Using photogrammetry to capture data in the round

With DigitalFossil 2012 in a few week's time it seemed appropriate to post some of the work I've been doing recently. Part of this has focussed on creating a workflow for capturing data a full 360-degrees with minimal loss of data, which leads to holes in the mesh and distortions. By way of an illustration here is an animation of an early 360 capture of the cast of a Conchoraptor sp. skull, showing the wireframe, mesh and textured model. It loops seamlessly for your viewing pleasure.

Neoichnology in the desert

Here in the UK we're a little short of deserts, so whilst in the US for last year's SVP we took advantage of visiting the Mojave and spend some time with the SVP field trip in Utah and northern Arizona. Below is a small selection of tracks we encountered whilst out and about.

Arthropod track. Coral Pink Sand Dunes, Utah.

Arthropod track. Coral Pink Sand Dunes, Utah. Notice other tracks crossing nearly perpendicular to
the double-lined track, possibly an arachnid trace.

Kangaroo Rat. Coral Pink Sand Dunes, Utah.

The Beehives, Valley of Fire, Nevada. This trackway, which obviously belongs to a large mammal
was a few hundred yards away from the car park. Note the paired footprints and tail drag mark.

Close-up of one of the footprints from the trackway pictured above.
Could this be a coyote trackway?

Finally . . . ichnology courtesy of the old ones. Vicinity of Atlatl Rock, Valley of Fire, Nevada.
My wife spotted this track on the underside of a large fallen boulder that had petroglyphs on the outer face. Note very narrow pace angulation, deep impressions and displacement rims suggesting
soft substrate and possible bioturbation traces on the surface. A beauty of a track
but we had zero time to record it as we were already being called back to the truck. Bah.

I wish I had more time to record all of these traces properly, but time didn't permit, especially on the Valley of Fire trip which was an excursion from Las Vegas, and was running to a strict schedule. Also, I wasn't so ready for photogrammetry at the time, now it would be very different!

Encounters with wildlife in the field

There's no doubt that seeing wildlife whilst doing fieldwork is one of the most exciting, entrancing and memorable experiences for a palaeontologist. Fieldwork helps a person feel a strong connection to the landscapes they work in, and seeing the animals and plants that actually live there is a massive thrill.

This set of photographs are records of some of the encounters I've had whilst engaged in fieldwork. I make no apologies for the bias to US species, as these trips had so much wildlife it was quite astonishing, and of course novel to have so many species of large mammals, reptiles and birds of prey to observe as we travel through and work the badlands. You might notice the images from North Dakota and Montana are surprisingly green for late June, this is because of the exceptionally damp year so far. As local garage owner Jim Martin said "You can tell it's been a wet spring when the clover's high on the gumbo banks".

Sea anemone (Sagartia elegans), Isle of Wight. Found in a rock pool whilst looking for dinosaur bones.

Bighorn Sheep, Zion National Park, Utah.
We came across a herd of these whilst on the 2011 SVP field trip.
I'm not sure, but I think this might be the subspecies Ovis canadensis nelsoni, or Desert Bighorn Sheep
which occurs in the Southwestern deserts of the US (wikipedia).

Unidentified invertebrate, Hell Creek Formation, North Dakota.
This intriguing little fellow was spotted by two of the
field crew when we went to check the sites at the start of the 2010 field season. It's head end
(unless it was in permanent reverse) is towards the top and it's around 4mm long. There was some
speculation it might be an aphid of some description, I wondered if it was a caterpillar.

Mule Deer (Odocoileus hemionus), South Rim, Grand Canyon, Arizona. Our guide Barry called these Kanab Deer, and These might be a subspecies of Mule Deer unique to Mexico and Arizona (wikipedia) known as the Desert Mule Deer, Odocoileus hemionus eremicus, although I think their range is further south. This handsome fellow was spotted from the trail that heads east from Grand Canyon Village. There were does and fawns around too.

Common Side-Blotched lizard (Uta stansburiana), Potter's Canyon, Arizona.
This attractive lizard was not for hanging about but did pose long enough for a couple of pics.

I have to be honest, I have no idea what this is but it was found by Professor Tom Hollocher
in the badlands of the Hell Creek Formation, North Dakota.

Plains pricklypear (Opuntia polycantha). Hell Creek Formation, North Dakota. 

