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 | 2 Comments

Going to Tristan the T. rex’s dig site

I guess it was kinda hard to miss that the Museum für Naturkunde in Berlin is getting a real Tyrannosaurus rex. I’ll have much to say about the beast here on dinosaurpalaeo over the course of the next few years. For now, I can show you a few photos and report on the trip to the site it was dug out. The Tyrannosaurus skeleton was named Tristan by its owner, Danish businessman Niels Nielsen, after his son. I’ll add some of the press photos of it below, but I won’t rehash what you’ve read in the press already. There’s tons more of photos on my hard drive, but anything that hasn’t been approved already by the PR people I would have to run by them, and they are quite busy enough already at this time. Patience, thus – you’ll see plenty of Tristan soon. maxilla

Medial view of the right maxilla. Photo: Niels Nielsen

all bones

Bones of Tristan during preparation. Photo: Niels Nielsen

Continue reading

Posted in Aves, Botany, Dinosauria, historical buildings etc., insects, landscapes, Mammal pic, Maniraptora, non-palaeo, photography, Theropoda, Travels, Tristan, Tyrannosauridae, Tyrannosaurus | 6 Comments

Urgent: Please reply! Can you get a bad reputation from poor academic etiquette?

Heinrich Mallison:

Jacquelyn’s post for your contemplation in case I am late replying/reviewing/authoring :)

Originally posted on The Contemplative Mammoth:

Academics juggle a lot of balls. The absent-minded professor stereotype is, for some of us, an apt one. Because our jobs involve multiple independent demands on our time, we’re often tossed (or hold on to) more balls than we can handle. Balls get dropped, neglected, or stay in the air for far too long after they should have been safely placed on the shelf.

We forget deadlines, studiously ignore emails we should be answering, miss meetings, triage our to-do lists based on which thing that’s most overdue. In my first couple of years as a PI, I’ve seen (and committed) my share of academic courtesy faux pas: never-returned emails, late reviews, late manuscripts, that one person who holds up the special issue, forgetting to notify co-authors of a conference abstract submission*, leaving names off of manuscripts or talks. We may be new PIs still figuring out academic workloads, we may suck at saying no…

View original 556 more words

Posted in Uncategorized | Leave a comment

GSA’s single article access scam

Note: I am not using the word scam in a legal sense here, but as an everyday language term. Maybe a case could be made that GSA’s behavior is in fact fraudulent, but I believe such a case would fail on a technicality (see below). Still, personally I’d feel scammed, defrauded, swindled if I had fallen for GSA’s trick.

A few days ago work required me to look for various scientific papers on the Hell Creek Formation, including one on its palaeobotany.

screenshot of GSA website

There it is, but as you can see the article is not open access, and the Museum für Naturkunde does not have institutional access. That’s not uncommon. And GSA offers a bunch of options to access the article PDF:

screenshot of GSA website

So, I can:

  1. Sign in, if I have a user account with access.
  2. Purchase short term access – 1 day from the very computer I am on, for US$ 25.00
  3. Use some weird thing I have never heard of that sounds like a publisher’s bad version of LEGO
  4. Sign up…..

Well, obviously, 1, 3 and 4 are not really good for anything. Bloc of Docs is nothing but a credit thing that reduced the number of separate credit card purchases, but doesn’t give you a rebate. Signing uP is for

Member/Fellow and Affiliate Student/K-12 Teacher

I ain’t any of that, so no good. And Signing in if I haven’t signed up….. well, you get the idea. In the end, this means I need to fork over a whopping US$ 25.00 for a single article. Ain’t gonna do do for sure! Thus, I started writing an email to our library, asking them to but the article – and then I stopped. After all, this article is part of a special issue, and it is highly likely that we will need more articles from it soon. Thus, I thought it worth checking if maybe there would be a rebate on the entire special issue. And lookie: You can’t buy it in print, but you can buy it in one go as an ebook!
screenshot of GSA website

And incidentally, the price is quite reasonable all of a sudden:  mere US$ 20.00 for both GSA members and non-members!

