Direct PDF download link for Mallison and Wings 2014

I keep getting emails requesting a PDF of the paper I wrote with Oliver Wings (link to blog post) on how to do photography for photogrammetry. That’s because the download link on the journal’s web page of the article is so well hidden that most people miss it.

Well, here it is!

Can you find it on the web page? It’s where it says “JPT No12” 😉

Posted in Open Access publishing, photogrammetry | 3 Comments

Speeding up Photoscan’s dense cloud generation

A while ago, Agisoft added GPU support to its wonderful photogrammetry program Photoscan. Calculation speed for the various processes that can make use of it went up a lot. Great!

However, many users complained that generation of the dense clouds suddenly took much longer in the new version. I’ve seen the same thing, and how posted a few images of ridiculously long (and ever increasing) projected calculation times to Facebook. Here’s one:

Given that this was running on my new PC, 14 hours plus was a ridiculous amount of time!

Luckily, Photoscan is getting a new update very soon! Version 1.4.0 is out as a pre-release, and the comments and questions thread on the Agisoft forum site is quite active. People are reporting bugs and asking all kinds of questions – and some of them are not really 1.4.0-specific! And in one comment, the slooo.oo.oooo…….oooowww dense cloud generation popped up, too – and was answered!

“In the version 1.3.0 the number of pairs for the depth filtering has a strict threshold: 50 pairs, in the later updates the limit has been removed.”


Well, the user asked the next logical question:

“It’s there a way to adjust the limit on the newer versions?”

and got this anser:

“You can use the following line input to the Console pane to limit the number of pairs:

Code:'main/depth_filtering_limit', N)

Here instead of N you need to input some integer value, for example, 80. Hopefully, it would reduce the processing time considerably without any visible issues. I do not recommend to go under 50-60 pairs, though.
To return the value to the default (unlimited) value, please use “-1”:

Code: [Select]'main/depth_filtering_limit', -1)

So, there you are:

open the console window via the View –> Panes menu, and enter'main/depth_filtering_limit', N)

Exchange the N for a suitable number and press RETURN – I have been using 80 for N and my dinosaur bones look good!
Unless you make a typo, you’ll simply see an empty line and a new prompt. GO run your dense cloud now 🙂

In my tests, calculation time dropped dramatically, and I saw no ill effects on the dense cloud.
🙂 Are you now happy? I sure am…..

Posted in Digitizing, photogrammetry | 2 Comments

EAVP 2016 at Haarlem’s Teylers Museum (2)

In the first post of this series I gave a short introduction to the town of Haarlem (NL), because although it is not very dinosaurian or otherwise palaeontological, and thus should not get a post of its own, it does play an important role for the experience of visiting Teylers Museum. This post I’ll show you the museum building inside and out, and tell you a bit of its history. In the first post, the museum’s front showed up already, and now let’s start this post with a closer look at it.

Quite a grandiose facade, and (to be perfectly honest) a bit overdone in my opinion. Part of that is the lighting, but even in daytime it looks rather like someone planned the entrance to a huge palace, then had to downsize it to 50% size and cut the wings due to monetary constraints, but kept the design.

To the right of that huge entrance door there is a sign – now outdated – giving the opening hours. The summer hours are nothing spectacular. Off the top of my head (I am an idiot and did not take a picture),  the museum used to be open from 10 a.m. to 6 p.m. or so. Things differed in winter. In October and March it was open 10 to 5, in November and February from 10:30 to 4:30, and in December and January it was open from 11 to 4. For a very simple reason: there was no artificial light in the building! Once it started to get dark outside, the museum interior went dark as well.

Today, things have changed a bit, mostly with the addition of a new wing with modern comforts, but also with the installation of emergency lights in the old rooms, plus a few additional lights. Still, in the late afternoon in winter you do not stand much of a chance of seeing the fossil halls too well.

Which brings us to the most important point, the thing that makes Teylers Museum so special: it hasn’t changed (much) for over 100 years! It is not only a museum of art, palaeontology, scientific instruments and many other things, it is also a museum of museums! In fact, it preserves a state of museum exhibit design from long ago so well that it managed to get audited when the museum foundation applied for World Heritage status. Now, museums are explicitly excluded, they can never be world heritage – and still Teylers Museum almost got in! Not as a museum of art, scientific instruments etc., but as a museum from ca. 1890! Let me show you…..

First, here’s a bit of history about the museum. It was established in 1778. A rich cloth merchant and banker named Pieter Teyler decided that his money should be used to do good after his death. Thus, he bequeathed his fortune to the city for the creation of foundations for the advancement of art, religion and science. Two foundations were established, one theological and one for all the rest, so to speak. Lumping poetry and physics pretty much fits the age, though, when researchers were often gentleman scientists interested in all of nature.

The first directors of the foundation of science decided to do what Pieter Teyler really had not wanted: they established a museum in his name. To be fair, however, it was supposed to be a study center that offered access to collections and library under one roof, while also serving for educational purposes. Pretty close the today’s concept of a research museum in the vein of AHMN and MfN Berlin, I must say.

Initially, the museum consisted of Teyler’s house. A pretty unassuming place, with a regular door with a small flap at eye level. Visitors had to apply for admission, and when thy got to the museum they had to hand their recommendation letters through that flap and then wait…… and wait…… until, if they were lucky, the door would open.

