Theropod Thursday 52: pulling a leg! Erhm….rather: pulling a tail!

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Hungry I am. An aardwolf (Proteles cristata), too. A hungry aardwolf. Yep, that’s it. A hungry aardwolf. Now get me my food. Now!

This is the elusive critter that David Hone, my esteemed colleague with plenty of zoo experience, and I totally missed seeing during our legendary winter visit. Legendary for me, as it made me aware of how much cooler a zoo the Tierpark is than I was previously taking note of. Dave kept repeating “I’ve never seen this animal before!” The aardwolf was the one animal that we really wanted to see but didn’t. And on my many other visits to the Tierpark – I place I practically live at during summer weekends – the aardwolf stayed elusive. I did see it, but generally just as a furry blur popping out of one hole in the ground and into another one.

So imagine my delight when the Tierpark, under the new director Dr. Knieriem, started announcing the feeding times of some of the animals, and included not only the echidna but also the aardwolf on this list! Obviously, I dragged my children there at the appointed time, 2:15 p.m. And lo and behold, the elusive aardwolf put in an appearance! He came out of his hiding place when fodder was presented and greedily gobbled it up.

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But, waitamoment!” you say. “What’s this to do with Theropod Thursday?

Well, here goes:

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A hooded crow (Corvus cornix) is paying a visit. And not a polite one, as we will quickly see.

Aardwolves feed mostly on termites, so the Tierpark feeds them a pretty yucky looking protein-rich slurry. And believe me, crows love anything protein-rich. And crows being crovids, some of the most inventive birds, they come up with ways to make you, me, and aardwolves involuntarily share that yummy protein cocktail.

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grab……..

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and pull!

Hm, ain’t nothing happening. Well, let’s do this again.

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Ouch!

Now, corvids have a pathological obsession with tail pulling. They just can’t help themselves! See here. If it’s got a tail, that tail’s gotta be pulled!

Still no effect? Here we go again!

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harder!

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Oh wow, finally there’s a reaction!

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aardwolf

and so, finally, the poor crow that risked life and wing got the deserved go at the trough!

To be honest, I don’t believe the aardwolf minded the tail pulling very much. He simply had had his fill, and thus would have wandered off anyways.
To end this on a more theropodish than mammalian way, here’s a Hooded crow proudly strutting around.

aardwolf

Posted in Aves, Dinosauria, Mammal pic, Mammalia, Maniraptora, Theropoda, Zoos | 1 Comment

Photogrammetry tutorial 9: Quick and dirty!

Over the course of previous tutorials and in my paper with Oliver Wings I’ve given quite a bit of advice on how to photogrammetrize objects properly. Today, I’ll address the other end of the spectrum: how to approach photogrammetry unprepared and without proper equipment. Oliver and I mentioned a minimum kit in our paper, but what if you’re really stuck with just a digital camera? What can you do with everyday materials to improve your results, and how do you approach the entire thing?

First of all, you really need to know how to handle your camera. If you have a tripod and control over the lighting, it is easy to take in-focus and well-lit images. But if the light is low, comes from one direction, and you must hand-hold your camera, then it becomes important that you know with which lens at what zoom setting you can reliably take good photographs with what ISO settings. There’s one thing that will help you a lot that usually I’d strongly recommend against: use flash! Yes, you read that right: it is better to use a flash, even your camera’s internal flash, than take blurry photos. (If your camera doesn’t have an internal flash, then it is a top notch DSLR and I can’t believe you don’t have a whole shitload of equipment with you). There’s an important thing to do when you use your internal flash, but I’ll save that for later when I talk about the process of photographing a specimen.

One thing to remember is that your zoom lenses will allow shorter exposure times / lower ISO / smaller apertures if you use them at a low extension length. So do consider stepping closer to the specimen rather than zooming in. As long as you do not go into the ultra-wide angles or use a fisheye, your models should turn out just fine. And if your modelling software happens to be Agisoft Photoscan Pro, you can even use a fisheye lens, as the program has a feature that allows dealing with fisheye distortion.

Another issue with q&d photogrammetry is usually the inability to use a turntable or optimize the background. Normally, you’ll want to use a background that doesn’t offer any features for the software to detect. However, given the lower quality of images you are wont to achieve, using a feature-rich background can actually be a boon! Normally, you’ll always want to aim for one-chunk model creation, where you toss all images into one chunk, even if the specimen was moved versus the background in between. Instead, now try to use a highly structured background, such as a colour ad newspaper page! And once you’ve finished shooting the specimen from one side and move it by flipping it over, use a different feature-rich background! This way, the background can be included in model creation and thus help with alignment, but doesn’t cause images to align based on the background that were taken with different specimen positions.

