more Juramuseum & the Kulturgutschutzgesetz

The previous post about the Juramuseum was full of fish, although it did end with a few higher vertebrates. All flattened, though. This time, there’ll be more higher verts, and the spineless stuff will be in 3D! Let’s start with more dinosaurs, theropod dinosaurs to be precise. However,


so please be patient and watch this space next Wednesday 🙂 Also, there is this German tapewormword Kulturgutschutzgesetz lurking at the end of the title. Thus beware!

Juravenator skull

This is a close-up of the skull of Juravenator starki (click to embiggen this and other images). It is an amazing little beast, and I love the teeth. But let me progress to what you likely are really waiting for: the Eichstätt specimen of Archaeopteryx lithographica!

Juravenator skull

Juravenator skull

This specimen is very small, and has an extremely good head, of which I have an extremely bad close-up photo:

Juravenator skull

For the sake of completeness, here’s the counterslab, too.

Juravenator skull

Knowing the Berlin specimen so well I was struck by three things right away: how dark the Eichstätt specimen’s limestone slabs are, how small the animal is, and how little the Juramuseum has done to make it stand out in the exhibit. It is just one of many specimens in a part of the exhibit that deals with birds and flights. There are a bunch of simple push-button experiments that try to explain how wings and feathers work in flight, there’s this display of different feather types:

Juravenator skull

and there are a bunch of models of the in vivo look of extinct dinobirds, too. Including a really huge one:




I didn’t take a pic of the label, thus I have no idea if this is supposed to be a Phorusrhacid or (more likely) Gastornis, and it is impossible for me to tell from the model. I’ve seen skeleton (casts) of terror birds and the Messel monster before, many times, and the always look amazingly big. Still, this model, which for once is not completely drab or exceedingly colorful, makes their size so much more real, especially the huge head and the sturdy feet – way cool!

Other models include Sinosauropteryx prima, Caudipteryx zoui and a Confuziusornis, all of which are also shown as casts. One can quibble about the feathers and colors and all of each of these, but overall I have seen much worse many times. These all do not look freaky.


Same goes for the inevitable model of Archaeopteryx.


Overall, it is a very nice exhibit about flight and volant and non-volant dinosaurs, but after being exposed to the Naturkundemuseum Berlin’s “Federflug” special exhibit it all looked a bit dull and grey. I guess there are two main reasons for this difference. One is that the MfN exhibitions team is just absolutely awesome. They can take anything and give it that noble, serious, quiet look that makes you feel it is special while making you focus on it. A far cry from the oh-so-common lights&sounds attack you experience especially in US museums. Eichstätt has that feel, too, just not at the top-of-the-league quality I am used to from Berlin. The other factor is probably as important, and quite mundane: money! While Berlin is horribly underfunded for a big Western natural history museum, there is always enough funding available to optimize the looks of exhibits. In any case, the Juramuseum Eichstätt is cool as is!

Now, I promised you fans of spineless stuff that there would be 3D spineless stuff. Here you go!


This is, a guess, the standard fossil associated with Southern Germany: an ammonite. In fact, it is a steinkern (literally: stone core), or natural cast of the inside of the shell, and even I with my long-forgotten haphazard training in ammonite taxonomy (I did study at Tübingen!) can tell it belongs into the Persisphinctoidea, by the splitting ribs and the constrictions (one is well visible on the lower right). In fact this is a Lithacoceras aff. ulmensis.  If you have ever collected fossils in the White Jurassic (limestone deposits of the latest Jurassic) of the Swabian Alb mountains you know these small to mid-sized shells only too well. Preservation as natural casts is the norm, and sometimes the suture pattern is pressed into the steinkern (top part of above specimen), too. The sutures is nothing but the negative of the contact area between the outer shell and the partitions between shell chambers. It plays a huge role for taxonomy.

