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Posts Tagged ‘CT’

Freezermas continues with track 3 of our rockin’ anatomy concept album! The number of the beast today is 5 (five days to go in Freezermas!), and I will deviate from the rock/metal theme to embrace the other side of the tracks: hip hop and rap. The Beastie Boys and I go way back: their “Licensed to Ill” album was the second cassette tape I bought (I remember proudly showing it off in Geometry class, circa 1986/7), and still ranks as one of my favourite albums ever. Everyone should own a copy of that, and of this next album…

The Five Felids, featuring KC

If only MCA were still alive to do this follow-up album…

The Beastie Boys’ superb, old school rap NYC-style (and themed) “To The Five Boroughs” (2004) satisfies my search for a #5-themed concept album/song. No track has that title, so I’m going with this one, “Triple Trouble” (song 3; day 3 of Freezermas… c’mon this is all just an excuse for me to talk about music I like and celebrate the concept album/freezers anyway!), as an introduction to a collaborative cat (felid) project we’ve started; and to continue the felid theme from Sunday (also be sure to check out the Snow Leopard dissection I posted on earlier!):

If You If You 
Wanna Know Wanna Know 
The real deal about the cats
Well let me tell you 
We’re felid funded ya’ll 
We’re gonna bring you some mad facts

(yes, that’s painful, I know… be relieved, I tried working some rap jargon into this post’s text but it just looked wack)

Dodgy-looking bagged-up skinned jaguar (bag-uar?) after delivery from Scotland.

Dodgy-looking bagged-up skinned jaguar (bag-uar?) after delivery from Scotland.

Anjali Goswami at University College London, myself, and Stephanie Pierce have teamed up to join the former’s skills in mammalian evolution, morphometrics, evo-devo and more together with our RVC team’s talents in biomechanics, evolution and modelling, and to apply them to resolving some key questions in felid evolution. We’ve hired a great postdoc from Bristol’s PhD programme, soon-to-be-Dr. Andrew Cuff, to do a lot of the experimental/modelling work, and then we have the marvellous Marcela Randau as a PhD student to tackle more of the morphometrics/evo-devo questions, which we’ll then tie together, as our Leverhulme Trust grant’s abstract explains:

“In studying the evolution of vertebrate locomotion, the focus for centuries has been on limb evolution. Despite significant evolutionary and developmental correlations among the limbs, vertebrae, and girdles, no biomechanical studies have examined the entire postcranial skeleton or explicitly considered the genetic and developmental processes that underly morphological variation, which are captured in phenotypic correlations. We propose to conduct experimental and geometric morphometric analyses of living and fossil cats, including the only large, crouching mammals, to study the evolution of locomotion, the mechanical consequences of size-related morphological evolution, and the evolution of correlations (modularity) in the postcranial musculoskeletal system.”

Above: snow leopard (headless) reconstructed and taken for a spin

Our study will integrate some prior studies from Anjali’s group, on modularity for example, and from my group, on the apparent lack of postural change with increasing size in felids (most other birds and mammals get more straight-legged as size increases, to aid in support, cats don’t– paper forthcoming). How does the neglected vertebral column fit into these limb-focused ideas? We’ll find out!

And it’s all very freezer-based research, using a growing stock of specimens that we’ve collected from zoo/park mortalities, many of which are kindly being supplied by Dr. Andrew Kitchener from the National Museums Scotland. We’ll be scanning, dissecting, measuring and modelling them and then returning the skeletons to be curated as museum specimens. This page features five sets of felid specimens involved in the research. We’ll be presenting plenty more about this research on this blog and elsewhere as it continues!

Above: ocelot from Freezermas day 1, now in 3D!

The Bag-o-Cats: whole specimens of a black-footed cat (Felis nigripes), juvenile cheetah, and juvenile snow leopard. I think. Sometimes you get a bag-o-cats and are not sure.

The Bag-o-Cats: x-ray CT slice showing whole specimens of a black-footed cat (Felis nigripes), juvenile cheetah, and juvenile snow leopard. I think. Sometimes you get a bag-o-cats and are not sure.

Panthera atrox (large American lion) from the NHM in LA. Oh yes we'll be applying our insights to strange extinct cats, too!

Panthera atrox (large American lion; “Naegele’s giant jaguar”) from the NHM in LA. Oh yes we’ll be applying our insights to strange extinct cats, too!