Why didn’t you say so in the first place? Why was there no link on the article’s page (the page I get directed to by Google and other searches) saying “Purchase entire Special Issue containing this article for US$ 20.00″?

I guess I know why there is no such link. Quite obviously, nobody in their right mind would spent US$ 25.00 for one-day access to one single individual article if they can instead spend LESS MONEY, US$ 20.00, to get PERMANENT ACCESS to MORE ARTICLES!

So, I click the ebook link and get this:

 

screenshot of GSA website

Oh, so now it is not an ebook format, but a PDF? Suits me, but why can’t GSA get things straight on their own freakin’ website? And it costs even less now, a mere US$ 9.99!

I did buy this, out of my own pocket, and successfully downloaded the entire PDF.

So, to sum up:

If you search for an article of this Special Issue by title, you are directed to a page where you can buy it for one day for US$ 25.00. The page does not inform you that you can buy this article along with the rest of the Special Issue for less than 40% of the cost of one-day-one-article access.

I guess GSA is making a hell of a lot of money by not telling you!

Why is this not legally fraud? In order to be illegal, GSA would have to falsify or misrepresent facts, and gain a financial advantage for them or others while causing you a financial loss. That’s arguably the case if they pretend you need to fork over US$25.00 when in fact US$ 9.99 is enough. But those prices are for two different items, one of which simply happens to contain the other. Nowhere does GSA claim explicitly that the only way to access this one single article is via buying it outright. They just implicitly pretend it is. Thus, any court would throw out a lawsuit.

Morally, GSA’s behavior is clearly wrong. That’s undeniable, and I am looking forward to what GSA has to say when I email them about this.

 

Posted in Open Access, Open Access publishing, rants, WTF? | 4 Comments

Less than 4 minutes to 3D digitize a large bone! (digiS project)

It’s been quiet here recently, and as is usually the case my work load is to blame. It’s not just that there is way more work than time to do it, but that I am currently doing a bunch of very tedious and a bunch of very thrilling things in parallel. The latter are mostly super-secret (sorry!), but I can tell you that a non-secret one deals with how fat dinosaur tails really were, and how their musculature was arranged. Yes, that old can of worms again. More on that soon!

The boooooooring stuff is, well, boooooring, so let’s skip right ahead. Let’s check out what remains in between totally exciting and secret and yawn-worthy: the latest developments in my digiS project. What I am currently doing for it has its tedious moments, but also some excitement, and a lot of quietly satisfying moments.

Recently, I showed the method for photographing bones I developed for the project. Well, it’s a method that has been shown to work very well indeed, thank you. But does it work reliably? What’s the percentage of failures? And how does it adapt to smaller bones, ones that can be set on a table instead of having to stay on the floor?

I’ve been busy photogrammetrizing more stuff, and trying to find out why my method works so well some of the time, and why I am admittedly getting some abject failures with it. My colleague Matteo Belvedere and I suspected that the cause of some of the failures I experienced was the lack of a sufficient number of overview images. What we saw were slight but noticeable offsets between the point clouds stemming from one set of photos showing one side of the bone and the other set showing the other side. Usually, I had been diligently trying to take photos at angles as low as possible in each set, so that the positions of some images in each of the sets were in fact near-identical – and still there was this odd offset.

Well, I must admit that I have solved the problem but not explained it with my latest tests. I simply took a lot more photos per set, and voilà! no more offset! But because these sets do not only include more photos, but also more overview images and more images of the bones’ “corners”, where th problem was usually most manifest, I can’t really tell what the cause of the issue was. Doesn’t really matter, though :) It’s not as if the additional photos take serious time to take.

Here’s an example of the bones of which “many” images were taken and that worked out just fine:

bone example

Yes, 23 million polygons. 23 MILLION! That’s from 117 images, taken in 2 minutes and 50 seconds, with a break in between to flip the bone over. In this case I spent nearly three minutes to do this, which means I was in fact talking to someone or doing something else. Typical flipping times are in the order of 20 seconds to one minute.

Let me say this in bold: Photographing this bone took less than 3 minutes!