In the Solnhofen Limestone deposition was very slow, and most fossils are therefore flattened, but the trough in which the layered limestone was deposited lay between small reefs. And in these we find 3D preservation, sometimes of incredibly good quality. The specimen above and those below come from a dolomitized reef in the Steinberg mountain near Großmehring, and the dolomitization has ruined the corals so they cannot be determined. The steinkerns, though, as exquisite.




A bunch of steinkerns of marine snails (Purpuroidea gigas, Pleurotomaria and I believe another Purpurodiea). And, below, a couple of Cossmanneas.


An almost-Nautilus! Pseudaganides belongs in a sister group to modern-day nautilids.


Let’s have some clam chowder: Isoarca explicata


Pholadomya sp.


Pinna. They often get quite big. I have one from near Dotternhausen that is some 20 cm long.


Pterocardia corallina. The left one is a steinkern, whereas the right one is preserved with its shell.


Paradiceras aequivalve. A clam that lived in places with stronger currents than the reef-dwellers shown above. Its thick shell anchored it well.

Now, before we get to the brachiopods and corals, there is something I must comment on. Currently, the German government is trying to develop a law to protect (national) cultural heritage. It is called Kulturgutschutzgesetz. That is, at first glance, an excellent idea! The law is supposed to make it much harder to sell art and archaeological artifacts of dubious provenance. Considering how much stuff is being smuggled out of Iraq and Syria and sold on the black market I believe it is high time that we force dealers to provide paperwork to show specimens are legal – period!

However, as is all too often the case, the German government and its entire executive support in the form of federal ministries and federal departments of all kinds makes the same uneducated stupid mistake so many laypeople make: they apparently believe that palaeontology and archaeology are the same discipline! And so the smart people working there actually made the law apply to palaeontological collections and specimens, too. Without, may I add, do the usual and ask palaeontologists to comment on the proposals! OOPS!

The first draft of the law, the second version of which by now has passed the cabinet(!), was so monstrously stupidly written that it actually forbade preparing fossils by defining them as unalterable Nationales Kulturgut (national cultural heritage) while still in the ground – provided they are either scientifically important or worth or more 50.000 €.

A twist I especially like – a particularly idiotic twist, too – is that depending on how you read the law some fossils would become cultural heritage because of scientific importance, which might be determined how? It is left open for debate in many cases. So one could interpret the law to mean that a fossil that was not cultural heritage becomes cultural heritage a posteriori because someone publishes a paper on it. A paper that may be based on data obtained by destruction of the fossils, which now a posteriori would become illegal and punishable by law.

Granted, that requires a pretty weird interpretation of the law, but until the courts decide on such matters you can’t be sure what’s gonna happen. Same for a fossil that, hypothetically, you sell while still in the ground, and that you sell for less than 50.000 €, and that nobody ever publishes on – is it now NOT national cultural heritage? Even if it is another Archaeopteryx? Idiots abound in certain Berlin circles…

A key problem with the law is that it does not do what, for example, Bavarian state law does: distinguish between opera and res. Opera is an opus – an object created by man. Res is a thing. If you define unprepared fossils as natural heritage (treat them as res), and prepared fossils as works of man, and differentiate the protection of the two, you avoid a hell of a lot of problems that you get when you merge the two into one category. An ammonite that has been prepared so it can be used for science, a meteorite that has been cored and thin-sectioned, and so on – these are clearly specimens that must be protected differently from the gazillions of microorganisms making up limestone that you could but nearly never do analyze.

Another issue is the incredible amount of paperwork that natural history collections will face with regards to loans, de-inventorying and other totally normal collection activities.

Oh yeah, and did I mention that you’re supposed to provide documentation of the provenance of cultural heritage specimens? That’s another good idea, but you have to do it retroactively back to 1992!

Yes, you read that correctly: retroactively back to 1992! Bought an ammonite at a fair in 1998? Well, please do contact the dealer-whose-address-you-never-had and ask him for documentation! What the goddamned freakin’ fuck????????? Until our beloved government starts handing out time machines this is utterly impossible! It is also a very unusual shift of the burden of proof: suddenly and retroactively, you need to prove that you own a fossil legally, instead of someone else having to prove that something about it is fishy.

