A photogrammetry primer for palaeontologists

One of the big advantages of photogrammetry is the ability to gather high-quality data quickly and easily. The tools are available to anyone and are often free, open-source or reasonably cheap. As mentioned in the previous post the work flow can be summed up as follows:

1. Take overlapping photographs.
2. Load into photogrammetry application.
3. Generate a point cloud (the software looks for points on the various photos and these are assigned a point in 3D virtual space).
4. Generate mesh and texture (if required).
5. Output, analyse and share.

The quickest way to start is using an online photogrammetry service. The best I have come across is Autodesk's 123D Catch, which is an easy and quick way to get started and produces pretty good results. You can use 123D Catch on your smartphone or tablet and as an internet service you need no other software to generate meshes and the app takes care of steps 2-4 in the workflow above. The app will generate .obj files which are read by every major 3D package including the excellent MeshLab, which I suggest you download (it's free) if you are thinking of incorporating photogrammetry into your own palaeontological skill set as it's useful for reviewing meshes.

Good though 123D Catch and similar online packages are, if you're serious about photogrammetry then  eventually you'll want to get dedicated software. The application I favour is called Agisoft Photoscan which comes in two flavours, Standard and Professional. I use the standard version and this is more than adequate for my needs plus is cheaper (the Standard version costs $179 and the Pro version is $3499 - ouch!), which counts as I am self-underfunded. An alternative is Peter Falkingham's excellent VisualSFM which is free but doesn't generate meshes, only point clouds. I say 'only', but the point cloud data is really the important bit and this is the basis for any analysis that might be performed on the data. However, the artist part of me likes to see images that look more solid so I prefer to generate meshes and for outreach and other purposes a mesh is desirable.

So here's a run through the workflow mentioned above, that should be enough if you wish to get started using photogrammetry.

1) Take overlapping photographs.

It's quite possible to generate usable 3D data by taking two overlapping photographs. However, the more data the better so I take a sequence of images, normally about nine but this can be far more according to the size and detail of the subject. There are some ground rules when taking images for photogrammetry: photos must overlap by no less than 60%, you must keep the camera a consistent distance for each shot, and you must keep the camera perpendicular to the subject.  As an example, for a single footprint you might take 3 shots with 60% overlap at the first pass with the camera in it's normal orientation, go back to your original and rotate the camera -90 degrees and take 3 more, rotate the camera 180 degrees and take the next sequence.

Eubrontes footprint from Warner Valley, Utah recorded using ye olde traditional digital photograph.

Here's a sequence I took of the same footprint ready for loading into Photoscan:

Sequence of images of the print.

2) Load into a photogrammetry application and 3) Generate a point cloud. 4) Generate mesh and texture.

Photoscan has a step-by-step approach to building meshes that is very easy to use. You load your images, the software then aligns them, generates a point cloud, then a mesh and finally a texture if desired.

This is a point cloud of the print, seen from above and generated from the image sequence above.

The same print, with mesh generated from the point cloud data and with a texture applied.

And that's it! The mesh can now be saved as any number of file types for loading into other programs for further analysis, and shared via email or cloud services with colleagues across the globe. If desired,  a 3D printer could be used to create a physical copy of the mesh, essentially returning the subject to the physical realm from the digital.

Uses for meshes:
Clockwise from top left: untextured mesh with adjustable lighting,
full textured mesh, colour elevation and contour generation,
anaglyphic stereo.

I hope this will encourage you to explore the technique of photogrammetry, and incorporate the method into your research workflow if applicable. This post has really only scratched the surface of what is possible with photogrammetry and associated techniques, such as recording objects in the round (see movie of cast below) and the methods used in processing to get really good results; these are subjects for a book rather than a blog!

If you do want to learn more and are heading to the SVP in Los Angeles this year then I highly recommend the workshop that Neffra Matthews and Brent Breithaupt are hosting during the meeting. They are two pioneers of the technique in the context of palaeontology and are excellent communicators to boot and there is no-one better to learn from.

Photogrammetry workflow. Click to embiggen.

Now go and get started!