Front door of Teylers Fundatiehuis, Haarlem
The old entrance. Teylers Museum, Haarlem, the Netherlands [CC BY-SA 3.0 nl (, via Wikimedia Commons

I won’t try to detail the museum’s history here – in fact, a lot of info can be found on its wikipedia page. Suffice to say here that collections sprouted up based on the research interest of the curators – whoever happened to be curator collected what happened to interest him. Thus, the museum ended up with an eclectic collection: fossils, minerals, scientific instruments, models of windmills, coins, paintings, whatnot. And obviously, the museum quickly became too small. A large expansion was constructed, and the architecture is rather impressive (although partly overdone). The entrance rotunda sets the tone, with lots of pillars and columns and marble and statues and reliefs and a gold-painted ceiling – even more opulent than the outside.

entrance rotunda

entrance rotunda

That entrance hall is really an amazing sight! It is not really huge, as you can see in the picture below, which has people for scale. But it is also not cramped with some 10 to 20 people in it (except when they are retirees – 3 of them make every place an obstacle course). It is opulent, a marvelous display of craftsmanship, a masterpiece of light and shadows! And – evidently owed to the constraints imposed by neighboring buildings, but you won’t notice that when inside – it is highly asymmetrical! The main axis takes a quite significant turn inside, but it doesn’t feel that way!

See, the rosetta’s dark grey arrow points at the next hall, Fossil Hall I – but the entrance lines up with the red marble arrow down left! However, unless you stand still and deliberately check angles, you will be distracted by the skylight and the exquisite detail throughout the room. And not just here: Throughout the museum, the decoration detail is amazing! Almost everything is carved out of wood, to the tiniest detail! The design varies, but each and very room is decorated to the fare-thee-well, to the point where you can spend an entire visit ignoring the exhibition and focusing on the rooms alone.

Yes, wood. Not marble. Wood!

OK, back to the tour…… From the entrance rotunda, one can either access the museum shop in a modern extension, or go straight into the first of the two fossil halls. Fossils…… yeah, let’s go there 🙂





ah, no, sorry!

Need to point this out again: this is carved wood! WOOD!!!!!!

OK, now for Fossil Hall I, here seen from the “back”, through the door of the hall behind it:

This is the first of two fossil halls, and although it is a small room, what a wonderful hodge-podge of everything one can find in Europe does it contain! Right when you walk in you have to walk around a large plesiosaur mounted as if it was a coffee table – smack in the middle of the room and rather low down. Only a glass cover makes it high enough that most people avoid bumping into it, it seems. If you turn to your left to walk around it, you face this cave bear:

It just sits there, unprotected by any glass or whatever, a reminder of the old times when museum visitors were (at least expected to) behave with respect and decorum. Although…… in Bonn, the Goldfuß Museum has a copy of the old visiting rules on show, and they include such gems as “sabres must be placed in the bin at the entrance” and “unruly behaviour and noise are strictly forbidden.” So much for “decorum”.

A characteristic of Teylers Museum very endearing to me is the lack of artificial light throughout this part of the museum. Used to spotlights picking out the key specimens (or parts) of exhibits and all the rest in the (semi-)dark (with only few, usually historical museum buildings defying this rule), I must say it is refreshing to come into a room where I am not subconsciously told where to look – and where not – by some designer’s concept of illumination! Specimens’ placement is dictated by construction necessities – walls for hanging specimens,  doors for not placing them, windows to give light as well as possible. This makes for a very calm and neutral atmosphere in the rooms.

Combined with the exquisite detail of just about everything in the room (note the metal grates covering the heating pipes in the floor!), the lack of electric lights can really make you feel like a ca. 1890’s visitor!  It has the effect of making all exhibits pieces somewhat equally weighted, a stark contrast to the weighing modern lighting brings to exhibits.
The first fossil hall is followed by – well, duh! – the second fossil hall………

Uh, no – sorry! Need to come back to the entrance rotunda once more, because it is so awesome:

OK, now that I have calmed down, let’s get back on track for the Tweede Fossielenzaal (God, I LOVE Dutch – to me, as a native German, Dutch will always sound and read like some sort of semi-comical baby German [blush] I guess the same is true vice versa!).

a long table with glass cover and cabinets below down the middle, and large glass-and-drawers cabinets set perpendicularly between windows – how much more gentleman-scientist can you get?

and check out the floors, the metal grates covering the space for pipes…… and the decor of the cabinets, the glass dome covers for the mineral specimens……. The first time I came into this room I noticed a sign pointing out an important whale skull specimen Cuvier himself worked on. On that glass table you can see in the last picture. But where – WHERE???? was the specimen?

Oh, there! ON the floor below the table! 🙂 The floor!

The entire place is cramped, cluttered, there is barely any order to the placement of specimens. And there are stories upon stories about the place, the specimens, the researchers…… the most famous of which is certainly (and obviously) the one about John Ostrom and the Archaeopteryx. A story that is wonderfully told here, so I won’t repeat it here. Go read it! It is a much better and more informative read than my ramblings.

After the second fossil hall, there is the hall of scientific instruments. There is way too much to tell about it and its content, so just go and see it all for yourself! There used to be a lot of info on the museum’s webpage, but they have revamped it into one of those annoying tablet-conformal abominations, and I refuse to peruse it. Thus, I can’t tell you if all the detailed info on the various apparatus is still there.

After the instrument hall, you pass a tiny cubicle on the left that has magician’s tools from 200 years ago and the entrance to the numismatic hall, and then you finally get into the inner sanctum: the oval room!