Let me explain step by step:

  1. Put specimen on a double-wide newspaper page with colour adverts, or some other crazy stuff. Persian rug or whatever.
  2. Clean, as far as possible, the area around or use additional newspaper etc. to hide anything that would be in the picture.
  3. Shoot images from all around.
  4. Remove specimen and all stuff you used to cover the table.
  5. Place different newspaper – maybe even something totally different like a tablecloth.
  6. Return specimen in different position (flipped over).
  7. Shoot images from all around.

Now, you can use multi-chunk alignment with points-based chunk alignment, as nothing but the specimen is there to make the chunks match each other. Granted, it may not work, but you can always resort to manually placed markers.

OK, now is the time to say that bit about using the internal flash. Obviously, in an ideal world, you have brought a ring light (usually LED) or ring flash, but let’s assume that you haven’t. If you point your camera at the specimen you’ll usually hold it upside up, so that the flash is above the lens. And in normal conditions, whether outside or indoors, the majority of the light will come form above. This means that you naturally get a darker, less-lit underside of the specimen, and that you add to this effect by having the flash light slightly from above, too. So, fix this: flip your camera upside-down! It sounds stupid, and it can be cumbersome, but having the flash under the lens gives you an extra 10% or so of surface you capture well-lit, right where it matters: on the outward edge of the specimen, where you want to find many good points to match one chunk to another.

What else? For one thing, do try out unusual camera programmes! Many DSRLs and even cheap point&shooters offer HDR modes. These modes take several images at different ISOs (usually) or exposures (better but rarer), and combine them into one image that is more evenly lit than any normal photo. As this post direly needs a photo now, here’s one – a HDR mode photo I took with my Canon EOS 650D of the AMNH’s Tyrannosaurus mount.

AMNH T. rex

AMNH T. rex

Oh well, it’s a cool mount, so two photographs instead of one ;) Notice how there are no black shadows and no white-outs? That’s the power of automated HDR. Sadly, the 650D does this via ISO variation, and that includes high ISO values, leading to a lot of noise in the image. But still: these images align and produce dense point clouds much better in Photoscan than normal, hand-held ones would. So, no tripod? Try the HDR mode! If you run Magic Lantern on your camera, you can do better, varying the exposure, not the ISO, too.

Anything else? Consider making a makeshift turntable from a sandbox or so for small specimens, or just using a smooth board on a smooth table. Use white pieces of paper or white shirts to reflect light onto specimens. And so on – happy digitizing! :)

 

Posted in AMNH, Digitizing, Dinopics, Dinosauria, How to, photogrammetry, Theropoda, Tyrannosauridae, Tyrannosaurus | 5 Comments

Photogrammetry tutorial 8: scaling “with hindsight”

Recently, I mentioned in passing that I took some photographs of specimens at the AMNH in New York so that I could better scale models I had calculated from photographs taken during my previous visit. Here’s how that worked out, with a step-by-step explanation.

Here’s one of the models again, as calculated before, without a proper large scale bar.

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If your name is Jaime H., click for a larger version ;)

This is a model of the Khaan mckennai holotype IGM 100/1127. It has only some 17.5 million polygons. Still, a nice model! Obviously, given the advances in the photogrammetry software that happened since I previously calculated the models, I could simply have re-run them from scratch, just with the new images added. In fact, I am doing that also, to compare the results. But with a calculation time of 183 hours for the alignment and 75 hours for dense point cloud generation – and that is for ONE of the models – it is a major task. If I can avoid it, that’s an option nice to have. I just recalculated on of my models, and that has 279 million points in the dense point cloud. So, “only” 17.5 million here, but a model that I certainly do not wish to re-calculate, as it is good enough for the vast majority of purposes.

So, how to proceed?
First of all, I created a new chunk in the project file, and added my new photographs with the big scale bars into it. I ran alignment, obviously at ‘High’ accuracy. Then, I added markers on my scale bars in the photographs:

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Obviously, the surroundings have changed. And if you look closely you will note that the specimen itself has changed a bit, due to further preparation work. However, the by far largest part of the area photographed has stayed the same. Therefore, it is now possible to align the two chunks to each other via points. And then I merged the chunks, which retained the already-calculated model.

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This is the chunk with the old photos, showing the alignment. And here’s the two chunks aligned and merged:

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Note that I set the alignment photos to “inactive” so that they are shown in a different colour.

Now, I just updated the merged chunks using two scale bars created from the four markers – and done!