Jeez, I get too worked up about this. I even can’t be sarcastic anymore. Let me get to one more key point and finish this. Why do I mention all this in the context of the Juramuseum? Because one area that the law – even before it has been finalized! – is having a massive impact on is the private collectors’ scene. Particularly, due to the wonderful German federal system creating wide variation between states, particularly to Bavarian private collectors. Bavaria, I do not need to remind you, is the state the Solnhofen Limestone deposits happen to occur in. What’s going on there is rather depressing and scary: private collectors, uncertain about how their fossils will be treated, have started pulling loaned specimens from museums!

This and other links below go to German language articles. These are must-reads for Germans, and all others should spare themselves the misery. So please be glad I am not linking English versions 😉

Now, the Juramuseum is lucky. As opposed to some other museums, notable the famous Bürgermeister Müller Museum in Solnhofen, most of its specimens are not loans, but are owned by the Bavarian state. For example, all he wonderful invertebrates from the Steinberg shown above and below were collected and prepared by one Heinz Haberl. Mr. Haberl started collecting in the quarry in 1972, and has given the many wonderful fossils to the Juramuseum as a gift. They are now owned by Bavaria, and thus not in any danger. They are – and this is a prime example of the importance of private collectors to science in Germany – the means by which scientists were able to time the quarry’s sediments to ca. 151-152 million years before present, i.e. upper Kimmerridgian to lowest Tithonian age, and thus slightly older than the Solnhofen limestone. Without Haberl’s diligent collection and preparation of ammonites, this dating would not have been possible at this accuracy.

This is just one of very many examples of laypeople helping science. There’s millions more. And all that is threatened in the future and also partly in the past (remember 1992?) by a sorry excuse for a draft of a law. Read, if you can bear it, a lawyer’s comments prepared at the request of the Mineralientage München. Admittedly, this is a brief written at the behest of a party with a special interest – but even if one takes that into account, it is still scary.

The German Palaeontological Society has some harsh words for the new proposed law (PDF download). I couldn’t find an English version, and believe me – unless you are German, you really do not with to delve into this any more. If you are German, though, consider contacting your political representatives and giving them an earful. The Swiss and Austrian Palaeontological Societies have joined the German one in the above-linked statement, by the way – they are equally appalled. By the way: Austria managed to write a 7-page law to coply with the EU directive. The German draft is 156 pages long.

So, per angusta ad augusta: let’s see some more beautiful fossils while we still can! Here’s some brachiopods from the Steinberg.

Juralina insignis

Torquirhynchia speciosa

and a sea urchin – a rather blurry picture, just to prove they were there.

The corals of the reef at the Steinberg were all rather ruined by dolomitization. Some of them still look pretty, but for science they are not that useful For one thing, you can’t determine the species.



It speaks volumes about Mr. Haberl and many other collectors that their specimens found their way into public exhibits, either as long-term loans or gifts. And not only the top, most beautiful or most scientifically publishable specimens, but also the more mundane fossils that should be collected and preserved for completeness sake. Science is about being doggonely thorough, not about glitz. And there are very many private collectors out there who understand this, and live by it. The proposed Kulturgutschutzgesetz is a kick into their faces as much as it is one into the face of thousands of scientists. I really hope that the law dies a quick and timely death, so that in about a year I can blog here about the many other museums in the Solnhofen area without having to show you a lot of photos of suddenly bare walls. 😦


Posted in Dinosauria, idiots abound!, rants, sad news, Solnhofen Limestone, spineless stuff (invertebrates), spineless stuff (politicians), Theropoda | 6 Comments

Juramuseum Eichstätt

Everybody knows fossils from the Solnhofen limestones. At least one fossil. This one: the Berlin specimen of Archaeopteryx lithographica.


