forelimb, left hind limb, right fibula and foot, three dorsals and their ribs, distal ~60% of the caudal vertebrae and all chevrons). How do I know? Because, laudably, the NHM L.A. has nice, big, obvious signs up that contain all the information you want:

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(click for larger, legible size)

Ain’t this cool? Specimen numbers, localities, and a nice coloured map showing you what on the mount comes from where. Plus info on when and by whom the fossils were excavated! That, people, is exemplary and highly commendable!

Ok, back to the mount. In lateral and oblique views it looks just like your run of the mill Trike. Once you get close to head-on, though, you’ll notice that the skull is transversely squashed.

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Looks rather outlandish, I must say.

Below, I’ll post two views from the right lateral and left anterolateral sides. They highlight the problem with lighting that this room has – a problem for which I do not believe a perfect solution exists.

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Here, I chose a fairly long exposure time, using a tripod, so the bones look well-lit. The right forefoot and the tail tip, in contrast, are overexposed, because of the sunlight streaming into the room. While the human eye is much better than a camera when dealing with bright-dark contrasts, but it still can be difficult to see the bones well when they are back-lit. My eyes are pretty good, but I did see others, especially elderly people, squinting quote a lot.

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This view also shows the effect of sunlight in the room: the head is over-lit, the rest of the skeleton is in the dark. Overall, however, the effect wasn’t too bad, because the exhibition planners intelligently employed ground-mounted spotlights to light the skeletons.

OK, time to finally take a closer look a the mount. The overall pose is nothing spectacular, with the animal having all four feet on the ground. It seems to be a very slow walking pose. Individual articulations between bones look good, although one might argue for a bit more room for cartilage in e.g. the knees. The ribs are nicely tucked close to each other, instead of the overinflated ribcage I have seen in some other ceratopsians. All in all, the mount looks good, it has the appearance of a real animal, not a freak.

As mentioned, the feet are mostly casts, but they sure look good! Still, I’ll limit closer views to the one real foot, the right front one.

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Classy: the bones are all held in cradles and can apparently be taken out easily. Not that this setup is a novel invention; as I’ve previously pointed out in one of the more popular posts on my blog, there are mounts that stem from the direct post-war ear that were done in this way.

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As is the case with many ornithischians, especially ceratopsians and stegosaurs, the lateral view of the lower forelimb is especially interesting. Just look at that absurdly massive ulna, and the absurdly huge olecranon process on it! It looks almost as if Triceratops wanted to play mammal, with regards to the moment arms, but the limb is far too heavy to be in any way comparable to mammals adapted to rapid locomotion. Maybe to rhinos, but although they are quite fast and surprisingly agile, they are still rather clumsy and ponderous compared to cows and other currently dominant terrestrial herbivores. Sadly, also, sometimes too ponderous for humans. Part of that strength is surely a result of the large percentage of weight the front limbs had to carry, just remember that huge skull!

What I also should mention, although the corresponding photo is way up at the top of this post, is the architecture of the hip. Check out how the ischia form a sort of chute for eggs to slide down. And how the broad sacrum displaces the acetabula laterally so that the limb clears the belly a lot easier than in basal dinosaurs. Both things are also seen in sauropods, for example. The former is a very dinosaurian way of doing things, the latter is again reminiscent of mammals. Other notable details? The loose connection of the shoulder girdle, the very ventral placement of the shoulder girdle, and the resulting large space for trachea, oesophagus  and neck muscles between the cervical vertebrae and the sternal plates. Also well visible in the photos above.

Overall, the Triceratops is a great mount, and its placement in the middle of the room makes the most of it: visitors can walk all around it and see it from all angles. It is well articulated, and consists in large parts of nicely preserved original material – what more can you ask for?

Next up will be another ornithischian: Camptosaurus dispar. For now, to end this post I have one more photo, a good-bye pic of the Trike, taken from the gallery at the end of the room. As you can see, despite the high base it is possible to get a good glimpse of the large dorsal surface of the sacrum.