It is a multipurpose room, exhibiting scientific tools and models of windmills and minerals and lots of other things on the ground floor, and housing part of the library and granting access to the rest of it on the mezzanine level (sadly closed to visitors these days). And the room is a sight worth seeing in itself: with its big windows, the slanting floor (it feels a bit like a ship’s cabin), the exquisite woodwork! With all the warm wood and its modest size, it is a cozy room, but at the same time it has a certain air of grandeur. And it has that grand white-and-windows ceiling that makes the ceiling shine like the sun 🙂

and on that high note, I will end this post. There are plenty more rooms, but I actually won’t mention the halls dedicated to art (Dutch masters, mostly), nor the modern annex. The oval hall is the pinnacle of museum architecture from 150 years ago, it is the fitting end to this description of the museum building. Next up will be a rather haphazard overview of some of the exhibits, before (finally) EAVP 2016 is on.

Posted in FUN!!!, historical buildings etc., history of science, Mammalia, non-palaeo, raves, Travels | 3 Comments

Giraffatitan in all its 3D digital glory (was Digitizing entire dinosaurs 2 (digiS 2016))

Quite a while ago I mentioned that for fiscal year 2016 I again received funding from the Berlin digiS program. Whereas 2015 saw Bone Cellar material digitized, the linked post shows one of the the first results of the 2016 effort, which concerned the mounted skeletons in the MfN Berlin. And obviously, the elephant in the room – erhm, the biggest sauropod in the room! – is Giraffatitan!

The aim of the digiS-funded program was to obtain high-resolution 3D models of the mounts’ bones, not just of each bone individually, but also of their spatial relation. Which allows creation of a high-resolution complete model of each mount as it exists in the exhibition, but also allows for correction of the virtual mounts. Real mounts are suboptimal, because they need to contain armatures to hold the bones, and these get in the way of a perfect mount. And they may have errors simply because of human error, or because of deformed fossils, and whatnot.

Initially, as shown for the Kentrosaurus mount in the post linked above, I had planned to create overview models at low resolution, as well as detailed models of individual bones, or small groups of bones. The latter were then to be inserted into the overview models, aligned perfectly, and exported again. Thus, they would be aligned perfectly with each other, but there would be no need to load them all at the same time. That’s an important point, because 3D data gets awefully big awfully quickly, and that means computer crashes. Obviously, one can always downscale data, but with an animal that has some 300 bones and each bone resolved to only ca. 1 mm, that’s still talking gigabytes of data.

In the end, things partly worked this way, and partly worked differently. Here’s how things went down with Giraffatitan!

Yep, that’s the entire sauropod group in ONE model! This is the sparse point cloud, i.e.: the points used to align the images. Each small white point is one camera position. In preview quality there are a few more points, and Giraffatitan looks like this:

Not too shabby, I say!
Now for a high resolution…..

Thank you very much, this will do!
In fact, it does extremely well, as can be seen in a closer view! This model, which as an entirety shows all the sauropod mounts good enough for “overview quality” shows individual bones at a sufficient resolution to serve as a “detail” model! Photogrammetry has come a long way since the day I planned this project 🙂

What you see above is really three integrated data sets, the biggest of which is again a lumping of several sub-sets:

- overview images that show the entire mount
- close-up shots of the ribcage, shoulder girdle and hips, 
  which are in fact
     close-up sets of
             - the shoulder girdle
             - the anterior ribs
             - the medial ribs
             - the posterior ribs
             - the ventral sides of the vertebrae
             - the dorsal sides of the vertebrae
             - the hip
             - the tail base
- overview images of the entire animal and the neck, shoulder girdle and back taken from a hydraulic lift.

In fact, when we took the photos we sub-divided them even more, although it proved to be difficult to stay consistent when working high up on a ladder in a sauropod ribcage. Especially because the ladder couldn’t be placed on the ground normally, but had to be set on hard foam plates to cushion it, as the special floor cover under the sauropods is easily damaged. So it all felt a bit like a high wire act, surrounded by fragile and irreplaceable fossils *gulp*

inside the ribcage

Here’s a shot of me sticking my camera up Giraffatitan‘s butt [the things we do for science *sigh* – if this was a life animal I might have gotten my face full of dung or egg] that shows the foam pads nicely.

ladder on stupid foam mats

We did two shots the first time around. One during the day, with natural light (you can see the shadows under the feet of the skeleton), during which my partner in crime Matteo Belvedere and I took turns.

Matteo inside the ribcage

Photographing the inside of the rib cage is a special challenge, as it is hard to put the camera on a tripod (which had worked well before for the overview images of Dicraeosaurus– images to come). First of all, you need one hell of a big tripod, then it has to be set on foam mats, too, and the ribs and the lamps in the floor and the feet and the hips… make it hard to put the tripod in all the locations you need it. Also, while a tripod allows long exposures, so that having sufficient light is not an issue, it doesn’t help with getting the recesses, nooks and crannies of the skeleton light properly. And dark recesses lead to holes in photogrammetric models, and that is the last thing we wanted. Thus, as I always do if I can, we used a ring light (a ring flash also does the job), as it gives lens-parallel light. This means that the images have no shadows on them, and that recesses are well lit. Personally, I prefer a LED ring light to a proper flash (but some of my colleagues vehemently argue for a proper flash), because it is not that heavy, and gives out a constant light. This makes it easier to shoot rapidly and without worrying about the exposure, as I can can use the auto-exposure mode of my camera. The drawback is that the amount of light it gives out is fairly low, so that I need to get close to the object I photograph. Which isn’t a problem when I want to create a high-resolution model, as I need to get close anyways to achieve sufficient resolution.