I’ve also tried more difficult shapes, including a dorsal vertebra of Giraffatitan brancai. That took a lot longer, but then the bone is huge and has a complex geometry.

spreadsheet

I really had to show this, just to get SV-POWer Mike Taylor salivating. As you can read on the mesh (no texture calculated) this is AR1, a posterior dorsal of G. brancai that was found isolated. I can’t access the collection database right now, so I can’t tell you the new collection number.

Let me give you a screenshot of part of the Excel sheet I use to document my work times:

spreadsheet

606 images of the posterior dorsal took nearly 12 minutes to take, and the model is excruciatingly beautiful. Longbones are typically done in less than 6 minutes overall, despite some chatting in between – hard pressed I could on average do one every 4 minutes, provided they are set out on a table for easy access. In fact, the average photography time of anything classified as a longbone of the entire spreadsheet (with some more bones than in the screenshot above) is 4:17 minutes, and the typical breaks without interruption are less than 30 seconds.

Yeeha! This photogrammetry thing is really cool :)

Posted in digiS, Digitizing, Dinosauria, Giraffatitan, Kentrosaurus, MfN Berlin, Ornithischa, photogrammetry, Sauropoda, Sauropodomorpha, Stegosauria | 13 Comments

Interspecific prey theft in extant theropod dinosaurs – Ardea vs. Spheniscus

Golly, what a science journal-worthy title! An unnecessarily complicated and grandiloquent Ersatz for a simple “Heron steals penguins’ fish!”

The Tierpark Friedrichsfelde in Berlin has started announcing feeding times a while ago, and the penguin feeding (Humboldt penguins, Spheniscus humboldti) is a huge favorite with many people. And with local Grey herons (Ardea cinerea), obviously, as they stand a not-too-shabby chance at nabbing a few fishes, too. The penguin keepers aren’t stupid, and feed the penguins individually, instead of just tossing the fish into the enclosure. But some penguins love dragging their fishes to their nesting holes and deposit them next to the entrance. And that’s when the herons see their chances.

Here’s the line-up and starting formation:

heron

A penguin couple has stashed two fish at the entrance of their den, and the heron stands a few feet away, trying to figure out how to get at the fish without getting nipped by the powerful penguin beaks.

heron
A quick stab – but the penguins are alert! Although the heron managed to grab a tiny bit of the fish skin, the defenders moved too fast to allow it to get a good grip, and the steal failed.

So, wait some more….

heron
STRIKE!
This time the heron didn’t just uncoil its neck in the heron-typical fish-grabbing motion they use when fishing, but also made full use of its wings to counterbalance the extremely rapid stab for the fish. And succeeded:

heron

But not every attempt is successful, and a determined defense combined with a strategically less inept fish storage location can work miracles. Keeping the fish not that far out and really going after the heron allowed these two penguins to keep their share for a relaxed dinner later on.

heron

heron

Some other birds are also on the scrounge. Not quite as daring in their approach, but then a heron is much bigger than a Humboldt penguin, whereas a Hooded crow is quite a bit less hefty. Still, some fish end up lying around……. and what proper crow would pass such a free meal by?

heron

heron

In the end, all those who were in the enclosure were well fed. Can’t say the same about some of the less daringly minded herons, though – each tree around the penguin pen had quite a few of them perched on top, and many of them stayed hungry. I’ll toss in a few gratuitous pics of them.

heron

I especially like this one:

heron

To wrap this up, below there is an animated gif I made of all the shots of the successful fish-grab. Sorry for the borders; I simply moved the camera so much that I can’t crop any better.

heron

Posted in "fish", Aves, Dinosauria, lower vertebrates, Maniraptora, Theropoda, Tierpark Berlin, Zoos | 2 Comments

My awesome digiS project: mass digitizing sauropod bones

Last year I applied for a grant from the Senatskanzlei Berlin for the 2015 digiS funding programme. digiS is a state-wide (i.e. Berlin-wide) programme intended to coordinate and support digitizing efforts.They have an about page on their website that is in English, all the rest is in German (sorry!).