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Posted in Ceratopsia, Dinopics, Dinosauria, NHM L.A., Ornithischa, Travels, Triceratops | 3 Comments

DigitalSpecimen 2014 – Call for Abstracts

DigitalFossil 2012 was a much bigger success than I imagined when I planned the conference and applied for funding. The excellent exchange of ideas and knowledge at the meeting was great fun, and now we aim to repeat the exercise:

DigitalSpecimen 2014

will take place at the MfN from July 14 through July 18, 2014.

You can find the conference abstract on the web page, or download the PDF version here. Presentations can be submitted here; for now only a title is needed.

As with DigtialFossil 2012, the focus is dual: 3D data generation and 3D data curation. Do you have a story to tell about how a scan project worked or failed? Is there a new, cool database for storing 3D files? A handy tool for searching or viewing them? Well, come and tell us about it!

:)

Posted in DigitalSpecimen 2014, MfN Berlin | Leave a comment

Dinosaurs in the Natural History Museum of LA County

The annual meetings of the Society of Vertebrate Paleontology (SVP) usually include an evening reception with a talk open to a wider audience at the local natural history museum. Usually OK food, expensive booze, and a lot of fun is involved – and a cool museum exhibition open only to several hundreds of crazy paleontologists. This year, in Los Angeles, things were a bit different: not only the museum was great, but the food was awesome, too! The talk was also interesting, which is not always the case. (and let me point out that talk and reception can be on the same day, but usually are not, as was the case in L.A.)

Obviously, an evening receptions is not the best time to get a complete overview of a museum exhibit, but I went back twice more, stealing a few hours from conference time. Not to sight-see, but rather to photogrammetrize some dinosaurs, with the very kind permission of Luis Chiappe, curator and director of the Dinosaur Institute at the NHM L.A.

The museum is built around a central atrium, and this atrium already sets the tone the way a dinosaur palaeontologist wants it set. In fact, the dino viewing starts from outside:

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Yes, a pair of mounts: a Tyrannosaurus rex attacking a Triceratops horridus. There even is a bronze version outside the museum, the dinosaurs fleshed-out, but somehow I managed not to take a photo. The shot above was taken through the glass doors (note the “forbidden” signs). More from inside:

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You can walk all around this mount, which is really nice! I didn’t have time to take many photos, though.

After this initial grounding you can lose yourself in a huge and very varied museum. There are 17 different permanent exhibit parts (see website) and plenty of special exhibits. I love how part of the exhibit is outdoors; too few museums actually take botany and zoology out of the building. The NHM in L.A. has beautiful gardens, and makes excellent use of them.

Inside, I quickly walked through a bunch of exhibits including the one on the history of LA – lots of cool stuff to see there. Took a peek into the bird part (lotsa!), but spent serious time only in the dinosaur part. Thus, below, all you get to see is dinosaurs. Let’s start with one of the best mounts they have.

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Yeah, I know: cheap shocker! Birds are dinosaurs, and not “descendants of dinosaurs”. Discussed this recently with TV people, and to their very great credit they not only struck the “descendants of”, but actually asked for an extra sentence explaining things better for the viewers.

Anyway, having real birds skeletons, and in this case not only the obligatory ostrich (Struthio camelus) but in addition a swan (sorry, no idea which, I forgot to photograph the label), allows showing the commonalities and differences between the various groups nicely. And in LA the extant bird skeletons are not shoved into a corner as an afterthought, but a prominent part of the display. I have two more photos of the pair, but they will have to wait for a different post.

So, OK, on for the “real” dinosaurs! The dinosaurs are spread out across two halls, one of them a long rectangle with a gallery covering one narrow end, the other a large hall with a less pronounced difference in length of the sides, and an all-around mezzanine level. What delight! Being able to skeletons not only from the bottom up, but also the top down! Here’s a view down the long hall.

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It starts with a quite majestic Triceratops mount, which you see from an oblique view as you enter, because the hallway comes into the room off-center. IN the background looms a Mamenchisaurs – and that’s at first all you see! Which is good. You’re not confused by tons of different stuff on all sides, but inexorably drawn to the first big mount.