OK, that’s it! And now, to tease certain colleague a bit more, another view of the model. This time without colour, so that the high quality is more apparent:

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Posted in AMNH, Digitizing, Dinopics, Dinosaur models, Dinosauria, Khaan, Maniraptora, Oviraptorosauridae, photogrammetry, Theropoda | 7 Comments

Attempts at macro photography of minerals

Software for photogrammetric 3D reconstructions pretty much doesn’t care what scale the photographs are that you feed it. As long as there are pixels and EXIF data, all is fine. Without EXIF it requires a bit of fiddling; see for example the wonderful Paluxy river trackway 3D model in this paper. Wish I’d done it! I had played with the idea, but Peter Falkingham was so much more obviously the guy to do it… well, anyways. Software doesn’t care about scale, so you can feed in satellite images or macro images – it will calculate ahead. I did some macro photogrammetry before (here and here), but in both cases I loaned the macro lens only for that specific purpose. However, I wanted to play around with the lens a bit for straightforward macro photography, too. Now, I finally got around to that.

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Markasite FeS2 and Lostlabelit (maybe Cerussite PbCO3 ?
I’m too lazy busy to check right now)

The lens in question is one of the coolest toys in this field you can imagine: a Canon MP-E 65 mm! What’s so cool about it is that, although it seems, from its name, to be  regular 65mm macro lens, it is in fact a 5:1 lens! Yes, you read that right: 5x magnification! You can go all the way from 1:1 to 5:1! Most macro lenses go from 0.5:1 to 2:1 or so.

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Vanadinite Pb5(VO4)3Cl

The huge magnification does have its drawbacks, though. For one thing, the lens does not have autofocus. When you see it in action, it becomes immediately clear, why an autofocus would not really be a good idea. The dinky 65 mm’s 98 mm total length turn into a whopping 300 or so mm (I didn’t measure) – this lens is longer when used at 5x magnification than many a good tele! And focusing via the focus ring and changing magnification is the same thing – therefore, I tend to set magnification first, then move the whole camera or the subject until it is in focus.

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Anapaite Ca2Fe2+(PO4)2·4H2O

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Bornite tarnish Cu5FeS4

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Calcite CaCO3

Overall, this lens quite clearly is not for the noobs and lazy out there! I count among the former, but I did have a lot of fun with it. It makes many of my at first glance boring minerals and crystals look really impressive, and the effort is tolerable. And it is surprisingly cheap (well, kinda) at currently slightly over 1000 €! As a colleague wrote on Facebook, he gets better results photographing microfossils with this lens than with the Senckenberg’s dedicated equipment that costs 40x as much.

Posted in macro, photography | Leave a comment

Absurd Addendum to Gut Check

Yesterday, I posted some pictures that I took with a fisheye lens. As mentioned, one has to be hellishly careful not to get into the picture by accident. Well, I mentioned lying down on the floor…….

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Note the camera under Diplodocus‘ belly.

Also, I took an unintended selfie. My tripod head allows tilting the camera down to 90°, and up to 45°. If I want to tilt it any further, I need to reverse it: take it off, loosen the screw that fixes the holder plate to the camera, turn the plate around 180°, then fasten the screw again and set the camera back onto the tripod. I did this without turning the camera off, and because it was in liveview mode, where you can release the shutter by touching the liveview screen, and because I happened to brush against the screen when I set the camera back into the bracket….. well, the camera was, due to the rotation, pointing in the exact opposite direction of “upward at Giraffatitan;)

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There you go, critical looking palaeontologist with Elaphrosaurus. Needs a shave ;)

Posted in FUN!!!, photography | 2 Comments

Sauropod gut check

In the past I have posted a few times on unusual perspectives of our MfN dinosaurs, especially the big sauropods Giraffatitan (ex Brachiosaurus), Diplodocus and Dicraeosaurus. There’s one view that I didn’t write much about before, and I won’t write much today – but I’ll show you a few pictures. Gut check pics. Can you tell which is which?

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These photographs were all taken with a Canon EF 8-15 mm Fisheye lens set to 15 mm. Obviously a fisheye, but there’s way more this lens allows! Below, a few more “gut check” and other views of the dinosaur hall I took today.

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If you look closely, you can see the low railing that runs around the low platform under the dinosaurs. The lens allows depicting almost a hemisphere! My colleague Matteo Belvedere, who helped me with the pic taking, and I had to hide ourselves well so we wouldn’t be in the photos! In fact, I used the 10 second timer release on the shutter and laid myself flat on the ground next to the platform – which gave Matteo a good laugh ;)

By now, I suspect every last reader of this blog has found out what wonderful image these photographs remind us of. Julius Csontonyi’s wonderful fisheye view of a sauropod. One of the coolest bits I’ve seen in a loooong time. Here‘s one version on the web. Isn’t it great? My images were taken from under the animals, not just next to them, but the oddness of ther perspective is similar.