A young rattlesnake (unsure of the species) warns us in no uncertain terms - stay away. Montana.

Common Raven (Corvax corax), South Rim, Grand Canyon, Arizona.
These magnificent birds frequent the trails around the canyon.

Desert Striped Whipsnake (Masticophis bilineatus lieolatus). Potter's Canyon, Arizona.
This fantastic snake was spotted during an SVP field trip. A shed skin was found nearby,
and it may well have come from this animal.

I think this a Woodhouse's Toad (Bufo woodhousii), Hell Creek Formation, North Dakota. 

Wild Turkey (Meleagris gallopavo), Montana. The first time I ever saw a wild galliforme in the US was
when a pair of these wonderful birds came close to our trucks when we stopped to
chat to the landowner to get the lowdown on conditions in the badlands.

Tarantula (Aphonopelma sp.), Warner Valley, Utah. This is a male possibly out on the hunt for
a female. It was small, a wonderful blue-grey and a real beauty.

Next: Tracks and traces in the desert.

Incidental finds in the field

One of the many joys of fieldwork is the fact you have no idea what each day might bring. Apart from the main focus of your work delivering up constant surprises, the environment you are working in is often as fascinating and throws up seemingly endless delights. If you are digging in a foreign country, then this effect seems magnified and everything around you becomes a vital part of the experience. The very nature of fieldwork means you are getting up close and personal to the land and the flora and fauna you share it with for the duration of the trip. On top of all this, there seems to be a sense of heightened awareness: in the rock you are working, the weather, the lay of the land, the sounds. . . . well, you understand. The context of the physical and mental activity that is fieldwork.

So here is the first of three posts that deal not with the fieldwork itself, but the incidental finds that over the years have attracted my attention. These may seem mundane or irrelevant and of course scientifically they are, but these finds are as much a part of the field experience as the fossils we strive to discover and understand. 

Three articulated vertebra, bleached by the sun.
No idea what they belonged too, but I'm guessing artiodactyl.
Hell Creek Formation, South Dakota, USA.

The wreck of The Carbon. Compton Bay, Isle of Wight, UK.
You need a low tide to get this close too the old metal-hulled boat, which came to grief on the rocks of the Wessex Formation, Wealden. She was a 175-ton steam tug that was under tow in November 1947 when she came loose and ran aground.

Deer leg. We saw Mule deer in the area of our quarry, but this also might be a Whitetail
or Pronghorn, both of which live on the prairie and badlands. Hell Creek Formation, South Dakota, USA.

Upper jaw fragment. Once more, I have no idea what this is from, but I'll go with artiodactyl as a guess.
Potter Canyon, Dinosaur Canyon Member, Moenave Formation, Arizona, USA.

Native American microlith. In the UK, this would come home but there are understandably
very strict laws regarding the removal of Native American artifacts, so it stayed in-situ.
Moccasin Mountain, Navajo Sandstone Formation, Utah, USA.

Petroglyphs, Fort Pierce, Utah, USA. These superb petroglyphs are carved into the desert varnish
on outcrops of Shinarump Member of the Chinle Formation.
We also heard a very loud boom at this point, possible sonic, mine or other blasting.
As for what these petroglyphs actually depict, there is plenty of debate and interpretations vary.

Where possible, I always bring incidental finds home as they act as not only objects of interest in themselves but reminders of a moment in time, which often have very happy memories. Antlers, skulls, sea glass, various sub-fossil bones, teeth, hagstones, feathers, shells minerals and one day a rather fine geological hammer all enter the collection and each has a memory attached. Wonderful.

Next: Critters

Photogrammetry: Two dinosaur footprints from The Isle of Wight

The Isle of Wight, which lies off the south coast of England, has long been a good spot to find dinosaur footprints and other traces of ancient life. The rocks of the Wessex and Vectis Formations, part of the Lower Cretaceous of the Wealden of southern England, contain numerous examples of trace fossils of many kinds, from dinosaur footprints and invertebrate traces to palaeoenvironmental indicators such as ripples and mud cracks.

At least two distinct palaeoenvironments are represented in these formations. The Wessex Formation is interpreted as representing a braided river system complete with crevasse splay sandstones, ephemeral ponds and lakeside margins, all containing trace fossils (Naish and Martill, 2001). The deposits of the Vectis Formation were laid down in a coastal lagoonal environment and contain facies interpreted as mudflats and storm coquinas, both of which also preserve traces of ancient life (Radley and Barker, 2000).

