Wednesday, 4 December 2013

PhD preparations in full swing

A way too spiky Polacanthus, with no sacral shield to boot.
I mean, we've known the dinosaur had one since 1881. Get a grip!

With less than a month to go before I start my Phd in earnest I am organising myself for the coming years of research. I already have a reasonable system of filing and directory structure that I've adapted from the methods I use in my day job as a motion graphics designer and 3D animator. I am used to handling large amounts of data (projects can run into hundreds of gigs for a large animation) and lots of footage is generated which means I need to keep track of exactly which versions I'm working on at any one point, and this has the potential to become very confusing if not careful. As I will be working on 3D data this system can be readily adapted to research, and I can use a similar system for writing and research.

Being self-funded also presents many challenges and I will have to choose activities such as visits to collections and meetings very carefully, and plan well ahead. Funding is going to be tight, and I could have called this blog 'Doing a PhD on a shoestring' as every penny will have to be watched and accounted for. This is not as bad as it sounds, as funding for the first couple of years is in place much of the software I use to earn a living shall be used in the course of research. The real issue will be affording hardware, and for the time being Im going to have to make do with what Ive got.

Part-time study needs to be reconciled with the day job and by necessity will be subordinate to paying work. I have no grants and no sponsorship and so need to keep working; l will be looking into both of these funding resources though, although part of me feels perhaps grants would be better off going to young researchers. I don't have the luxury of a permanent office in my institution and I will be studying from home most of the time although Im set up for this already (my institution, the University of Southampton is actually 200 miles away from where I live).

Even though I am working and studying at the same time I can turn this to my advantage. I will be creating a crossover between work and research which means I shall use the skills developed in either, in both. As much if my day job involves scientific visualisation I will be able to communicate more clearly with my customers as a consequence of being immersed in scientific method. Clients will appreciate having an artist that is also a scientist working for them, helping them to communicate.

Conversely, the years I have spent working in the cut and thrust of the commercial world should hold me in good stead when doing research. The work ethic is a given; I routinely work on high-pressure projects with tight deadlines and for very long hours in extensive stretches, so the volume of work isn't intimidating (yet). More important are the skills I have acquired using complex software for scientific visualisation and animation, and these will be put to good use and expanded upon in my research. Also, I will be looking at how some of the methodologies of the commercial world might be used in science outreach, for instance when assessing how the best delivery systems for 3D meshes and other data, including the re-use of data and assets generated during research and making the presentation of this data engaging whilst retaining scientific integrity. These will be part of the palaeontology outreach solutions I will be working on.

Another step closer to the mountain.

Thursday, 7 November 2013

PaleoIllustrata is dead. Long live PaleoIllustrata!



Palaeontologists spend a lot of time looking at rocks and fossils that have endured for eons and now provide us with a glimpse back into the past of our planet and its inhabitants, a journey into the vastness of deep time. Studying these specimens you get a real idea of the transience and impermanence of our world, a realisation that everything we see about us is in a state of constant flux; from the weathering of the sediments containing the fossils we study, the appearance and extinction of species, the uplift of mountain ranges and the constant drift of tectonic plates across the surface of the planet. Always in motion is the earth.

This sense of transience also applies to our everyday lives and the last year has, for me been a case in point. When I started PaleoIllustrata I intended it to be a portal for palaeoart on the internet, my own work and other oddments that caught my eye. However, as I became more involved in research at the National Oceanography Centre Southampton (NOCS), University of Southampton then I started posting more about events such as the SVP, SVPCA and Jehol meetings, my own research and things palaeontological in general, and less of the art. As it happens, palaeoart is well-served online by sites such as the excellent Love in theTime of Chasmosaurs and picfest Paleoillustration (to name but two) and so my contribution was, with hindsight, superfluous. PaleoIllustrata wasn't realising it's potential, and that's because I was not focussed enough and needed to alter the way I was approaching research. As it happens, a solution presented itself at just the right moment.