Now, to round this off, for two shots of the hall from a more conventional viewpoint.

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The latter shows off the huge size of Giraffatitan very well, as well as the hall’s overall classical proportions and architecture. And the great skylight. I makes for great lighting, but I must admit that it can be a challenge to photograph something big, as one invariably ends up photographing it against the light. In this case, shooting a series of different exposures and HDR-merging them helped ;)

 

 

 

 

 

Posted in Dicraeosaurus, Dinopics, Dinosauria, Diplodocus, Giraffatitan, MfN Berlin, photography, Sauropoda, Sauropodomorpha | 10 Comments

AMNH Feb 2015

A short while ago I paid a rather unexpected and sudden visit to the AMNH in New York. American Museum of Natural History – that name stands for one of the greatest museums in the world, and it has much more to offer than just absolutely cool dinosaur galleries. But hey, I’m a dino researcher, so guess where I was headed ;)

Aside from being the first ‘big’ natural history museum I remember visiting at age 10 (I do not count the back-then small and cramped SMNS in Stuttgart; mucho has changed there since, including an additional building much bigger than the old one), the AMNH has been a special place for my own research career. It has, therefore, popped up here and there on this blog a few times. Well, many times. Very many times.

This time, I happened to have a flight back to Germany on a Monday evening, but learned after booking it that I would run out of work in Pennsylvania on Thursday evening. So the question was: change the flight, or make use of the time in NY? As not staying for one Saturday night in the US makes the flights become some $220 more expensive, and as the rescheduling fee was another $210, the decision was simple: stay in NY and try to get into the AMNH collections! Luckily, I know collection manager Carl Mehling pretty well by now, and luckily Carl is a really great guy. I posted a fun photo of him a while ago, and he’s still a big, knowledgeable, kind and funny bear of a man. I emailed him about my predicament of being stuck in NY, and sent along the required official letter requesting access – and got back a rather short email: “Sounds good to me Heinrich. See you soon.” Typical Carl :)

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The AMNH’s  Central Park entrance with Teddy Roosevelt on his horse.

Thus I found myself at the entrance punctually at 9:30 in the morning, ready to fill my camera’s memory card….. One of the things I hoped to achieve during this short visit was going back to the wonderful oviraptor specimens from Mongolia stored at the AMNH. I had photogrammetrized them during my last visit (see here and here), but because I was young an stupid I forgot to use a big scale bar. ‘big’ being important because when you scale the 3D model, the error of where you place your marker on the photo is pretty much the same, absolutely, however big or small your scale bar is. So a longer scale bar means that the error in each marker’s position becomes proportionally less! Thus, the accuracy overall goes up. So this time, I brought bigger scale bars, and was hoping to be able to take a few additional photos of each specimen, with the big scale bars draped around them.

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Well, as those two samples show, I was able to access the specimens. Now I just had to find my old Photoscan project files, put the new photographs with the big scale bars into them, and re-scale. Here we go…… two scale bars of 50 cm each, and Photoscan calculates their errors as very slightly over 0.002 m (i.e., 2 mm!) each.

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I also took photographs of the Edmontonia mount and the Protoceratops mount I digitized last time, for the same purpose. However, as they are encased in glass, I had to lean the scale bars against the glass on one side of the mount, then go around to the other side and take photographs from there. Any distance from the glass means there will be too many reflections. No idea if this will work out; I’ll let you know!

Obviously, I checked out a bunch of other things, too. Some of this I can’t write about right now, but you’ll be let in on the secret in a few months – promise! What I can say is that I spent a lot of time photogrammetrizing some of the many well preserved foot bones of Albertosaurus the AMNH keeps in the collection.

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Bones like those in this drawer. I am always struck by a bit of institutional envy when I enter the AMNH main collections or the big bone room. Proper shelves and cabinets! A fairly flat and level floor! Our bone cellar has its own charm, with the wooden shelves and the brick floor, but for doing actual work in the room the AMNH is two leagues above us.

 

 

Posted in AMNH, Digitizing, Dinopics, Dinosauria, Khaan, Maniraptora, Oviraptorosauridae, photogrammetry, photography, Theropoda, Travels, Tyrannosauridae, Tyrannosaurus | 11 Comments