Quite an issue in this room is the lighting. There are two big windows going down to ground level, and in the morning the sun shines in through them. Therefore, there are two big splotches of light in the room, with the rest in shadows. I’ve left the photo above unadjusted, so you can see the darkness that surrounds the Trike, and the left-side-only light on the sauropod. It lends a lot of atmosphere to the room, but it also can make things very restive. What it does beautifully, though, is draw the eye to the giant mural you can see on the left, a wonderful painting by Julius Csotonyi (website; he’s really good!). Here’s another view:

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Yes, it is too big and the Trike too much in the way to photograph it in one go without foreshortening! And it is very impressive, and in the near-ideal spot next to the skeleton Mamenchisaurus.

Here, now, a view from the other end of the hall:

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In the area of the hall I stood in there are some non-dinosaurian animals mixed in, marine reptiles. That’s OK, as they aren’t much in the way and nicely mounted. Still, I fear it will reinforce in the public’s opinion the misbelief that they are also dinosaurs.

Overall, the dino exhibit uses a lot of stuff besides mounted skeletons to teach people about dinosaurs. I must admit that my attempts to do photogrammetry of the mounts didn’t give me much time to check out the rest of the exhibit, but what I saw impressed me. There is, for example, a long wall with isolated bones mounted, in front of which you can find a touch screen that displays information on the specimens. You can see that wall in the background of the Triceratops photo above. There are also TVs around, and lots of graphics that are simple enough to readily understandable, but accurate. I wasn’t too impressed with some of the educational stuff, but then I realized that I was thinking of European audiences. US visitors were very well served, I guess. Three classes with students of varying ages visited while I was there, and I was quite struck by the differences in teaching culture.

OK, enough of that, you want juicy dino pics. Here goes!

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A beautiful specimen, a bunch of articulated sauropod dorsal vertebrae. This specimen fills a spot in the area connecting the two big halls, where there also is a staircase leading up the to mezzanine. Being set in the middle of the room in an all-around-glass case, it became a center of attention for many visitors, who devoted far more time to a much more thorough study of it than they otherwise would have. A lesson to remember: don#t drown people in specimens.

On we go into the big hall. Here’s a view of the main attraction, the tyrannosaur mounts.

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Another big display, which holds an Allosaurus mount and a Stegosaurus mount (yes, the allosaur attacking), as well as an articulated bas-relief Edmontosaurus juvenile, the ostrich and swan, and some other things, was behind me when I took the photo, and to the right there is a big case with ceratopsian skulls (below). Overall, quite a lot of dinosaurs, and with ample space!

Overall, a wonderful hall! I certainly enjoyed the fact that one can walk around all mounts (even if there is some glass and stuff in the way on the far side of the Stegallosaurus mount), and the top views are just awesome. More goodies are also hidden away upstairs; you can just make out a wall mounted hadrosaur in the photo above. The room has excellent lighting, whereas nearly every other dinosaur hall I know has issues. Here, a plethora of windows downstairs combine with the glass ceiling to flood the entire room with light. Spotlights in the bases under the skeletons are used to even the lighting from below.

Oh, by the way: the bases! I love how they have changing heights that allow children to see well, but structure the room as well. Their very simple geometric shapes and dark metal finish makes them unobtrusive, and they provide ample room for texts and figures (all on exchangeable plates) at good angles: not too steep, not to flat, so the lights do not mirror in them.

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The good lighting does in some places bring with it a problem with reflections on the glass used to protect many specimens. On the skull cabinet above you can see that even the use of a polarizing filter can’t amend it enough to get good photos. Thus, you end up waiting for a cloud to pass by, or have to come back later in the day, to get tolerable shots at best. But that’s rare: 95% of all glass in the exhibit does not suffer from this problem.

That’s all I have to say about the halls in general for now. The next posts will address the mounts in detail.

Posted in Allosaurus, Aves, Aves, Ceratopsia, Conferences, Dinopics, Dinosauria, NHM L.A., Ornithischa, Reptilia (non-archosaur), Sauropoda, SVP 2013, Theropoda, Triceratops, Tyrannosauridae | 3 Comments

Photogrammetry tutorial 2: picture taking, general remarks

In the first part of the photogrammetry tutorial I listed all the equipment you need. Now, it is time to look at the basics of photography as applied to the method: what are the general set-ups, and how do you have to adjust your camera settings to take optimal photos. And how do you judge the crop.