Just under a year ago it was suggested I might consider applying for a part-time, self-funded PhD at NOCS. I had never considered studying at this level before so took my time and sought advice off trusted colleagues and friends before looking for a suitable project. There were some issues with the practicalities of how this course of action might work. Firstly, it had to accommodate my job, as I am self-employed and the need to work is paramount and comes before everything (including sleep). Secondly, any degree I did would have to draw on my quarter-century as a commercial artist, animator and designer, especially as regards to my 3D work; in fact I wanted the exchange to be two-way, as a fair few my clients are scientific communicators and they will benefit from skills learned in the course of my research.

More importantly, was I capable of doing a PhD? I have learnt a lot since I started more structured research at NOCS, have attended and presented at meetings so was out of the blocks so to speak, but this was a major step and I spent a lot of time reflecting on and considering if I had the intellectual capacity, discipline and thoroughness to be a successful postgrad student. In some respects, I still don't know whether I do have these qualities or not, and time will tell. However, nearly a decade of being a sole trader has taught me much about my ability to draw on my own resources and tough out the hard times, so I was less worried by my work ethic.

Once it was established that I could make a part-time PhD work for me, I set out to find a project. I made many calls and spent many hours in conversation with friends who are established palaeontologists and patiently talked over the various research ideas I had. I spent time at meetings talking it over with colleagues who were generous with their advice and offered their opinions. I am so very grateful for this help which was massively important. I owe some beers.

I had my interview in September and accepted an offer a couple of weeks ago, and I start on the 1st January, with Dr. Gareth Dyke as my supervisor. I'll still be living up north at the edge of the Peak District and doing the day job (which I love and involves scientific visualisation, 3D and motion graphics and graphic design) so will be studying from a distance. However, my second supervisor is in Manchester and we're frequently on the south coast anyway. In fact, despite being raised a Brummie I was actually born in Winchester, so it feels right to be at Southampton.

Obviously, this means I am going to be pretty busy, and I can't see me continuing to post to PaleoIllustrata as I have been doing, so I am sorry to say the blog in its old form has passed. Gone. It has ceased to be. It is an ex-blog.

However . . . as outreach is a major part of my research proposal I need an online presence to document my research and my journey as a Phd student in his late forties. A blog would be ideal! So the next post will be on the new-look PaleoIllustrata, relaunched as one of the methods I will use to disseminate my research and write about the whole process of studying for a doctorate for someone like me, coming from a non-academic background. I'll still be posting about meetings and field trips as previously, but with a bigger dose of science and research. I will feature my artwork here too, as before but the focus has changed; indeed there is now a real focus to my research.

So what am I going to be working on? I'll expand on that in future post(s), but mainly on the Early Cretaceous nodosaurid Polacanthus, including biomechanics and soft tissue reconstruction.

A new journey, a new stage in my life. As a palaeontologist. Here goes! 

Thursday, 26 September 2013

Celebrating Dinosaur Isle: Jehol-Wealden International Conference. 2013

Last week saw the first ever ‘Celebrating Dinosaur Isle: Jehol-Wealden International Conference’ at the National Oceanography Centre (NOCs), Southampton, UK and hosted by the University of Southampton Ocean and Earth Sciences and the Confucius Institute. There were around 90 delegates for the talks and 40 for the field trip, including palaeontologists from all over the UK, Europe, China and the USA. As a venue NOCs is hard to beat as the building sits on the dock front and from the cafe are excellent views down Southampton Water, across the Solent to the Isle of Wight in the distance and has superb facilities. A room was dedicated to displays and vendors and next door was the lecture theatre, with lunch and refreshments served on the wide landing right outside the two, the proximity of which was useful as it maximised the time spent with other delegates. 

The exhibit room at the conference.


As the title suggests, the whole meeting concentrated on the Early Cretaceous of the Jehol of China and the Wealden of Europe.  The day kicked off with an introduction by conference organiser Gareth Dyke of the University of Southampton, followed by a brief welcome by Mark Cranshaw of the Confucius Institute. The first talk was John Radley on the Geological Conservation Review and featured the work of Percival Allen on the Wealden climate, work that is still relevant today. In an entertaining talk Hugh Torrens than discussed the ‘first dinosaur’ as recognised by Richard Owen and discovered on the Isle of Wight. In the next room was the specimen itself, kindly lent by the National History Museum, and naturally it attracted a lot of attention. Jeff Liston then talked about the legalities of fossil collecting in China, where there are strict rules about moving fossils across even provincial boundaries. Pascal Godefroit was unable to attend but Mark Witton finished the first session with a typically excellent talk on Jurassic pterosaurs and their importance in understanding the evolution of Early Cretaceous forms.