Still, this means hand-holding a hefty DSLR with lens and the ring light at arm’s length for hours at a time, which can be quite exhausting. Doesn’t take the fun out of the project, though.


Now, it wasn’t me alone doing the shoot, so Matteo and I could spell each other. But that doesn’t mean that one of us could laze around half the time as he pleased. The rather rickety ladder support meant that most of the “off” time was spent like this:

Booooring! You get to spend hours at a time watching your colleague’s butt sway around a dinosaur 😀

The last photo shows the second, night-time data capture session. You can see that even the dinky LED ringlight gives quite a splash of light on the skeleton! This shot was at the height of a summer heat wave in Germany, and despite only wearing shorts and T I was sweating profusely, to the point where holding the camera was a challenge because my hands were so slippery. Also, I had to wipe my brow all the time to keep sweat from trickling down into my eyes. High time the Museum für Naturkunde gets air conditioning – not just for comfort, but to protect the exhibit specimens!

So, did it all work out smoothly? Far from it! This project was a major pain in the rear end, simply because of the complexity of the capture process and the humongous amount of raw data we had to handle. Also, the mounted bones proved a bigger challenge in many respects that I had hoped. For example, many bones reconstructed badly because they are partly hidden from view by other bones. We can see a lot of their surfaces that a photogrammetric model cannot capture too well, because we can peer into deep recesses, but it is difficult or even impossible to get several photos of the surfaces in the recess at not-too-shallow angles. Think, for example, of the acetabulum and the femur head in it. We can easily look into the gap, but despite trying really hard my models would only show about half of the femur head surface in acceptable quality.

Additionally, for really high resolution models it is important to capture the surface at high resolution, which means taking a lot of images with small offsets and angles between camera positions. Now comes another bone, one that articulates with the one I am  digitizing, and hides a big chunk of it – say, worth a 20° angle.  My chance of photos of one part and those on the other on the other side of the obnoxious interfering bone aligning well is not too great. In fact, this turned out to be a major issue! Obviously, I can just digitize the two bones together – but then we are talking project with some 2000 to 3000 images in one model! EEK!!!! Calculation times of several hundreds of hours are a major drain, but if that’s for uncertain gain…….. I tried a different, much faster software, Reality Capture (from which is the Giraffatitan model above), but it has its ow issues. Among them it demands very small angles between images, which makes the issue of one bone hiding part of another even more of a problem.

And as if that wasn’t enough to deal with, the mounted bones all have been treated lavishly with a wide variety of glues and lacquers (remember, most were originally prepared a century ago!), making them quite shiny. Baaaaad for photogrammery! And their upper sides are all rather dusty, which – like shininess – induces a color change depending on te angle you photograph them. UGH!

Thus, a lot of models failed or at least didn’t work as well as I had hoped. With the new, GPU-supporting version of Agisoft Photoscan out now, and the MfN IT wizard having re-shuffled a lot of the CPU and RAM and GPU at his disposal, I will run a bunch of model again and expect to get good results. But…. it’s been a bother.

Anyways, overall this was and (contra planning) still is a fun project, made possible (I should mention again) not by some palaeontology-related grant, or by the MfN’s (already overstretched) budget, but by the state of Berlin funding digitizing initiatives with the explicit aim of making assets accessible. So do expect our scans to go online at some time, hopefully soon!

Posted in 3D modeling, digiS, Digitizing, Dinopics, Dinosaur models, Dinosauria, FUN!!!, Giraffatitan, MfN Berlin, photogrammetry, Sauropoda, Sauropodomorpha, Tendaguru | 4 Comments

EAVP 2016 at Haarlem’s Teylers Museum (1)

After all the recent photogrammetry posts it is high time to get away from “stuff that somehow has to do with dinosaurs a little bit” and finally write again about dinosaurs themselves. Which is why I now will write about something that has nothing much to do with dinosaurs at all: 2016’s EAVP (European Association of Vertebrate Palaeontologists) conference, which took place in the wonderful Teylers Museum in the wonderful town of Haarlem (wikipedia). But fear not – dinosaurs will feature in a post later this week 😉

The trip to EAVP 2016 wasn’t my first visit to Haarlem. I went there a few years ago when I applied for a job at Teylers Museum. A job I didn’t get, in the end. Back then I was quite disappointed, because it would have been a very cool job to do in some regards – you’ll see why, when I get around to describing the museum. On the other hand, it would have meant some pretty radical changes to my family’s plans and a pay cut. In the end, I guess I would have been happy there, but I am also happy where I am now.

When I went to Haarlem the first time, for the job interview, it was February, and grey cold weather. I arrived in the early evening, by train, and walked to my hotel – and already I had fallen in love with the city! It is very much cliché: canals, small brick houses built wall-to-wall, cobblestone roads in the city center. And a windmill! Which I promptly photographed the next morning.


Here are some more views of the town, both during the day and in the evening. I am posting them here, although they have no relevance whatsoever to dinosaurs or palaeontology, because the town has quite a relevance for the way a visitor will experience Teylers Museum: the museum is special due to its history and the state it is preserved in (intentional choice of words here), and it fits into the town in a way other museum of natural history don’t. So bear with me, get to know Haarlem a bit.

downtown street

Lots of small shops, cafés, and most certainly a huge number of bicycles! Well, it’s Holland, so what should one expect? This road is obviously one of the more picturesque ones, but there are plenty of them in the old downtown of Haarlem. It is an old town, having gained city rights in 1245 A.D., which doesn’t make it very old compared to many other places in Western Europe, but does mean – given the lack of WWII carpet bombing and other devastation – that it has an old, grown city center.