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Seven dead old limbs
Seven science wins
Seven icy forms beheld
And our trip begins

Seven anat’my jokes
Seven bloody posts
Seven are our sci-comm fires
Seven frozen choirs…

(props to Iron Maiden’s “Moonchild” opening lyrics, from the iconic “Seventh Son of a Seventh Son” concept album, of lofty, epic, frozen, anatomy-bearing motifs)

7th Son

So we come full circle to another Freezermas, another foolhardy attempt to honour Charles Darwin (his birthday is Weds 12th Feb) with seven blog posts in seven days!

There will be mysterious morphology! Expositions of new projects and a new paper! Detailed dissections showing amazing anatomy! Silly songs and other nonsense! So much more that I have no idea about at this writing but will surely come to me! (there is an amorphous plan)

Last year I invoked the 7 days of Freezermas song, but this year the songcraft has changed. Christmas is so 2013! Time for a 1970smodern approach! We’re doing hard rock/heavy metal concept album songs and motifs each day. I started off with one above. Future posts will try to stick to a theme of songs/albums featuring numbers, counting down from seven. Because we all know that Darwin loved to rock. But let’s get on with the real rockin’: the freezer-based anatomical science!

Today we’ll ease you in to Freezermas: The Concept Album, like the acoustic intro of Moonchild did, with some simple Mystery CT Anatomy…

(insert guitar solo here while you mentally prepare yourself)

Stomach-Churning Rating: 2/10; simple CT scan of a body.

Mystery Anatomy 2014: same rules as before; remember that the scoreboard has been reset.

Identify the animal in the CT scout/pilot image below, as specifically as you can. 

Today’s special rule: Your answer must be in the form of a lyric (at least 2 lines) from a song by Queen (Google some if you’re unfamiliar– but how?).

Why Queen? One should never question Queen; not a little or a lot.

Difficulty: Is this the real life? Is this just fantasy?

You will probably want to click to emgiganticate the image below.

Mystery CT 11

Don’t let this one drive you Stone Cold Crazy! I know you’re feeling Under Pressure; just Tie Your Mother Down and play The Game.

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Well lookie here… it’s a new Mystery CT slice challenge! And it’s appearing while Society of Vertebrate Paleontology members are busy drinking and eating at the conference’s welcome reception– how naughty of me!

What is it, what species, etc.– tell me what you can.

RULE: Your answer must involve excessive alliteration!!!

Prodigious perambulations of appropriate prose promise to procure prodigious points!

Remember: the scoreboard is here.

Difficulty: lumpy + alliteration + possible intoxication if you are an SVP attendee (John whistles innocently).

Stomach-Churning Rating: 1/10 unless you have lump-associated PTSD.

Proceed, plucky puzzle ponderers!

Mystery CT 10

EDIT: These images give the answer and show some cool features. It’s an Asian elephant skull, NHMUK 1984.516, of a juvenile animal (probably a UK zoo animal). Gotta love that pneumaticity!
Elephant skull _Se1_Im002

And another view:

Elephant skull _Se1_Im001

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Just a quickie here! I’m finishing a little sabbatical at Brown University and had a bit of downtime, then ran across this confusing image that seems to have loveable, sometimes-superhero Sesame Street character Grover in it, and also poses a tough but solveable Mystery CT Slice post! So go for it! Can you find Grover? (no points for that) and can you tell us (1) what the image is of (animal/species, region of anatomy, identifiable bits), and (2) what the heck is wrong with this image and why?

Scoreboard is here for easy reference.

Difficulty: fuzzy image, amusing childhood memories.

Stomach-Churning Rating: 1/10 unless you have bad childhood memories associated with Grover.

This is the mystery image below, not the Grover image above! You cheeky monkey.

No rhyming in your answers or you lose 10000000 points! Grover is grumpy today and hates rhymes. He had a bit too much Hefeweissen and polka music last night. Pity the poor creature.

MysteryCT9

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I have a rant to do, and an anatomy vignette or two, but before I do, here is a puzzleroo: It’s a reconstructed CT scan. I’ve digitally cut off the head to be tricksy. Come on man, I ain’t just whistlin’ Dixie! What is this beastie? Not hard in the leasty.

(your answer needs neither rhyme nor Shakespearean meter, but do take the time and provide the Latin binomen for reala– don’t just call it Peter or Sheila!)

Stomach-Churning Rating: 1/10. It won’t bite.

Difficulty: decapitation.