After coffee Paul Barrett delivered a comprehensive and well-illustrated review of dinosaurs from the Jehol Biota. He was followed by Darren Naish who has been working on the Eotyrannus monograph and whose description of the specimen was very thorough, providing lots of information along with great images of the fossil. Dave Martill discussed the dentition of the pterosaurs Istiodactylus and Longchengpterus, again with excellent hi-res photos of the specimens which looked spectacular on NOCs’ excellent projector system. Unfortunately M. Matsukawa was also unable to attend the meeting but Martin Lockley delivered his talk in his place, no easy task considering the complexity of recreating ancient food webs and trophic cascades.

Lunch gave everyone a chance to really study the exhibits in the room next door to the lecture theatre. Apart from the thrill of seeing the ‘first dinosaur’ there were parts of a Polacanthus on display, with a very impressive ilium and sections of the sacral shield, as well as various vertebrae and parts of the pectoral girdle and limbs. A team from Dinosaur Isle had various specimens on show, including a complete Iguanodon mandible and some large Baryonyx teeth. The model of Microraptor featured in Dyle et al’s Nature paper was present along its balsa wood counterpart, more on that later. The chaps from Lyme Regis had fetched over a selection of fossils for sale and The Bristol Dinosaur Project also had a display on their local dinosaur, Thecodontosaurus antiquus.

The first of the afternoon sessions started with Zihui Zhang from Beijing discussing an enantiornithine bird skull and its implication for other enantiornithines. A small enantiornithine was also the subject of Dongyu Hu’s (Shenyang) talk, and he was followed by Colin Palmer who gave an excellent talk on the work that went into the Microraptor paper mentioned earlier. Colin’s talk finished with video of the balsa model  of Microraptor being flown, and demonstrating the flightpath predicted by computer simulations was pretty accurate. Next up was Mike Howgate, who was expounding his view that Microraptor was in fact a ‘archaeopterygid’ bird and Eoraptor was a possible bird ancestor. Mark Young then talked about the “Shanklin Shocker”, a large metriorhynchid with teeth similar to may extant fish species such as piraƱa in that when the jaw is closed they give a shearing motion, very effective for tearing lumps of flesh off prey. The images of the damage a cookie-cutter shark can do to a human leg could put a person off paddling for life.

The final session started with my own review of dinosaur ichnology on the Isle of Wight, and this was followed by Martin Lockley (who needs no introduction to vertebrate ichnologists) who showed some of the work being done in China at the moment, including some of the quite astonishing museums being built to house collections and cover track sites, including one shaped like a huge tridactyl print. Steve Sweetmen then talked about his fascinating work on Wealden microvertebrate assemblages, and also showed a spectacular print from Cowlease Chine, in-situ in the cliff, made in mudstone and infilled with sandstone. Pam Gill closed the session with a comprehensive review of Wealden-Jehol mammals.

The evening was spent in the Red Lion in Southampton, a 12th century pub where delegates were entertained by Luke Muscutt and friends. Luke is a PhD student at the university and a brilliant musician. Needless to say, a good time was had by all and much discussion was had, including an impromptu ichthyosaur mini-conference in the back room.

Walking through the upper Wessex and Vectis formations, first stop on the field trip.
Next morning the field trip started out from the Red Jet terminal in Southampton and were soon heading across the Solent to East Cowes on the Isle of Wight, where everyone boarded a bus and headed to Sandown, home of Dinosaur Isle. The first stop was the beach at Yaverland, where under the guidance of expert Trevor Price delegates inspected the uppermost section of the Wessex Fm and the whole of the Vectis Fm, both of which are exposed in this small but very productive stretch of coast. The beach conditions meant the footprint layers were covered by sand, but everyone could search for fossils in the shingle and along the cliffs. Next up the trip visited the Wessex-Vectis junction and then spent some time examining the section, including the footprint-bearing beds of the Shepherd’s Chine Member, eventually making its way towards to Lower Greensand and its beautifully preserved shelly fossils. I’m pleased to say dinosaur bone was found!