Haarlem is – what a surprise! – full of canals. On the smaller canals – wait one, let’s clear up terminology first: a canal is called a gracht in Dutch if there are roads on both sides and it is in a town, a singel if it is or used to be a moat surrounding a city, even it the city has grown to include it and it now looks like a gracht, a kanaal if it is in the countryside and mostly for drainage, or a vaart if it is in the countryside and mainly a transportation route. This out of the way, let me say that there are a lot of small boats, but also sometimes bigger ones that, for example, which for example may serve as flower shops.

sail night

The big river of Haarlem, the Spaarne, which runs right past hte city center and has quite a lot of ship traffic going on, is virtually indistinguishable from any other gracht but for its width and runs by Teylers Museum, with its quite overboardingly decorated facade.

Here’s a closer view.

But I am getting ahead of myself, as I wanted to show you the town before I show you the museum building, which then is to be followed by the museum’s content. And then soem words on the EAVP meeting. So, here’s another view of that windmill, this time with the sun out:


Also, some views of the city hall and the Grote Kerk St. Bavo (“Great church”, i.e. cathedral), which both (and a bunch of nice restaurants) are located on Grote Markt (I guess there is no need to translate this name).

town hall

town hall

The Grote Markt is still being used as a market square, Monday and Saturday, and has not only a large number of stalls selling all kinds of things, but also a bunch of theropod ne’er-do-wells hanging around.

town hall

All this sounds quite quaint, and there is much more to like about Haarlem that makes it appear more like a country village than a bustling town. For example, although most roads are narrow and the sidewalks narrow, with little to no room for anything green, there are still a lot of flowers in view as soon as you leave the (indeed bustling) shopping streets of downtown, and walk into the residential areas of the owl town. Aside from balcony flower boxes, quite a lot of houses have Alceas (wikipedia) growing in front, not in flower beds or pots, but simply between the pavement stones.

town hall

Compared to Germany, a lot of Haarlem looks very British to me, considering the bricks, doorframes styles, window styles, door styles and so on, but the huge Alceas combined with the plethora of bikes somehow dispel that notion and make the place distinctly un-British.

Many shops in the city enter are still small and non-chain, and have individual signs hanging out in front.

And, obviously, a lot of grachts mean a lot of bridges. Many of these are drawbridges that will be pulled up for larger ships, and quite many are pedestrian/bike only. Overall, the narrow streets and the no-car bridges make Haarlem a very nice town to walk in.

Now let me close up this post with a few sunny daytime views, both of the Grote Kerk, seen from a nice restaurant we had lunch at during the conference, and of Teylers Museum seen from across the Spaarne river

Enough for today! It is time I introduce you to Teylers Museum and a few bits about its history in the next post.


Posted in "fish", Conferences, historical buildings etc., history of science, ichthyosaur, lower vertebrates, Mammal pic, Mammalia, non-palaeo, raves, Reptilia (non-archosaur), Travels | 5 Comments

Photogrammetry tutorial 12: How to preserve strike and dip or cardinal directions in your 3D model

Photogrammetry is a really nice and easy way of surface digitizing specimens in collections, but also useful in the field. Recently, Marie Attard, a colleague working in England, asked me to help with a project that deals with rock surface shapes. I don’t want to say too much, but this I can tell: she wants to capture rock surfaces on cliff on which birds lay eggs. Obviously, in this case, it is not only of interest what the surface shape is, but also what the surfaces tilt is in the field: is it level, or does it tilt toward the cliff edge or toward the cliff wall? And while you can simply use a geological compass to measure this, write the info down and be done with it, wouldn’t it be nice if the same info is also included in your 3D file?

If you follow the tutorials I previously posted here, you’ll be using long scale bars placed around and maybe even on your specimen for scaling. These scale bars will usually rest on the ground or table under your specimen more or less horizontally, but they are not useful for “leveling” your model. Well, they kinda are, and there is a neat trick for how you can make a model come out right-side-up (roughly), but that’s not good enough for the bird nesting site thingy.

So, Marie and I thought about this a bit, and soon came up with an elegant solution, one that actually does a bit more than we aimed for! Here’s how you

Preserve strike and dip of a surface in a Photoscan model

First of all, you best use a special kind of scale bar. It should be L-shaped, and for convenient in-program marker placement in Agisoft Photoscan it should have three of the automatically recognizable markers printed on the ends of the two arms of the L and at their meeting, with the distances between them known exactly. Here’s how they can look (screenshot of print file created by Marie Attard)

Lshaped scale bars

(As you can see, Marie ingeniously also added a label at one edge saying “cliff edge”. In the field, you simply align that side of the scale bar with the cliff edge and already you have preserved the information of the cliff edge’s strike in your model. This means that you can’t preserve the geographic direction using the same scale, though. You then need two scales)

So how do you use such scale bars to preserve strike and dip of a surface? First, you place one scale bar flat on the surface. Then, you put a compass on it, aligned with the edge of the scale bar, and rotate the entire thing until the edge points due North. Now, you level the scale bar. If you use a geological compass, or any other that has a round precision bubble level, you can use that. However, I personally find it easier to use a tool that you can buy cheaply for e.g. caravans: two combined bubble levels.