(from Wikipedia under Creative Commons Attribution-Share Alike 3.0 Unported license)

But the Solnhofen Limestone is about much more than dinobirds, and in fact the entire area is about much more than just the Solnhofen Limestone! And a great place to see a lot of fossils and more is the Juramuseum Eichstätt, which is located in the Willibaldsburg above Eichstätt.

The whole area is incredibly picturesque, with the town of Eichstätt on the Altmühl river itself being a Bavarian Baroque church town, which means plenty of pretty imposing buildings in a wonderful landscape. The Willibaldsburg is a huge castle, the medieval part in its various stages of construction well preserved and with equally well preserved bastions from the 1600’s surrounding it. It offers a stunning view of Eichstätt and the sharp bend in the Altmühl’s course, and houses a very nice Biergarten (no need to translate that term, I guess), a museum that shows archaeological finds (Roman, Celtic, and so on) and palaeoanthropological as well as palaeontological exhibits from ice age times, and the Jura Museum.


The Willibaldsburg as shown on the museum’s tickets.

I recently spent a very short visit there, less than an hour in fact, and with three small children in tow (however, they loved it and didn’t whine!). During that time I managed to take a few photos of some of the more amazing exhibits, so let’s dive into the Jurassic World of Bavaria.

One thing most people don’t realize about the Solnhofen Limestone is that it is a marine deposit, and as such so beautiful, so mysterious… so full of fish. Lemme show you some.




Top to bottom, these are Asthenocormus giganteus with a bit of prey in its stomach,  Sauropsis sp., and Aspidorynchus acutirostris, a gar-like fish. The museum features a number of aquaria, too, trying to show what the Jurassic coral-reef and lagoon dominated landscape looked like, and in one of the them show gars (Lepisosteus oculatus) – not a fish you will see often.

spotted gar

Similarly, the museum has a tank with Limulus polyphemus, which matches very nicely indeed with the fossils:



What’s preserved here is a track of a horseshoe crab that for some reason got into the oxygen-deprived waters at the lagoon bottom, ran around for a bit trying to get out, and succumbed. One of the really rare cases where a trackmaker actually can be found dead at the end of the track. If only most dinosaurs had died that way, too 😉

Some more cool fossils from the Solnhofen Limestone:


fish scales close up


Aspidorynchus acutirostris again, this time in dorsoventral instead of lateral compression.

Enough fish?
Well, you ain’t seen nothing yet! Some of the fish are just incredible 🙂


These look more like fish flattened in a printer’s press yesterday, or prints of color photographs on limestone, than real fossils. But they are oh so very real! Click to zoom in on the images. I hope to go back soon, with time on my hands to get really good photos of the fossils and the labels 🙂


close-up of the above


This Turbomesodon relegans is so amazingly beautiful that I could look at it for hours on end!

not all fish are that exquisitely preserved, but even tiny Leptoleptides sprattiformis are often extremely detailed.




the absolute whopper, though, as the fishes in the special exhibit “the best fishes” (or so) that they added somewhen after my previous visit. Check this out (and excuse the poor photo, I was in a hurry).

The color! THE COLOR!!!!!!

Makes me long for smoked trout with lemon 😉


OK, enough fish already, on to other creatures.


A somewhat pornographic-looking view of a turtle. The museum thoughtfully placed the specimen on top of a mirror, so that we can also see the upper side of the shell.


and a lizard, which under UV light shows soft tissues very nicely. The posterior tail has been regenerated.


and finally, a dinosaur: Juravenator starki!


so, although….


and although this post hasn’t arrived at Plateosaurus, I still think this is a good opportunity for a break. More soon – I am not even half done with my very hasty tour of the wonderful Juramuseum!