On my last visit to the island I took the opportunity of recording some of these footprints using photogrammetry, and here are a couple of the meshes I was able to create. These are both from the trackway at Hanover Point, and are well-known; perhaps too well known as one print has been removed with a rock saw, and a second was in the process of being removed when the it finally dawned on the not-so-smart thieves that the rock was way too unstable to make the operation worthwhile, but not before one footprint was lost forever.

Figure 1: 3D mesh of tridactyl footprint from the Wessex Formation
of the Isle of Wight, UK.

Figure 1 shows the footprint that was in the process of being removed. This is the best preserved of the remaining prints. It's a tridactyl pes print, and has a distinct claw-mark on the leftmost digit.

Figure 2: 3D mesh of a second footprint from the same trackway as the footnoting illustrated
in figure 1.

The second print is much less well-defined and demonstrates how much variation is possible in footprint morphology within a single trackway.  The left most digit has one clearly defined node, the rest of the print indistinct; this might indicate the substrate might have variable texture and/or consistency, or the footprint was subject to alteration after being made. The line running throughout the print is a natural fault.

This trackway is well worth seeking out if you're visiting the island, although you'll need a low tide and some time to find them out on the rocks. Professionally guided tours are available from Dinosaur Isle. Please note it is illegal to remove or attempt to remove any footprint found on the south-east coast of the Island.

References:

Martill, D. and Naish, D (Eds). 2001. Dinosaurs of the Isle of Wight, 319pp. The Palaeontological Association, London.

Radley, J. and Barker, M. Paleoenvironmental significance of storm conquinas in a Lower Cretaceous lagoonal succession (Vectis Formation, Isle of Wight, England). 2000. Geological Magazine, 137. pp193-205. Cambridge University Press.

Neoichnology: bioturbation around ephemeral ponds

Randomly oriented dinosaur track assemblages occur frequently in the fossil record (Thulborn, 1990) and form under a variety of conditions. Thulborn states that these random assemblages can appear to represent a patch of ground with high dinosaur traffic that are passing through, but some sites have been interpreted as being the margins around water holes (Martill and Naish, 2001).

I went to check out a local ephemeral pond situated on farmland to see if there was evidence of bioturbation, and was able to do some photogrammetry on what I found. All images were taken between 1pm - 1.30pm on a bright, sunny day (at last!) in late May.

Ephemeral pond in grass crop grown for silage.

The pond is located in a field used for growing grass for silage, after each cutting (which occurs three times a year) cattle are allowed to graze briefly before being excluded again as the crop resumes growth. The small pond is present during the winter months and occasionally re-appears after extended wet spells over summer, however the pond gradually dries up as spring progresses. The pond appears to be fed by water draining off adjacent fields; no streams fed into the pond and it is situated in a shallow natural hollow.

I have often seen mallards at the site of this pond, and fully expected to find evidence of their presence in the form of footprints and tracks, as this site is close to where I recorded duck tracks in mud alongside a small stream; this photograph is taken from the foot of the levee which separates the stream from the field (this stream feeds into a reservoir around half a mile away and never floods into the adjacent field).

Zones of substrate consistency surrounding the pond.

As can be seen from the photo above there are three possible zones of substrate consistency. The outer margin is dry and hard, and coated with slurry applied by the farmer when wetter conditions persisted. A dried out microbial mat might also be present here. Red Deer footprints are present in this zone and these too were made when the substrate was wetter.  There was one canine trackway which was too big for a Red Fox and probably represents a pet dog. Goose and other bird droppings were present. The middle zone consists of slightly dryer area containing some deer footprints and is covered by a microbial mat which has formed over the decomposing slurry. The layer constituting the pond margin is waterlogged, and like the rest of the site consists of fine-grained sediment. There is no evidence of slurry or microbial mat in this zone. So we have a homogenous substrate with varying consistencies with a surface covered with fibrous, decomposing vegetable material and a microbial mat present in at least one zone.

3D model generated by photogrammetry.
Bioturbation in the pond margin, consisting of monotypic, randomly orientated bird footprints.

The pond margin zone was heavily bioturbated. The tridactyl tracks are randomly orientated, monotypic and all of uniform morphology. It's likely this represents a single species of bird visiting the pond to drink or feed, although no signs of probing appears present in the substrate. The term for a fossil association of tracks preserved in a single horizon is ichnocoenosis (Leonardi, 1987), I so I guess this assemblage would be termed a neoichnocoenosis.