Heading towards Hanover Point.

After an introduction by Jeremy Lockwood a superb lunch was had at Dinosaur Isle, where the lab was open and local collectors were present with their finds and palaeontologist Steve Hutt was present to discuss the collection. This included new Iguanodon material from Nick Chase (who donates to the museum), a piece of thyreophoran armour and some quite incredible Baryonyx material representing at least two animals; let us hope these important specimens not lost to science.

The multicoloured sands of Alum Bay. My Nan had a small glass tube of these on her
sideboard, but this was the first time I'd seen them first hand.

Next on the itinerary was a visit to Hanover Point and Brook Bay on the west coast of the island, led by Steve Hutt, Penny Newbery and Trevor Price. There delegates inspected the dinosaur footcasts that litter the beach on this part of the coast and which were particularly abundant given the time year (I’m pleased to say) and spent time prospecting in the shingle for fossils. More bone was found. Following pickup by the bus, everyone was taken to the Needles Park where many brave souls rode the chair lift to the beach to look at the famous Alum coloured sands, and upon re-ascent were treated to a fine buffet and drinks. We took the Red Jet back to Southampton around 9.15pm and the conference ended.

The chairlift down to the beach at Alum Bay. Gulp.
This meeting was a resounding success. The talks were all fascinating (I’m excluding mine here, others can be the judge of that), the venue and organisation spot on, as was the field trip. It was great to see so many Early Cretaceous workers in one space, and personally I’m hoping a lot will come out of the discussions had during the coffee breaks, in the pub and on the field trip. Having so many experts on the field trip was a real treat, and I personally learnt much for their generous and patient instruction despite having spent many years visiting some of these sites. Thanks are due to Gareth Dyke for organising the conference and Jessica Lawrence who assisted, as well as Dinosaur Isle and The Needles Park for their hospitality.

I am sure I join many others in hoping this conference will be repeated in years to come.

Thursday, 5 September 2013

Jehol-Wealden Conference schedule

The schedule for the upcoming Celebrating Dinosaur Isle: Jehol-Wealden Conference at the National Oceanography Centre in Southampton is now available, and is posted below (get a pdf version here). The conference consists of a full programme of international speakers on the 20th September and a very busy field trip (including two site visits) to the Isle of Wight on the 21st September. This will be an essential meeting for anyone working on or interested in Early Cretaceous research, and will provide a great networking opportunity. Booking via the conference web page at the University of Southampton web site.





Wednesday, 21 August 2013

Jehol-Wealden Conference Second Circular



The second circular for Celebrating Dinosaur Island: Jehol-Wealden international conference has been released. With a programme of international speakers and a trip to the Isle of Wight included it's going to be an exciting chance to get together with researchers working on Early Cretaceous palaeontology from all over the world at the outstanding University of Southampton facility at the National Oceanography Centre, located on the quay beside Southampton Water.


Wednesday, 3 July 2013

Triceratops 3D update

After another comment from Jamie Headden from essential palaeontology blog The Bite Stuff, I made a couple more alterations to the Triceratops sculpt, focussing on the rostral region. Here's the final mesh, and that's it (until I change it again).

Triceratops horridus. Click to embiggen.

Thursday, 6 June 2013

Building a dinosaur: the finished Triceratops sculpt

It's been a while coming, but the Triceratops sculpt is finally finished. At this advanced stage the fine detailing is added to the mesh as well as any adjustments that may be needed to  morphology.