Putting this on the scale bar you now need to level it by shoving tiny pieces of cardboard or so under it. That can be a bit of a bother, and Marie came up with some ingenious solution: she bought a mini tripod on which she mounts the scale bar. Either way – once the scale bar is level, you start taking your photos of the surface as you normally would. If you wish to preserve some other information, e.g. the cliff edge direction mentioned above, you can use a second scale bar aligned with it.

Then, once you have taken the photos you need for scaling the mode, you remove the scale bars and proceed to take your photos for model creation – otherwise your 3D model will have the scale bars in it.

And all the rest is done in Photoscan!

Align your photos normally, including the scaling images. Remember to make them inactive afterwards, so that they do not contribute to the dense point cloud and thus the 3D model. Now, let Photoscan detect markers, or manually place the markers on the scale bars on your images. Make sure, if you do this manually, to name the in-program markers so that you recognize them properly.

Now, create your scale bars in Photoscan, scale the model – all as you would always do it.

Finally, go the the “markers” section of the reference pane. Here, you will find all your markers, and here you can set world coordinates for them. The marker at the meeting point of the two scale bars that form the L gets the coordinates 0,0,0, the two others get the same plus the respective length of the scale bars added to the X for one and the Y for the other. Click UPDATE and voila, your model is level!

Obviously, you can preserve any direction in the field by placing a scale bar edge along it. It need not be due North, it can also be a cliff edge, or whatever.



Posted in Digitizing, How to, photogrammetry | 3 Comments

Making Mike Taylor gloriously green-eyed

It has become a bit of a tradition that I use this blog to make Mike Taylor of SV-POW! (and much other) fame a tiny bit jealous. By posting photos of the Museum für Naturkunde Berlin dinosaurs, for example a selfie with the skull of the Giraffatitan mount, or from other unusual perspectives – photos a normal visitor can’t ever take, and photos Mike (despite getting better access as a researcher) didn’t take during his short Berlin visits. His real-life job has given him far too little time to come visit. Still, the MfN Berlin dinosaurs have featured prominently on SV-POW! again and again. In fact a very special bone, the 8th cervical of Giraffatitan individual SII featured in the very first post there.

Mike, aside from being a very esteemed colleague in the same league as Eric Snively, Larry Witmer, Matt Wedel, Andy Farke, “Dino” Frey, Aki Watanabe, Michael Pittman, John Hutchinson, Viv Allen, …..    oh, jeez, I better stop before this becomes a ten page list of cool people in paleo!
Anyways, Mike is not “only” a really cool colleague and (American-style) friend, but also someone I personally trust in the way Germans trust their friends (which is on a totally different level than a US-style friend).

Given the affinity of Mike for the Giraffatitan‘s 8th cervical it is, I guess, especially suitable for making Mike all green-eyed. After all, while it was on display in 2005, today it has a new number (MB.R.2181.47 or MB_R_2181_47 in the computer-palatable version), rests in a wooden box in the bone cellar, inaccessible and hidden from view, and gathers dust – except for Wednesday two months ago. On that Wednesday, it was moved out by the MfN preparators to the hallway, and the sides of the wooden box were taken off, and the sand bags that stabilize the vert were taken away. For this:



Artist Alicja Kwade wanted high resolution scans of various bones, and for this very special occasion the museum OKed access. Alicja payed for the scanning of several vertebrae and ammonites by a professional surveying firm, matthiasgrote PLANUNGSBURO. Now, a lot of people have told me that they know some firm or other, and that said firm will quickly create perfect scans. A lot of people simply buy an expensive scanner, know roughly how to handle the software that comes with it, and them call themselves “experts”. Well, typically I have these conceited scanning “expert” for breakfast…… but not these guys! I was very impressed by their knowledge and experience. They know exactly what they are doing, know how to work to order (e.g., not creating a model at far too high a resolution, which means unnecessary cost), can do top-notch models if needed, brought a wide range of tools, all of which they knew exactly how to employ – it was great fun and quite informative to see them at work! And both the boss, Mr. Grote, and his two employees are very nice people, with whom I had some fun conversations.

Still, any such opportunity to scan difficult objects is a challenge for me, and this is especially true when someone else is scanning the same object at the same time! Can I scan as fast, as accurate, as detailed as them? Can I predict my data capture time and scan resolution and accuracy accurately? Does my data capture approach work at all? In short, can I hack it? I have recently become pretty cocky, given the success of the digiS bone cellar project‘s success, but that concerned rather simple bone shapes. This time, as I quickly saw, I was pitted against the elite of 3D scanning, and the specimens were of an entirely different level of complexity. Not that I expected the experts to beat the resolution of the model I was going to try and make with the scan they needed to do for Alicja – theirs would be for rapid prototyping on a CNC milling machine, and therefore of limited resolution, whereas mine would be aimed at way-more-then-enough for all science and exhibition uses I can currently imagine. But , knowing how scanning people tick, I was expecting them to additionally go for a top-notch scan anyways, going way beyond the ordered level of detail and resolution. And given the tools they brought and their expertise, I must admit that I was a bit afraid of working too quickly, taking too few photos and ending up with a model that has errors or big gaps, and compared badly to theirs.