Ref:
Pond, S., et al.,The ichnologists guide to 3D models: from the field to the cloud. DigitalFossil Berlin 2012 Abstracts of Presentations. Available at: http://www.naturkundemuseum-berlin.de/forschung/tagungen/digitalfossil-berlin-2012/home/abstracts-of-presentations/#c24993

The Photogrammetrical Palaeontologist

I don't get out into the field anywhere as much as I would like to, and when I am out there I want to be sure I can record as much data as possible, as accurately as I can. In the past this has meant using tracings, drawings, field notes, measurements and photographs to record tracks*, the location of a specimen or if excavating a specimen, the site itself. All good techniques and methods no palaeontologist worth their salt is likely to abandon in the foreseeable future, but what if you could record field localities in a way that you meant you could analyse, share with colleagues and present them back at your workstation, with sub-millimetre accuracy and all the detail visible in the field? What if you could have a scaled-down, physical section of a partially excavated skeleton from your quarry to help plan the next field season? In fact, you could be sharing not just data from the field, but specimens from collections or that you're working on right now. In the past the tools for acquiring high-quality 3D data have often been expensive and not available to all workers; we can't all afford a luggable Lidar unit to record our quarries or outcrops. As the shiny digital future becomes everyday reality a number of imaging techniques are now being used to analyse 3D data from specimens and field locations on equipment we all have, such as laptops and mobile devices.

A large ornithopod footprint in the back garden of a collector on the Isle of Wight.
Not so easy to share with your colleagues across the world? You can with photogrammetry!

Photogrammetry is one of these techniques. Most palaeontologists and amateurs will already have the tools to practice photogrammetry in their field kit: a camera and a laptop. In fact, your mobile phone and an internet connection will enable you to produce reasonable quality 3D data very little time using free software, downloadable right now.

So what is photogrammetry? It's the technique of generating a 3D point cloud from a series of overlapping photographs and at it's most basic a mesh can be generated from a stereo pair, but in most cases more images are better. It is capable of sub-millimetre accuracy and can capture virtually any subject, including outcrops and objects in the round. Photogrammetry has several advantages over traditional techniques. As mentioned earlier most of us having the equipment needed as part of our regular field kit and  vitally photogrammetry is totally non-destructive and this is important when recording delicate fossils as well as tracks and traces as often a traditional technique (for example creating a mould) will cause some damage to the fossil as part of the process. The software used to generate the 3D data is free, multi-platform, open-source or relatively cheap and capable of excellent results.

Chirotherium footprint, textured 3D mesh.

One example of a photogrammetry workflow is as follows:

1. Take overlapping photographs.
2. Load into photogrammetry application.
3. Generate a point cloud (the software looks for points on the various photos and these are assigned a point in 3D virtual space).
4. Generate mesh and texture (if required).
5. Output, analyse and share.

The 3D data has one huge advantage over traditional data: it's very easy to share. You could record a specimen in the field, generate a point cloud and the a mesh, save it into any one of a variety of formats read by a variety of apps. This data could then be emailed, uploaded and shared with colleagues across the world, all from your position in the field (provided you have internet access).

Another Isle of Wight footprint, this time a theropod track which some gooner has
tried to remove with a rocksaw. I recorded it using photogrammetry and did no damage at all.
An untextured 3D mesh.

This data has a wide variety of uses. The point cloud and mesh generated from it can be used for morphological analysis, measurements, false colour and contour analysis and light sources etc can be manipulated to aid interpretation. The meshes can also be 3D printed to bring the specimen back into the physical realm; want to have a scaled 3D version of that Allosaurus skull you excavated last field season on your desk? Use your photogrammetry data!

PG data also has potential as uses when publishing research, as stills in a paper and animations and meshes supplied as part of the supplementary data of papers. 3D works particularly well for outreach too, with animations and 3D video particularly useful for encouraging engagement.

So how to start in photogrammetry? Watch this space!

*You might notice this post is ichnology-centric. For that, I make no apology at all.

Scientific illustration: Cell schematic

Generic human cell illustration. Click to embiggen.

I've recently been working on a piece that I thought might be of interest to readers of this blog as although it's not palaeontology, who can resist a bit of biology?