Depth of field

Whatever you want to make a 3D model of, the first thing you need to understand is how to produce photos with a suitable depth of field. Basically, this means getting as much of the object into proper focus, instead of having the parts closest to and farthest from you all blurry, and only the middle ground properly in focus. Or, if you use a point&shoot camera, whatever happens to be near the point of focus (i.e., often in the centre of the image) perfectly crisp, and all the rest just a washout.

Depth of field is influenced by several factors, for practical purposes (i.e., thing you can do something about) these are

- f-Number

And that’s it! Yes, indeed – that’s the one thing you can do directly on your camera to get a huge depth of field!

Now, there are a bunch of things you can do aside from that, but let’s stick to the basics for now. And there are a bunch of things you can adjust, but that you should not touch. More on that later.

F-Number, what does that do? It means making the aperture of your lens smaller or bigger. The bigger, the more light per time gets into the camera, and the lower will your depth of field be. Thus, you want a very tiny aperture, and that means very little light gets in. This increases the time the aperture must be open, i.e. the time it takes to take a well-exposed photo. Hence the need for a tripod: unless you have very unusual lighting conditions (basically, the sun directly behind you), you normally won’t be able to hand-hold your camera. Exceptions are flat objects that do not need a massive depth of field, like track fossils.

One thing to keep in mind is that you can change the focal length you use – which directly changes the distance to the specimen that you have to keep. Focal length also directly influences how much light gets into the camera. The longer, the less light – thus it can be a good idea to step closer to the object and shorten focal length. If you use a tripod, that doesn’t matter much, though: there is no big difference between a 5 s and a 15 s exposure time. And stepping close and using a wide view (18 to ~35 mm) can carry it’s own risks (photo alignment will sometimes fail), so personally, I rather go for something between 35 and 80 mm and live with the longer exposure time.

So, Rule #1 is: Maximize your f-number! It gives your greater depth of field, thus better images for photogrammetry.

Rule #2 stem directly from Rule #1: Use a tripod!

On to the other things you can do:
Obviously, for the same f-number your exposure time will be shorter if there is generally more light. So don’t try photogrammetry in a dank basement without turning on the room lights. Or bring additional light sources, if you can set them up. You can also, if you really really REALLY have to, up your ISO. Don’t ever think of going up from base ISO (typically 100) unless you really must. But yes, higher ISO numbers mean shorter exposure time, thus if you can’t use a tripod using ISOs up to 800 may save your day.

Also, obviously, you can just buy a faster lens. Be careful, though – you’ll easily spend several hundreds or more of bucks to gain a reduction in exposure time from 25 s to 5 s. Still way out of the window of hand-held shooting, thus irrelevant. Remember Rule #2!

Balancing exposure

Besides being out-of-focus, the easiest way for a point on your specimen not to show up in the model is to have it under- or overexposed. If your photo has washed-out highlights, the program will not find points in these areas, nor will it pick up blacked-out shadows. So you have to try to get all parts of the specimen well lit, and that without overexposing other parts.

Again, long exposure helps, and thus high f-numbers. Simply because it allows you to shoot without strong lights on the specimen, which invariably will create strong shadows. Especially if specimen are covered with lacquer, or otherwise have very smooth surfaces, on which directional light creates reflections.

So how do you find the correct exposure? The first step is using your camera’s automatic suggestion as a starting point. Do not auto-expose, but use the manual mode (M program on Canon cameras). Tap the shutter release and the camera will suggest an exposure time for the aperture and ISO settings you chose. Now check out your specimen and its surroundings. If you are using a turntable and a white background, and the specimen doesn’t fill your picture very well (e.g. because it is long and narrow), overexpose a bit, especially for dark specimens. If you have a darker background and a light-coloured specimen, underexpose a bit. Take a test shot and check it out on the computer screen – you’ll quickly get a feel for what’s too light and what’s too dark.