In the end, as the photo above shows, along with an Artec Spider scanner they did bring the Big Gun – the Faro ScanArm with laser scanner. And they did go for a very high resolution and high accuracy scan. Which means that my best scan would have to measure up to a really excellent scans by them……. *gulp* I was quite a bit tempted to forego my usual happy-go-lucky high-speed scanning routine for a calmer, more thorough approach, maybe even using a tripod, simply to make sure that I drive quality up as high as I can. But then, the comparison is only fair if I stick to the same effort expended and use the same tools that I normally do!

So, they scanned with the Faro Scanarm and an Artec Spider scanner, and I used my trusty old Canon EOS 70D with a cheap LED ringlight. No tripod, no extended scan planning. Just my usual happy-go-lucky approach.  Several vertebrae were set out on the work table in the Bone Cellar – not much room to work in, but sufficient for the artec scanner and my camera. The huge cervical 8 of Giraffatitan was moved to the hallway outside the bone cellar to allow better access with the Faro scanner, as can be seen in the photo above. And there it was that I went at it with my camera.

Overall, I took 754 images, the first 20 with scale bars placed all around the bone, the rest overview and close up photos without scale bars. Here’s one of the former:

overview image with scale bars

The scale bars use the pre-made markers that come with Photoscan, so that the software can automatically detect them. This time it worked like a charm, saving me quite a bit of time. Matteo Belvedere is to be thanked for fighting with Photoshop to create the file from which we had the scales printed – thank you very much, Matteo! I used a bunch of 0.5 m scales, because scales half as long to slightly longer than the specimen you scan are best: they provide the least proportional error without causing extra work capturing them. And I must say that the resulting accuracy is pretty pleasing! Below you can see a screenshot showing the scale bars and their respective errors:


note that the average deviation between the scales, each 500 mm long, is less than 0.33 mm, i.e. less than 1/15th of a percent 😀 Photogrammery FTW!

After taking the scale bar photos I removed the scale bars from the bone. The same process – removing the photos with scale bars – I later repeated in the Photoscan project file, after alignment: I made the images unavailable for model creation. This way, they are there for scaling, but are ignored for construction of the dense point cloud, and do not litter the model. Because of this approach I can place scale bars ON the bone itself, instead of just around it, which gives me more flexibility. In some cases, like digitizing trackways, placing the scales on the specimen you wish to digitize is the only way to place them, so remembering the trick of using them for alignment and scaling but blocking them later is helpful.

The additional 734 photos fall into three distinct categories:

  • images I took while “rastering” the bone
  • images where I deliberately pointed the camera into recesses and at other difficult points
  • overview images

The first category obviously is necessary to deliver a model that shows the entire bone at high resolution. I makes up about 1/3 of the total, because the photos need to overlap quite a bit. The second category makes up more than 1/3, not because I really needed that many (despite the plethora of deep, air-sac-caused depressions in the bone), but because I took way too many images, to make sure that I had enough to cover all the many nooks and crannies. Better having too many photos resulting in extraordinary calculation times than ending up with a model with unnecessary holes! Last but not least, the overview images are necessary to guarantee a good alignment of the other images. Yes, you can omit them, but if you take a series of images down one side of the bone and another up the other side, there is a high risk that your model will “warp” a bit. Overview photos keep this in check.

Rastering is best done by doing one set of photos with the camera pointed at the center of the specimen, then (for complex shapes like verts), another with the camera tilted left by ca. 30°, and another with the camera tilted right at 30°. Or up and down, depending on the shape of your specimen and how you place it. Or all of them – up, down, left, right….. and so on. Here, I made sure I used “straight”, “left” and “right”, as well as “up”. “down” images weren’t needed as a separate set, because of the geometry of the vertebra.

Then came the “recesses” part, which basically means pointing the camera at the midpoint if a hole, then moving it on the surface of an imaginary sphere but keeping it pointed at the same location. I did this for every single freakin’ depression….. *sigh*. I much prefer proper titanosaurs; they relocated their air sacs into the bone and have rather smooth outer bone surfaces. Much easier to digitize!

All in all, I spent 45 minutes and 21 seconds on photography, which does include a short 20 meter walk to a door and back to let some people in, as well as the time required to pick up and toss aside the scale bars. Divided by 754 images this means I took a photo every ~3.6 seconds. That may sound impressive, but it is actually slow work for me. Usually, I just aim the camera by eyeballing the brightness of the ring LED light on the bone. In this case, however, I felt the need for a more thorough approach, and used the 70D’s twistable touch live view screen to aim the camera and select the focus point. Usually, I achieve photo rates of 0.8/s, not .02777/s, but the live view screen makes shutter release slower, and the process of taping the screen each time to select the focus point and trigger the camera also is slower than simple blind point&shoot. Still, if I can’t easily go back and re-shoot a specimen, I’d rather spend more time and make sure I can guarantee a good model.