This is a 3D model created in entirely in Maxon's excellent Cinema4D of a cell that is gracing the front page of my day job website (www.stupond.com), and is a schematic of a generic human cell showing the basic structures and organelles commonly present in many cells. This could be animated or labelled is needed.

Next on the personal learning curve is getting to grips with Maya, one of the real heavy-hitters in the world of 3D modelling with a learning curve to match. Exciting stuff!

I hope you like the illustration.

Building a dinosaur: Starting to detail Triceratops

The next stage in the construction of our Triceratops model is one on the fun parts of creating 3D models: detailing. This is mainly carried out in zBrush and takes full advantage of the symmetry option which allows the artist to mirror brush stokes over the axis of choice. This means you can add detail without having to do it twice and as dinosaurs are symmetrical this is extremely useful. Of course, there will be subtle asymmetrical details that will need to be added but these can wait until we have the main details sculpted.

As with the rest of the modelling process, detailing is best approached by starting out with the larger details first and working in ever-increasing resolution as the finer details are added. There are decisions to be made at this stage too, deciding how much to actually model with geometry and how much to add using displacement maps and texturing. For the time being, I'm going to continue adding to the geometry as we're still dealing with larger details rather than the tiny stuff.

As you can see I've started to refine some areas that were difficult to model by pulling polygons and points, such as much of the skull detailing including the rostral and orbit areas, the epioccipitals and general refinements around the skull. I'm also adding wrinkles to the skin, especially in limb areas. I'm also attempting to keep the animal looking quite fleshy as I'm anxious too avoid an overly skinny look with bones poking through everywhere. Most of this work is done using standard zBrush brushes and alphas; the need for custom alphas will be when the finer detailing such as skin texture is being applied.

Many of the decisions on how the muscles look are based on our earlier reconstruction of the musculature of Triceratops, but at this stage it's worth considering how the integument of the animal affects the way the skin might fold and fall across the skin and muscles. Keep referring to any reference you have gathered and be mindful of the analogues you choose; elephant skin is probably very different to ceratopsian skin, so do the research. More on this in the next post.

Celebrating Dinosaur Island in September 2013

The University of Southampton has announced it will be hosting a meeting called Celebrating Dinosaur Isle: A Jehol-Wealden International Conference on 20th and 21st September 2013 at the National Oceanography Centre in Southampton. UK and Chinese palaeontologists will present their research, and the meeting will be an excellent opportunity to forge new contacts and discuss future research. There will also be an opportunity to visit some of the main fossil sites on the Isle of Wight, which is a hop over the Solent from Southampton.

More programme information as it comes through, in the meantime here is the poster.

In the interests of full disclosure I have to state I am a research associate with the University of Southampton and also designed the poster. The image on the poster is a reconstruction of the skull of Neovenator salerii, a theropod dinosaur unique to the Isle of Wight.

The Chooks got the look: the soft tissues of Gallus gallus domesticus

Like many people, my experience with Gallus gallus domesticus is largely confined to consuming the poor creature in variety of rather tasty dishes; indeed, as I write this a deceased, plucked, eviscerated and recently defrosted Gallus gallus domesticus is on a plate in the fridge awaiting its fate as tonights Sunday roast dinner. This is a shame because for all it's familiarity the humble domestic chicken is a beautiful bird that is deserving of more attention outside of supermarket freezers and specialist breeders.  Darren over at Tet Zoo has discussed them briefly but yesterday I had the good fortune to visit the High Peak Poultry Show which was being held in Bakewell, Derbyshire and got the chance to see these birds in a different context to the usual.

Palaeontologists spend a lot of time wondering about how dinosaurs looked and moved in real life, and these thoughts recently were expressed by the recent shift in ideas about external appearance of dinosaurs that move away from the more traditional scaly-hided, shrink-wrapped Paulian beasts of the last forty years to the new anatomically rigorous yet rationally speculative reconstructions illustrated in the brilliant All Yesterdays or Matthew Martyniuk's equally inspirational Field Guide to Mesozoic Birds and Other Winged Dinosaurs.