Posted in "fish", Aquariums, Dinopics, Dinosauria, ichnofossil, Lacertilia, lower vertebrates, Solnhofen Limestone, Theropoda | 7 Comments

Tristan 3D printing

So, you’ve all been faithfully following this place in the hope of catching an early glimpse of the greatest T. rex to ever grace a European museum? A preview that shows a tiny bit of the majestic bones? Or maybe a few terse comments on the bones, their preservation or the number of them preserved? Maybe you’ve seen photos on Facebook of some 3D prints of individual skull bones of Tristan?

Well, today I can do a bit better than that. This is exactly the theropod you are looking for!


Well OK, this is a 1:10 scale selective laser sintering copy of the photogrammetric files I made of all the skull bones, with a handful of CT-based files thrown in: the missing bones that were added as hand-crafted models and the bones that do far didn’t work out as photogrammetry. There’s very little CT in this, because the skull is quite complete, and because I’ve gotten quite good at photogrammetry of even the most insidious objects. I’ve had some important help with the latter, too – from Uwe Moldrzyk, the head of the MfN’s exhibition team found out about cylcododecane spray for me (it makes a non-glossy cover and evaporated off, slowly enough for photogrammetry), and especially from Matteo Belevedere, who spent many a day shooting the hell outta Tristan with me. Many thanks to you two! 🙂


In fact, the real skull is even better than this 3D print, because there are two teeth missing in the model that are present as fossils, but weren’t attached to the maxilla when I took the photos that led to this model. So it is now time to get all excited!

I have posted and will post more about the difficulties of photogrammetrizing such difficult objects – black, shiny, and with complex shapes, but obviously there is much more to say about Tristan than just the technical aspects of scanning. How did the skull bones fit together (and how did I mount them)? How complete is the skull, and the postcranium, and in what state are the individual bones? Can’t say much today, but I can promise that my colleague Daniela Schwarz will be very busy producing an anatomical description, and my colleague Oliver Hampe is taking a very close look at a bunch of pathologies.

For now, I’ll end this teaser with a photo that is part of my digitizing effort, in which you can see nicely how the cyclododecan spray helps creating photogrammetrizable surface properties.


Posted in Digitizing, Dinopics, Dinosaur models, Dinosauria, MfN Berlin, photogrammetry, Theropoda, Tristan, Tyrannosauridae, Tyrannosaurus | 5 Comments

Photogrammetry tutorial add-on: The consequences of optimizing a sparse point cloud

If you build a photogrammetric model following the workflow I suggest in this post, one of the steps is optimizing the sparse point cloud (tie point cloud) via gradual selection and deletion of points. Here’s why that matters.

Below you see a screenshot of a model of a sauropod bone. The sparse point cloud is shown as produced in-program by aligning the 190 images (one image doesn’t count, as it shows the label, and accordingly wasn’t aligned).


(click to enlarge)

Note that there are close to 200,000 tie points connecting the images.
Now, I used Gradual Selection to select lower-confidence tie points, and deleted them. After optimizing the alignment the point cloud looks like this:

(click to enlarge)

In this case, I deleted nearly 50% of the tie points, which are down to just over 100,000. Now compare the errors shown in the screenshots! The very same two scale bars of 25 cm length that differed by 0.000557 m (you need to add the two errors to get the total discrepancy), slightly over half a millimeter, now differ by only 0.00032 m, i.e. 57% of the previous error!

Ok, admittedly this almost-doubling of accuracy doesn’t make much difference in this case, but imagine you’re modelling a specimen with fine details. Sauropod vertebrae with their fine laminae come to mind. Decreasing the error by half means that your chances of getting the fine details modelled without too much error and messy edges doubles!

Let me end this with a view of the derived mesh. Ain’t sauropod bones beautiful? (oh, and this is medium density only! The mesh could be much better resolved).


(click to enlarge)

Posted in Dinosauria, How to, photogrammetry, Sauropoda, Sauropodomorpha, Tendaguru | 8 Comments

Photogrammetry tutorial 11: How to handle a project in Agisoft Photoscan

Over the course of the last year I have helped a bunch of people with their photogrammetry projects. Usually, they needed help with the photography – understanding how the program works, so that they take the right amounts of photographs in the right places. Or with camera settings. Or with the set-up for easy and quick models that show the underside of a specimen, too.