Central to this stage of the process is gathering reference; in fact this task runs through every stage during the creation process. This involves looking for papers on integument, lesions on the skin as well as gathering references on colour and skin texture. Using extant phyogenetic bracketing (EPB) we can infer certain things about how a Triceratops might have looked; for instance we know birds have very bright colouration and the males often have structures designed for display, so we can consider whether ceratopsians used their head ornamentation for only for display or perhaps defence or species recognition too. We have fossil impressions of chasmosaurine skin so we have a reasonable idea how parts of the skin of Triceratops looked in terms of topology and we can look at extant animals and observe their colouration and how it relates to their ecology. One tool I've started using a fair amount to gather reference is Pinterest, which allows me to 'pin' images from the web to virtual boards, and works both in the browser on my desktop and in a standalone app on the iPad and iPhone. Using this tool it's possible to gather good reference quickly and easily, and store it all at one location that is accessible online.

Although we're not actually texturing this model at this stage, to my mind it's essential to consider integument when detailing a sculpt as it may well affect some of the decisions you make when adding detail will be reflected if you decide to texture a model.

I did all the detailing in zBrush, as this allows the artist to work at high resolution and at speed. I tend to create my own alphas as this gives me more control, but the built-in alphas are usable and a Google search will turn up many sources of free alphas to download. These can be resized to give different sized brushes and for the scales of Triceratops I created this alpha:

Ceratopsian scales. Oh yes.
I traced some scales from a reference image of ornithischian skin and blurred the image slightly to avoid jagged edges on the geometry. As scale size is not uniform over the body on either extant or extinct animals the ability to adjust the draw size gives flexibility when adding scales.

Next I added wrinkles, scars and detail to the horns and claws. I turn off symmetry on whatever brush I'm using for the final part of this to ensure variation which adds visual interest. I roughen up the skin here and there, add a few lumpy bits and other marks as this Triceratops is an older animal that bears the scars from it's years living in the Late Cretaceous world.

Detail of the hoary head.


Finally, I seek the comments of palaeontologists and other illustrators and make any suggested amendments. This is an important stage; it's very easy to get too close to your work sometimes, and you can end up making errors that are, when pointed out, embarrassingly obvious. Moreover, getting someone with experience to critique your work means you will have the most subtle of subtle changes pointed out to you, and this is a great opportunity to learn. It will help you immensely with the interpretation of the reference material used when creating artwork in the future.

So that's it! I'm now looking to get a 3D print made of the model, and I will texture and pose it of course, but that's it for the time being. I will hopefully get around to animating it at some point too.

Big thanks to all those who have commented during the process and especially to Scott Hartman for his invaluable input.

Tuesday, 28 May 2013

Jehol-Wealden International Conference 1st Circular




The first circular for Celebrating Dinosaur Island: Jehol-Wealden International Conference is now available for download here. For further information and proposals for presentations and posters contact: gareth.dyke@soton.ac.uk

I hope to see you there!

Friday, 10 May 2013

A photogrammetry primer for palaeontologists

video


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!

video


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

Tuesday, 23 April 2013

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.

Friday, 29 March 2013

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.


Monday, 11 March 2013

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.

Sunday, 17 February 2013

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.

Sunday, 3 February 2013

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.


Friday, 18 January 2013

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.

video

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!


Saturday, 5 January 2013

2013 and setting out on the path

The Christmas and New Year break gave me some time to reflect on the last couple of years of my life, on palaeontology and where I am now, and where I might be heading in the future. This introspective mood was triggered by the events of the last four months of the year which saw a distinct change in the way I was engaging with palaeontology and research, part of a wider arc of activity that had its roots back in the summer of 2010.

In July 2010 my wife and I went to dig dinosaurs in the Hell Creek of North Dakota and Montana. We'd been regular visitors to the Isle of Wight (off the south coast of the UK) for many years, going to search for dinosaur bones washed out of the island's cliffs of Wealden marl and sandstone. Nothing prepared us for the badlands: the searing heat, the biting insects; the rattlesnakes . . . also the sheer beauty of the place, the scale of the prairie and the badlands, and of course the dinosaurs. Lots of bits of dinosaurs. Heaven. During the week we were there we dug turtle graveyards, dinosaurs, prospected and found dinosaurs, dug some more, worked in the prep lab and talked palaeontology for a week . It would no exaggeration to say that week in the field (which wasn't all plain sailing due to circumstances beyond our control) was one of the best of my life, and I felt I had found my direction. But how to take this passion forward?