My trip to the poultry show added plenty of fuel to the fires of imagination when it comes to thinking about the reconstruction of the soft tissues of dinosaurs, as the various breeds of chicken present had a bewildering array of wattles, combs and other ornamentations. They were equally diverse in terms of body shape and type of feathery integument as well as the placement of feathers over the body. In short, some looked they had really funny haircuts, some quite weird faces and fleshy bits and others looked duller but distinctly dinosaurian and at least one breed looked cuddly. Never thought I'd say that about a chicken.

Here are the pictures. I took these with my iPhone and so they're not great quality and them chucks have a habit of not staying still at all. I didn't get the breed names of most of these birds so apologies for the lack of clear labelling. However, I hope they convey some of the beauty of a bird it's all too easy to take for granted.

First up, this chicken with a mostly naked head.

A more traditional looking bird, with an elaborate, flat comb.

The cuddly chicken.

This bird would not stay still hence the motion blur, but has very distinctive ear lobes.

Another chicken with prominent fleshy wattles, ear lobes and comb.

A lovely wattle/comb/feather combo on display here.

This breed is quite spectacular, and slightly weird (in a good way).
In the Tet Zoo Gallus post Darren notes this breed is a Transylvanian Naked-Necked Chicken. 

A very solid comb and prominent fleshy eyelid, plus feathery ear coverts.

Er, obviously not a chicken, but a Dewlap Toulouse gander.

Foot casts and photogrammetry in the Isle of Wight

I managed to get out into the field for a couple of days in early December with the intention of recording (using photogrammetry) some of the footcasts on the beach at Hanover Point on the Isle of Wight. I'd spent some time at the National Oceanography Centre in Southampton where I'd given a scientific illustration and photogrammetry workshop and discussed current and future projects with a colleague at the University of Southampton.

It is possible the stretch of beach of the Isle of Wight at that runs from where the chalk cliffs meet the Vectis Formation at Compton Bay, along through the Wessex Formation eroding out at Brook and Brighstone Bays until the end of the Vectis at Cowlease Chine is my favourite place in the world. I can't afford to get there as much as I'd like, but it's never too far from my thoughts and I've spent many happy hours over the last two decades looking for dinosaur bones and other fossils with my wife and dog, and now it's the site of my research and has become even more important.

3D mesh of an ornithopod foot cast at Hanover Point, IOW.

Once on the beach I met my UoS colleague and a local collector from the island and we headed off to look over the site. The cliff at Hanover Point is famous for its foot casts, which originate from the crevasse splay sandstone that is interbedded with the green, red and grey marls that make up much of the Wessex Formation in this section of coastline. The sandstone outcrops on the beach north of Hanover Point and then rises through the cliff as you proceed south-east; at this point we're close the axis of the Brighstone anticline and a mile down the coast the beds dip in the other direction and disappear under the beach.

3D mesh of a large ornithopod footprint, Brook Bay, IOW. This cast is especially
deep and shows distinct edges crated by the ungual phalanges as they sank into the substrate.
Note it goes vertically down (we are looking at the base of the print).

There are many loose blocks on the beach and a fair few of these show some evidence of dinoturbation; the number runs into several tens over the length of the exposure and the whole underside of the bed probably represents a bioturbated surface. Traditionally these prints have been interpreted as being made by ornithopods but theropod, and possibly thyrephoran and sauropod prints can be found here too and some casts contain more than one print. All of the prints are individual and drop out of the lower surface of the sandstone bed as the softer sediment it sits on erodes from underneath it. The area is managed by the National Trust and it is against the law to remove any casts without permission; the site is widely visited by students and other interested parties specifically to view the prints, and this makes them a valuable resource for education and outreach.

I collected data on several casts and we inspected the full exposure before heading off to another site. A couple of the prints are shown here as 3D meshes processed in Photoscan and rendered in Cinema R13. Also here are the results of an experiment I tried whilst on site, where I attempted to record the crevasse splay sandstone in-situ in the cliff face. This was my first attempt at recording an outcrop using photogrammetry and the results speak for themselves, affirming it is possible to get good data on exposures of this size using this method over more expensive technologies such as Lidar. The above animation was created from data processed in Photoscan and rendered using Cinema R13.

You got to love photogrammetry!