Recently, however, I realized that a lot of people also have problems making the most out of their photographs in their photogrammetry software, most of them using Agisoft‘s really easy to use Photoscan. They’d run through the “Workflow” menu of Photoscan and end up with model that were OK or so-so, based on photographs that should deliver really excellent models.

Below, therefore, I’ll describe how I use Photoscan to create high-quality models. Models like the one in this screenshot:

Screenshot from Photoscan

(click for larger size. note that I decreased model size from ca. 45 million polygons to 10 million)

PLEASE NOTE: this post assumes that you are using Photoscan Pro, not the standard version! Some steps described below are not available in the Standard Version!

Continue reading

Posted in Conferences, digiS, DigitalSpecimen 2014, Digitizing, How to, MfN Berlin, photogrammetry | 21 Comments

I thought I knew what ACAB means

Walking from the msueum to my car I recently happened upon a trashcan in a public park. It had some grafitti on it, and lots of stickers. One read ACAB, which normally means All Cops Are Bastards. Not a sentiment I agree with. But coming closer I could read the smaller-print full text…..




What the hell??????

All curators are bastards?

First of all, nearly all curators I ever met are really cool people. The rest may not be the nicest people in the world, and I may not want to be friends with some of them, but I have never met a curator whom I would call names. Not one.

Secondly, the generalization has me stumped: all? What insane idiot is so weirdly twisted that s/he believes that an entire group of people, and a large one at that, are all mean – and then curators?

Lastly, who in their semi-right minds would go to the bother of actually having stickers printed with this slogan?


Colour me totally confused…..

Posted in WTF? | 4 Comments

3D digitizing black, shiny bones


I know you all wait for news on Tristan, the Tyrannosaurus rex that will soon grace the exhibition spaces of the Museum für Naturkunde Berlin. I know, and I understand, and I feel with you. Really, I do. But…. see above: this post has nothing whatsoever to do with Tristan. Rather, it deals with a hypothetical. Let’s say that you need to digitize a large number of fossils, fossils that are of a very dark colour and very shiny, and that have a complex surface shape with many holes and deep depressions. Fossils like…. the skull bones of a very large theropod from a sediment that is rich in organic materials. If – and this is entirely hypothetical – if you wish to mount such a skull so that museum visitors can see it up close, and so that researchers can have good and easy access, then you can’t mount the real skull with the rest of the skeleton. It would end up several meters above the heads of visitors, laypeople and researchers alike. So what, then, do you mount in front of cervical 1 (atlas) of the skeleton? A cast? That means making moulds of all the oh-so-fragile skull bones, and if in any way possible the damage that may (and often does) associate with casting is something a curator will wish to avoid. Quite obviously, you can CT scan the bones, and have them rapid protyped. But if the bones are a bit bigger – say, like those of a megapredator of Late Cretaceous times – then 0.25 mm slices, the best really good large medical CTs can do, just do not cut it. One point per 0.25 mm translates to 4 dpmm (dots per millimeter), i.e. 10.16 dpi. Your screen on which you are reading this text has 72 dpi. So, we need a data capture method that has a much better resolution. Laser scanning – requires a really nice laser scanner. No money no laser scanner. Structured light scanning – requires a really nice structured light scanner. No money…. you get the drift.

Photogrammetry to the rescue!

Yeah, I know, this is getting kinda old. But then, photogrammetry offers really high resolution 3D digitizing at relatively low cost, with relatively little effort. Just perfect for Tristan the megapredator skull bones.