I had heard that there were a lot of applications in 2014, and that it would be difficult to get an application funded. However, the rules for applications were fairly straightforward, and they didn’t ask for a lot – just a clear description of the intended project with some background, a short discussion of why it is important, and who will benefit from the results. Along with that a short financial plan – a really simple one. And that was all that they asked for! In sum, I decided that the programme was worth a shot, as the cost of writing an application was not out of proportional to the potential gain.

I decided to go for a 3D digitizing project that has showcase character, with scientific gain, methods development, and room for outreach: 3D digitizing the long bones and girdle bones of Tendaguru sauropods stored in the Museum für Naturkunde’s Bone Cellar. These bones:

BoneCellar_06

bone cellar OLYMPUS DIGITAL CAMERA

The digiS programme limits individual projects to 100,000 € and a maximum run-time of one year (i.e., starting at the earliest on January 1, 2015 and ending at the latest on December 31, 2015 in this case), but I was unofficially informed that successful projects in the past had never received more than 50,000 €. Given the overall limits, digiS obviously wants to fund not just one or two projects a year, but a wide diversity. After all, digitization has many forms, and the cultural heritage institutions in Berlin have diverse needs. Therefore, I decided to design a program plan that stayed below 40,000 €, but still offered plenty of data for the public in the end.

The largest item in such a plan would then have to be personnel, and not tools. A nice hand-held laser scanner easily costs over 10,000 €, and squandering more than 25% of my total budget on one just wasn’t on. As usually the case, I therefore had to plan the digitizing via photogrammetry. Given the confined space available in the Bone Cellar, photogrammetry also seemed a good idea. After all, I didn’t want to have to carry the bones elsewhere, especially as there currently is no lift due to construction work at the museum.

In the end, I sent in a proposal that promised to digitize 360 long bones and girdle elements of the Tendaguru sauropods and Kentrosaurus, bones that are difficult to handle and should see more study than they do. Additionally, I will also clean up scans of the old dig diaries’ excavation sketches in which these bones are mentioned. All the data goes online via a special web interface, so that people all over the world can easily find the data, check out the 3D files, and request high-resolution versions for their research.

And lo and behold! – my project was granted in full! I got a call a few days in advance of the official decision, and was told that it was the first 3D digitizing project digiS would fund, because for the first time they saw a real use for the 3D files, and that although the project was very ambitious, the digiS team felt that if anyone could do it, I could. They had looked at my publications and at my blog, and basically wanted to see if I was all talk or if I would do the job :) Well, here goes!

disigmethod01

One thing I really needed to find was a very quick method to digitize all the bone in the confines of the Bone Cellar. And by now I have perfected my first rough idea, by trial and error, into something that works quite smoothly! I’ve already posted about the photography method, including a video, in the last post. Here, let me quickly explain how I create my models from the photos.

As you can see above, the images from all photography sets (two sets, in the example above) all go into one chunk in Agisoft Photoscan Pro. Because the background has been completely changed in between the sets, the resulting alignment and sparse point cloud has two floors:
disigmethod01

I put a styrofoam support under the bone for both sets. Obviously, that’s visible in the sparse point cloud as well. However, it is important to do this, as you will see in a second.

The really cool thing here is that the only points that both sets of photographs have in common are those that are on the bone! This means that all photos can only be aligned based on the camera position relative to the bone, not to the background. Which means a near-perfect alignment in one chunk – which mans practically no work effort for me :)

Next, I optimized the sparse point cloud and re-optimized camera positions. More on how to do that in a later post. Then, I calculated the dense point cloud:

disigmethod01

Well, that’s quite a bunch of floating nonsense data there, but as you can (I hope) see in this screenshot, the floating stuff does not touch the bone! That’s because the bone projects beyond its support all around, instead of lying flat on the ground. And it means that cutting away the excess points is quick and easy.

So there you are: a quick and reliable method for taking photos that results in very little manual editing later on :) I am quite confident that I can digitize a huge number of bones for the digiS project :D

 

Posted in Berlin, Dicraeosaurus, digiS, Digitizing, Dinosauria, Giraffatitan, Kentrosaurus, Ornithischa, photogrammetry, Sauropoda, Sauropodomorpha, Stegosauria | 10 Comments