Close-up of untextured mesh which shows the chaotic nature of the bioturbation.
Footprints and partial footprints are overlain

Textured version of the mesh. Note quality of mesh is so good the individual nodes
of each digit are clearly visible in some footprints, especially the central print.

The two images above are close-ups of the mesh, untextured and textured. The print in the middle of the image clearly shows the nodes of each digit, as well as displacement rims and is impressed deeply into the wet substrate.

The tracks are different form the duck tracks recorded in the local area. They are smaller, show no sign of interdigital webbing (as can be seen, the footprint impressions are deep) and there is a large hallux present. However, the prints are large enough to rule out many of the smaller birds to be found in the local area, and it might be that the track maker was a corvid, gull or pheasant, all of which are abundant locally. The pheasant can probably be ruled out as it has a very short hallux (see image below), and no interdigital webbing would rule out gulls as track makers. The most likely candidates are corvids and the pond lies below the route which rooks use twice daily between the local roost and the fields where they feed, and jackdaws, magpies and common crows are all present.

Of course, the prints we're looking at here are concave epireliefs, or moulds. It would be impossible to see the cast (or convex hyporelief) of these prints in the real world, but photogrammetry allows us to look underneath and view the bioturbated surface from below. The ability to look at tracks as moulds with adjustable light angles is a useful tool in footprint morphology interpretation.

The underside of the mesh, showing the tracks as casts instead of moulds.

References:

Thulborn, R.A. 1990. Dinosaur Tracks, 310pp. Chapman and Hall, London.

Martill, D. and Naish, D (Eds). 2001. Dinosaurs of the Isle of Wight, 319pp. The Palaeontological Association, London.

Leonardi, G. 1987. Glossary and Manual of Tetrapod Footprint Palaeoichnology, 43pp. Departamento Nacional de Produçao Mineral. Brazil.

Laridae vs Columbidae - guess who won.

We took a trip out yesterday to Chester and the North Wales coast. Having never visited Chester before I was looking forward to seeing the famous medieval Rows and visit the cathedral. The Rows were fascinating, the cathedral we didn't get to see as it cost 6 quid to get in if you weren't a worshipper; as we're not religious we departed.

What we did get to see was slightly less aesthetically pleasing to the eye but equally fascinating. In a nearby area hard to the city walls called the Kaleyards we spotted a Lesser Black-backed Gull attacking and eating a feral pigeon; avian dinosaur predation in an urban centre.

Feral pigeons seek respite from the weather in the lee of the city walls.
The large stones in the bottom of the image are Roman.

This area (named as the spot was where monks grew vegetables in days of yore) has an impressive coop and the area is home a large number of feral pigeons (and the odd duck, not in shot) all of whom use the city walls as shelter from the elements. When we arrived the gull had already disabled the pigeon, and whether it had attacked a healthy bird or picked on an injured or weak one we did't see.

Gull attacking still-alive pigeon.

The pigeon was still very much alive however, and the gull was pecking towards the rear of the bird. After several minutes the unfortunate pigeon gave up the ghost and the gull continued to feed, before a parking motorist scared it off. It waited a while on a nearby lamppost for a while, then flew out of sight and then returned after a few minutes and continued to feed. Lesser Black-Backed gulls have been noted as predators, and intraspecific predation in colonies of the species have been recorded by Davis et al.

The prey had been dragged a few metres away by now, and had expired.

It was a gully day. We saw Herring gulls nesting on the roof of the railway bridge, Herring gulls nesting in a window seat in a tower at Conwy castle and lotsa gulls in Llandudno, as you would expect. Here's some pics for all admirers of the Laridae out there.

Room with a view: a brooding Herring Gull at the magnificent Conwy Castle.

Adult Herring Gull on the pier at Llandudno. Ever the opportunists, these gulls are
quite bold when scavenging from the food discarded by humans.

Immature Herring Gull, also at Llandudno and keeping a close eye on the activities
of the anglers fishing of the end of the pier.

Refrences:

J.W.F. Davis, E.K. Dunn (1976). Intraspecific predation in Lesser Black-Backed Gulls Larus fuscus. International Journal of Avian Science 118, 65-77.