So, photogrammetry…. if you are using a regular lens, say an 18-135 mm Canon EF-S lens, you can easily get files with a resolution of 1/20th of a millimeter. That’s roughly 500 dpi. And once you have such files, bone for bone can be laser sintered. Those of you who talked to me at SVP 2014 in Berlin probably remember my poor imitation of a beach watch salesman, pulling some bone replicas out of my jacket pockets. Those were laser sintered, by the very helpful and capable 3D Lab of Technical University Berlin. The folks there, especially Joachim Weinhold and Ben Jastram, have been a joy to work with, and now we take our cooperation a step further, with the skull of Tristan a large dinosaur skull. The layer thickness if 0.1 mm, or ca. 260 dpi. THAT’s cool, because it means that at half of arm’s length you can’t see the difference between original and print, and if the prints are properly coloured you can’t even see the difference at a much shorter distance.

printed bones

3D laser sintered bones of the stegosaurian dinosaur absolute king bad-ass of the Jurassic of Africa, Kentrosaurus aethiopicus Hennig 1915, at various degrees of scaling. The big femur at the bottom with the hole in it is hollow, with a wall thickness of less than 1/2 mm (< 1/50th of an inch for my ex-British-colonial friends). The walls are so thin they actually flex when pressed, but the models are tough enough to toss (hard) at anything without taking damage!

But before any printing there is digitizing and data editing. And that’s where the problems begin with our entirely hypothetical large theropod skull….. black, shiny bones, is turns out, aren’t giving anything up easily!

In the field our hypothetical black bone often looks like fossil charcoal. I was only able to distinguish wood from bone in the field this summer because there is a layer of white matter around bones, but not around wood, and because a guy who excavated a dinosaur at that site actually told me which is which. Let me show you:

bone in the field

Fossil bone eroding out of a hillside at a dig site in Montana. Estwing hammer for scale – you ain’t no true geologist unless you own and use(!) a regular Estwing rock pick (pointed tip) – and no, rock picks with a chisel edge do not count, they are good only for archaeologists and other mud scrapers 😉 Both leather covered and blue grips are acceptable, and the grey colouring or the naked metal looks are interchangable, too. Just don’t show up with an ACE-brand hammer. Just……. don’t……. EVER!

OK, so the bones are black, and they are shiny. For photogrammetry that normally means  that any light on the bones will cause strong reflections, and that I need to expose the photographs so that the black bone is not uniform black, but actually has colour variation in the images. Looooong exposures, as a consequence, because I can’t just use a strong flash (remember: reflections!), which again means using a tripod. With a good image stabiliser I can handhold a 20th of a second, but not hundreds of times in a row. Sometimes.
The next problem is that of lighting – if I shine enough light on the bone to get rid of the usual shadows on the underside of projections and the outside rim, and light up deep recesses sufficiently, I end up creating more highlight…… impasse!
There is obviously no way around putting a lot of light on the specimen. Necessarily lens-parallel, as anything else would lead to deep shadows in recesses. This means a ring light or ring flash. And lots of reflections. Therefore, I need to take so many photos that either there are enough images for each spot on the bone that happen to have no reflection, or that there are enough photos with the same brightness of reflection in it. In the former case, the software can build the model from the good bits, in the latter I’ll end up with a nearly white model – but I will get a model!
Here’s the set-up I am using:


The turntable is huge, and in fact that is a nice thing I should have realized long ago: if the turntable is much bigger than a specimen, the photos will show practically no background that doesn’t turn with the specimen. Also note how I am using styrofoam to make the background all-white. Photoscan is so incredibly good at finding points (real or fake) even on totally out-of-focus parts of an image that a structured background that doesn’t rotate with the specimen can really mess up the alignment.

So, with this setup I take a few photos from a steep angle (as in the photo above), then I bring the camera down ot a shallow angle and take many photos – one every 5° of rotation or so. And then I bring the camera down all the way, so that it looks perfectly sideways at the specimen, and again take very many photos. If necessary, I add more rings of images, so that the part of the specimen that is currently up is well-covered. Notice that there are scale bars on the turntable – obviously, I make sure that they can be seen in many images.