Thus, Rule #3: aim for a balanced exposure! This can sometimes involve moving your camera that tiny bit that hides a spotlight in a museum behind a pillar or even part of the skeleton you are trying to photograph. Or timing your photo session so the sun is on the other side of the building, and therefore doesn’t cast light and shadow patches on the mount.

Obviously, sometimes it will be very difficult to find the perfect exposure. Dark bone in cream-coloured limestone would be one of those things where you’ll likely end up with problems whatever you do. Here, it is possible to take two shots, one slightly over-, the other slightly under-exposed. Later, you can mask the bad parts of each image. But depending on what camera you buy there may even be a more elegant solution.

HDR-photos for photogrammetry

HDR captures a greater dynamic range between the lightest and darkest areas of an image than normal photography. HDR photos therefore can resemble the impression you get a lot more than any single photograph can. Basically, if you have a bright sky and a dark ground, you will see more of each than in any single photo, so you need to combine at least two photos to create the same effect. That’s what HDR programs do. So why not use such photos?

The big problem is that most HDR programs (or HDR functions in photo editing programs) do not spit out photos with “correct” EXIF information. But you need EXIF information for photogrammetry. Also, creating HDR images from several shots takes quite some time. Also, it can be quite an iffy task of fiddling with lots of parameters to achieve realistically coloured images – remember that all images you use need to “look” the same with regards to hue and tone, or photogrammetry will not work because no matching points can be found. Thus, the classic way of taking over- and under-exposed shots and calculating one image from them is something you should only do if you really have to. Luckily, some cameras have a built-in HDR mode, which creates images from usually three shots. If you use  a tripod (here we go again!), the motion between the shots will be minimal, thus there will be no large crop and practically no loss of sharpness, and the photos can be used for photogrammetry.

So why did I not say right from the start that HDR photos are the way to go? Because they aren’t! For one thing, most automatic HDR modes do not vary exposure time, but ISO. Which means that one of the usually three photos that go into the final image is shot at a high ISO value, with all the dire consequences. Lotsa noise, which does show in the final photo. If you are rich and buy an really expensive DSRL, however, there often is a manual mode in the recent models that allows varying exposure time, and you will end up with perfect pictures.

Also, the blended images tend to be somewhat less crips, which can throw your point-detection algorithm. Not good, it will ruin your model. Overall, you’ll just have to experiment with your camera.

Thus, Rule #4: Try unconventional stuff, including HDR, if things don’t work well otherwise!

Crop

One thing that many people miss out on is that there is no need at all to hold your camera perfectly horizontal or vertical. Turn it any way you like, for photogrammetry it doesn’t matter! Thus, if you specimen is longer than wide, turn the camera so that the long axis fills the diagonal of your crop, and gain some resolution! The bigger the specimen in your photos, the higher will the maximum possible resolution of your model turn out. Thus,

Rule #5: maximize the size of your specimen in your images!

An expansion of this rule means that you should take a handful of overview images of a very large specimen, then get lots of closer-up shots of all parts, in order to get high resolution of the actual surface(s). I’ll explain that in detail in another post.

OK, next step is explaining the setups you can use for different types of specimens, and how to take pictures of actual specimens.

Posted in Digitizing, photogrammetry | 2 Comments

Photogrammetry tutorial 1: equipment

Taking photos for photogrammetry can be dead simple, or it can be a fiendishly difficult task. It all depends on the specimen you want to get a 3D model of. Here’s a not-so-short guide on how to ensure that your photos will get you a good model. Often, much less effort is required, so please experiment on your own. This part 1 will give you a list of tools you need.

There’s four things you really need:

  • Digital camera with quality lens (and polarizing filter)
  • tripod
  • tiny white stickers and a pen
  • scale bar

Optionals include

  • turntable
  • lights
  • ring flash

Digital camera & lens

You can use your phone or a cheap (or expensive) point&shoot camera. But if you want really good models, there is no way around a really good DSLR camera. I use a Canon EOS 650D with a Canon 18-135 mm lens or a Canon 50 mm prime lens. The lenses are OK, but a better one would sometimes help photogrammetry. Same for the camera: if you can get the funding to get an EOS 1D X or another professional model (Nikons are excellent, too, as are some other brands), go for it! The maximum resolution you can achieve depends, among other thins, directly on the number of megapixels your camera’s sensor has. Also, if the circumstances of your photography are suboptimal (bad lighting comes to mind), a better camera may help.