So, did all this effort give me a model I can be proud of? Can I hold my own against one of the best scanning crews out there? I can’t really judge, because I haven’t seen their models yet, but on the other hand I believe the results speak for themselves:


Yes, you read that correctly: the model has, in the highest resolution possible, some 484 million points in the dense cloud! Meshing a tiny part of itdelivers a 80+ million polygon mesh!

dense cloud

This is the full dense point cloud in all its glory! Note the hole at the bottom, where the vertebra rests on a plaster support made to fit. No way was anyone going to lift the vert up so I could take photos of its ventral side. It is way too heavy and fragile! We have very accommodating collections curators and managers at MfN, but lifting this bone is way outside anything they would ever consider – and rightly so! And a close-up – click for full size:

dense cloud close-up

This area is less than 15 cm wide… oh yes, the resolution is amazing 🙂 Now let me show you the mesh…… below is a total of the dense cloud with a small part I meshed right away superimposed. Note that I did NOT yet clean the dense cloud at this stage, which is why there are ugly black rims on top and so on. The meshed area resulted in >80 million polygons, here decimated to 1 million.

dense cloud with mesh

and a zoom-in on the mesh (with slight smoothing):


yes, that hole you see is real! The bone really is that thin 🙂 I put two markers on the two sides of the neural arch that the mesh happened to cut. You can use Photoscan as a measuring tool by simply scaling a model creating markers and a scale bar from them, setting it to length 0, and checking the error – that’s the length of the scale bar (assuming you scaled your model correctly before). The thickness of the bone is really just


~4.569 mm! And despite the enormous size of the specimen, my happy-go-lucky model managed to keep the two sides consistently separate, except for the spot where there is a real-life hole in them, too:

hole in bone

So, overall, I am *very* pleased with my results! I haven’t seen the scans by Grote yet, so I can’ really say how I measure up against them, but I have once again been able to capture a very high detail model of a difficult object with simple, affordable and mobile equipment.

So, Mike, here it is now in all it’s glory – or should I say, in a small percentage of all its glory? As this is only a 74 million polygon model after clean-up, and if I ran this at ultra high resolution I’d expect it to have around 600 million. It is detailed enough, though, as it is….

click to embiggen

click to embiggen

Posted in digiS, Digitizing, Dinopics, Dinosauria, FUN!!!, Giraffatitan, MfN Berlin, photogrammetry, Sauropoda, Sauropodomorpha, Tendaguru | 1 Comment

“Liberation from the Bone Cellar” – a progress report

Here’s a short update on how my digiS 2015 project is coming along. Yes, 2015 is still running, due to a bunch of unforeseen circumstances a huge theropod sticking its ugly skull into my affairs and demanding to be photogrammetrized in a big hurry. digiS 2016 is also running, which means that I have about 50% of the computing power at hand that I need – ugh! Our IT is doing all they can to keep me happy, which is way more that their jobs dictate they should do, but they can’t work miracles. I am enormously grateful, and really hope that my work makes the higher-ups in the museum realize how excellent the support is IT gives researchers at the museum.

Now, where are we with regards to “Liberation from the Bone Cellar” – a project title not quite as tongue in cheek as it may sound, as the work conditions in the basement are really suboptimal enough to make many research approaches barely feasible that really should be easy in an ideal world.

Well, I am glad to report that things are finally chugging along nicely! Both my computer screen and that of my colleague Bernhard Schurian are usually populated with views like this:

batch process result

(click to embiggen for readability)

What you see here is a batch process file in Agisoft’s awesome Photoscan Pro. Each batch contains the photos taken of one bone (both top and bottom side), and we run an overnight batch process for photo alignment for all chunks. Then, we optimize the resulting sparse point cloud, scale the models, and run another batch process for dense point cloud calculation. Then, the results must be manually cleaned – after all, we do not want to have all kinds of background data in the files. The screenshot was taken just after cleaning of the dense clouds. As you can see, in this case there are 6 chunks, i.e. 6 bones. The second and third are marked inactive, which means that we had some sort of problem with them. Usually, what gives us trouble are photo sets that do not align perfectly, usually because we run the models with fairly low sample point ratios (max 10.000 per image). Instead of stopping work on the other chunks while we fix these problems, we typically just ignore them, finish the rest of the chunk, and then come back and deal with the problems. Usually, this simply means re-running the alignment with more sample points (40.000 or unlimited).

Each of the six chunks has been aligned, and you can see the number of photos per chunk, the number of resulting points in the sparse cloud, as well as the number of markers we already assigned. In the two chunks that have been expanded you can also see the number of aligned images each: in the first 169 of 175, but in reality 173 as the first two show the label, which equates to an alignment quota of over 95%, and in the second 163 of 165-2=163, a quote of 100%. Considering the free-hand photography at close quarters that we did this is a pleasing result 🙂

You can also see the setting (Medium quality) and resulting number of points of the dense point clouds: over 7 and 9 million points, respectively. That’s way more than 99% of all science uses of the models will ever need, and in fact way more than 99% of all science uses can handle! I expect to get meshes with around 9 to 13 million polygons, and such big files are a bother to load. Mounting a full skeleton, or even just a girdle + limbs, at this resolution will crash most computers!

The key thing we are proud of you can see at the bottom left of the image: the average error between our scale bars. For the “small” bone fragment in the open chunk we used four scale bars, one of which is 20 cm long, and the other three are 25 cm long. The average distance between them in the model, which in an ideal model would be zero, here is 1.3 mm, i.e. slightly over half of a percent of the average scale bar length – and this is one of the worst models we produced (which is why I show you this one). Most have three zeros after the comma, not two! That is an amazing accuracy when you consider the far-from-optimal conditions in the Bone Cellar and the speed with which we acquire the data: I usually take less than 7 minutes per bone including transport!

So, overall, I’d call digiS 2015 an overwhelming success – for us, for paleontology as a whole, and for all our colleagues out there who want to quickly capture a lot of data during collection visits. While our photography method is physically exhausting, the results show that digitizing 10 to 20 big bones per day in collections is entirely feasible.


Posted in digiS, Digitizing, MfN Berlin, photogrammetry, Tendaguru | 2 Comments