Skip to just over a year later, and we're sat in the back of a truck bouncing along a rough track in the desert of Utah. Along with the rest of the attendees in this and the other six trucks on the SVP field trip before the Las Vegas meeting, we're heading back to the highway after visiting a remote dinosaur trackway in the Warner Valley. During the hour or so we spent at this breathtaking location, I took some photographs of a dinosaur footprint that were my first attempts at photogrammetry and when Neffra Matthews handed me her laptop and I saw my images turned into a 3D model I knew this was it: science I could do myself. My world shifted on it's axis a fraction and things would never be the same. At the meeting itself I picked up a leaflet for a course at the University of Southampton, put it in my folder with all the other stuff I was collecting and headed off to the next presentation.

Back at home I started pursing the Southampton course, but it became apparent that it wasn't going to happen for various reasons including the dire economic situation. There was no way I could give up work and move south for a year (we live 200 miles to the north of Southampton) so it was deemed impractical. I was gutted (as a 45-year old man it felt as though my options were narrowing) as I knew I wanted to be more involved in palaeontology, and I wanted to learn and contribute. But how?

This blog was a starting point; one man's journey into the art of palaeontology. I had originally intended to make it solely about palaeo art and scientific illustration, and as I do scientific visualisations for the day job (mainly drug interactions at the molecular level) it made sense to blog about a subject I loved. I am surrounded by palaeontology books I have collected over the years and did a little myself so there was no shortage of material to go at. So I launched this blog and got a great reception from the mesozoic blogosphere and things were hunky-dory. I was off and doing something.

In the meantime, I became a research associate at Southampton and started doing science in earnest. I was concentrating on ichnology alongside photogrammetry and was working on my first poster, which was co-authored with Matteo Belvedere and Gareth Dyke and which was presented at EAVP in Spain in the summer of 2012. As the year progressed I became more involved, attending and presenting at DigitalFossil 2012 in Berlin and going to the SVP meeting at Raleigh, NC. Berlin was the highlight to be sure. I had never presented before and I got great feedback, and I was invited to co-host a photogrammetry workshop at the same meeting alongside Neffra Matthews, Brent Breithaupt and Peter Falkingham and this went very well, with high attendance and more very positive feedback; I hope we can do more in the future.

By this point though, Paleo Illustrata had lost its way a bit, and it had become 'One man's journey into the art and science of paleontology'. It dropped off one or two of the blogrolls for some reason despite getting a hit rate I was happy with, although it had become less about the art and more about the science. What I had realised was how much the science needed to inform the art, and as I got more into the science I got further away from my original art-based concept. It became less consistent in terms of subject and slightly more scattergun as I tried to cover all the bases as well as my deepening interest in the science of palaeontology. My research was continuing and as 2012 came to a close I presented a scientific illustration workshop at UoS and a couple of papers are being worked upon as the new year starts.

I have big plans for the coming year, and this blog will be a vital part of them. It will include more science, and the reason for this will become apparent in due course (if all goes to plan). It will include more personal observations and opinion because that's part of the journey. I will of course be continuing to address the subject of scientific illustration and paleoart, but it will be less from the angle of an enthusiastic amateur and more from a palaeotologist's point of view and I hope the merger of science and art will become more of a practical resource rather just than me commenting on other people's work (a task successfully fulfilled by people far more better at it than I).

So here goes for 2013. To all my loyal readers - thank you for sticking with me. For any new or returning readers, please stick around and hopefully some of my blather will be of interest. I've received encouragement and valuable advice from many of the people I've met in the last couple of years (and the years before, here in England) from professional palaeontologists to amateurs like myself with a deep love of the subject, and many of them I am proud to call my friends; their patience and generosity has been amazing. I'm very lucky to have a wonderful wife who has supported me throughout these two years, without that support I'd not have come as far as I have. For everyone, have a great 2013 and here's to a new year of palaeontology, ichnology and art. 

Finally a path is emerging and although I doubt it will be straightforward or without bumps and crossroads, but I can't wait to see where it takes me. Come along for the ride.