Then, I take the specimen off the turntable and completely exchange the cover. A blue trash bag that covers the cushioning material serves well. Or a different type of cushioning material. I also take the scale bars off. Now, I put the specimen down again, but upside down. And then I repeat the above photo sequence. Here’s how the alignment looks with one side done (blue rectangles represent photos), and the other side just started (red rectangles).

alignment example

In theory you can now toss all images into one chunk. There are no features on the two backgrounds for the two sets of images that connect them – after all I exchanged the entire background. That’s why I don’t use scale bars for the second round: they might give features that match between set 1 and set 2. So if all works out I get a very nice alignment of all images in one go.

In reality, this worked very well for many of the ca. 30 bones I have worked on during the last week. The more photos I took, however, the more problems surfaced. For one thing, Photoscan kept being unable to align the vast majority of images. In the example above, only 155 out of 828 photos were initially aligned. I was able to manually align the rest (i.e., select them in the image list and ask Photoscan to align them without running point detection and matching first), but I ended up with several groups of images aligned well within the groups, but not between the groups.

So now I decided to help Photoscan along. The obvious big issue was that the bone in question has a thin margin, it is essentially a flat piece. Thus, the overlap between the two image sets is a small area with a high curvature, and thus prone to produce photos with lots of reflections and few features. I therefore manually aligned all images of one side – 514 in all worked out, and some 12 or so didn’t. Now, I optimized that alignment by using Gradual Selection (setting 10 for Reconstruction Uncertainty and setting 1 for Reprojection error). This led to a very nice sparse point cloud, less than 10% of the initially calculated one, but already a lot of bone detail was recognizable. It also dumped a few photos due to lack of points, so I ended up with 495 still aligned.

Now I chose those images of the second set that were shot with the camera level with the edge of the bone, and manually aligned them one by one. This worked quite well (see photo above; it’s the red images that got aligned to the whole set of blue ones), because now Photoscan had an excellent tie point set with a nice bone rim available that it could match the points on the new photo to. And once the first circle of photos from the second set was aligned, I could align all the rest of the second set to the sparse cloud, as this now contained also all the tie points that connected the second set’s first circle between themselves, including features on the background (i.e. on the turntable and the cushioning material).

During this process, the tie point cloud went from a very nice recognizable bone to ape-shit. In order to be able to recognize if a newly aligned group was totally out of whack I intermittently ran Gradual Selection again – and the sparse cloud always popped back to a nice one. With only one or two images tossed out, this repetitive optimization kept new alignments tight and nice. After a while, I began to see not only the medial side of the bone, corresponding to the first set of images, but also the lateral side, corresponding to the second set of images.

I ended up with 769 photos aligned, nice and tight! Not too shabby, given the original number of 155, and the total chaos that erupted when I simply asked Photoscan to align all non-aligned images willy-nilly. The time I spent sorting which images to align at what time, and to optimize the point cloud in between, turned chaos into a solid alignment.

alignment example

This is the final result, with the last few aligned images in red. As you can see from the small peek you get at the tie point cloud, the bone is not all over, but concise. Now I look forward to the dense cloud, which will be computed in a day or two…. *sigh* The punishment for a large number of high-res images.

The take-home lesson

If you digitize dark, glossy stuff,

  • take very many photos
  • make sure that you use lens-parallel light
  • make sure that you take two circles of photos of the connecting area between the various specimen positions that are near-identical, to maximize your chance of the sets aligning
  • be willing to invest a lot of time into manually helping the alignment along
  • intermittently, use sparse point cloud optimization to keep the alignment on track
  • do not give up too early!

To end this post, here’s a view of the alignment from a different angle, which shows the tie point cloud a bit better.
alignment example
Oh, and please remember:


Posted in 3D modeling, Conferences, Digitizing, Dinosaur models, Dinosauria, Kentrosaurus, MfN Berlin, Ornithischa, Stegosauria, SVP 2014, Theropoda, Tristan, Tyrannosauridae, Tyrannosaurus | 15 Comments