A key advantage of my 650D over many other cameras is the touch-screen display with Life View – you can see, on the display, exactly what the sensor sees, and you can choose your focus point by touching the screen in the right place. Additionally, the 650D screen can be flipped out and rotated so that it points to wherever I want it to point to. That allows very easy handling of the camera even if it is far above my head, or if it is under a mounted skeleton pointing up. Get a camera with such a display! If it means that the sensor is a bit less good, so be it! The ease with which you can take hundreds of photographs that without a rotatable screen would be a real contortionists act simply outweighs the small difference in megapixels between a top-of-the-line camera and an EOS 650D.

Additionally, a circular polarizing filter can work wonders with specimens behind glass. Examples to come – Edmontonia and Protoceratops at the AMNH worked out much better than they would have without a filter. They cost between 70 and 100 USD, quite cheap considering what they allow you to do.

Tripod

A key factor influencing the quality of your final models is the sharpness of your photos. Blurry photos mean less good alignment and especially a bad surface resolution. A tripod allows you to
a) take blur-free photos under bad lighting conditions, but also
b) take photos with long shutter speeds (also called exposure times) and narrow apertures under any conditions.
The latter point is important, because narrower apertures mean large depth of field. And that means that more of your specimen is in focus.

Thus, for a good model, you want to max your f-stop and thus have to use long exposure times (I often use 30 s). That means high quality lenses and a tripod to keep your camera perfectly still.

You should not try to be very economical when buying a tripod. Nor is it good advise to hunt for the least heavy one. Aluminium tripods, or plastic ones, can be significantly lighter than steel ones, but you will rarely get the size and flexibility as well as durability you really want for serious photogrammetry work in the field or collections all across the world.

The size of the tripod you need depends on the types of objects you want to digitize. Assuming you are like me, and want to be able to produce high quality models or any sort of dinosaur bone as well as of complete sauropod mounts, you need a tripod that can put the camera well above your head. Also, it should be able to put the camera just above the floor. Also, you should be able to flip the camera into any direction you want, which means a highly versatile tripod head.

Overall, a good tripod will cost you roughly $300 or more, but that is money well spent. However, any tripod is better than hand-held shooting!

Stickers

Yes, an odd item to list, but sometimes a great help. Usually, you can’t digitize a specimen completely in one go. Gravity gets in the way and results in the object touching the ground in some places. Thus, you will need to flip it upside down to get photos of the underside. Under ideal conditions (more on that later) you can then simply throw all photos into your software and get a perfect results, but normally this means that you need to run the model as two parts: a first and a second half. These need to be stitched, and putting small markers on the specimen helps you aligning the halves properly.

Scale bar

Well, duh! You do not necessarily need an actual scale bar, but you need to have something in your model that
a) you can easily identify the ends of in your model and
b) you know the exact length of.
No, a bone’s maximum length will not do, because you really can’t ever find the exact two spots you measured the length in between on the digital model. Well, almost never. So get something bit in there (the bigger the less will your percentage error be), like a yardstick or a camera lens cover (they are perfectly round, so the biggest distance you can measure is the correct one).

Turntable

For objects that can be set on a turntable there is no better and more comfortable method than using a turntable. Granted, you may end up having to mask out the background on some images, but in my experience you’ll be twice as fast.

Lights

You may, not really need them, but a 5 to 10 LED light you can use to illuminate specimens from below can be really useful, and is small enough to be taken along.

Ring flash

Another method for getting equal and good lighting onto the object is a rung flash. Not too expensive, and very useful for smaller objects, especially on a turntable.

OK, that about covers it! Anything else you need can be gotten locally at short notice. Next post will address the various set-ups you can use. then comes the camera options.

Posted in 3D modeling, Digitizing, How to, photogrammetry | 4 Comments