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…a daily picture of anatomy! And today it is five pictures; zza-zza-zee! ♫

Welcome back againagain, (gasp, pant) and again to Freezermas

I’m letting the dogs out today. Science gone barking mad! Hopefully my puns will not screw the pooch.

Stomach-Churning Rating: 4/10; a dog cadaver’s leg (not messy), then just tame digital images of anatomy.

I am working with Rich Ellis, a former MSc student at Univ. Colorado (see his cool new paper here!), for a fun new collaboration this year. He was awarded a prestigious Whitaker Foundation scholarship to do this research, which focuses on how different animals stand up from a squatting position, with the legs about as bent as they can be.

We want to know how animals do this standing up movement, because it is in some ways a very demanding activity. Very flexed/bent limb joints mean that the muscles (and some tendons) are stretched about as far as they ever will be. So this places them at disadvantageous lengths (and leverage, or mechanical advantage) for producing force. We know almost nothing about how any animal, even humans, does this-- how close to their limits of length are their muscles? Which muscles are closest? Does this change in animals with different numbers of legs, postures, anatomy, size, etc? Such fundamental questions are totally unaddressed. It’s an exciting area to blaze a new trail in, as Rich is doing. So far, we’ve worked with quail, humans, and now greyhounds; in the past I did some simple studies with horses and elephants, too. Jeff Rankin from my team and other collaborators have also worked on six species of birds, of varying sizes, to see how their squat-stand mechanics change.  Thus we’ve covered a wide diversity of animals, and now we’re learning from that diversity. “Diversity enables discovery,” one of my former PhD mentors Prof. Bob Full always says. Too true.

Greyhounds are interesting because they are medium-sized, long-legged, quadrupedal, quite erect in posture, and very specialized for fast running. Fast runners tend to have big muscles with fairly short fibres. Short fibres are bad for moving the joints through very large ranges of motion. So how does a greyhound stand up? Obviously they can do it, but they might have some interesting strategies for doing so- the demands for large joint motion may require a compromise with the demands for fast running. Or maybe the two demands actually can both be optimized without conflict. We don’t know. But we’re going to find out, and then we’ll see how greyhounds compare with other animals.

To find out, we first have to measure some dogs standing up. We’ve done that for about 8 greyhounds. Here is an example of a cooperative pooch:

Those harmless experiments, if you follow me on Twitter, were live-tweeted under the hashtag #StandSpotStand… I dropped the ball there and didn’t continue the tweeting long after data collection, but we got the point across– it’s fun science addressing useful questions. Anyway, the experiments went well, thanks to cooperative pooches like the one above, and Rich has analyzed most of the data.

Now the next step involves the cadaver of a dog. We could anaesthetize our subjects and do this next procedure to obtain subject-specific anatomy. But it really wouldn’t be ethically justified (and if I were an owner I wouldn’t allow it either!) and so we don’t. A greyhound is a greyhound as far as we’re concerned; they’ll be more like each other than either is like a quail or a human. Individual variation is a whole other subject, and there are published data on this that we can compare with.

We get a dead dog’s leg — we don’t kill them; we get cadavers and re-use them:

Greyhound hindlimb for CT

We study the hindlimb because birds and humans don’t use their forelimbs much to stand up normally, so this makes comparisons simpler. We’re collecting forelimb data, though, as we work with quadrupeds, for a rainy day.

We then CT scan the leg, getting a stack of slices like this– see what you can identify here:

It’s not so clear in these images, but I was impressed to see that the muscles showed up very clearly with this leg. That was doggone cool! Perhaps some combination of formalin preservation, fresh condition, and freezing made the CT images clearer than I am used to. Anyway, this turned out to be a treat for our research, as follows.

We then use commercial software (we like Mimics; others use Amira or other packages) to “segment” (make digital representations in 3D) the CT scan data into 3D anatomy, partitioning the greyscale CT images into coloured individual objects– two views of one part of the thigh are shown below.

What can you identify as different colours here? There are lots of clues in the images (click to embiggen):

Hindlimb segmentation of greyhound

And here is what the whole thigh looks like when you switch to the 3D imaging view:

Quite fetching image, eh?!

The next steps after we finish the limb segmentation are to apply the experimental data we observed for greyhounds of comparable size by importing the model and those data into biomechanics software (SIMM/OpenSim). We’ve done about 40 models like this for various species. I detailed this procedure for an elephant here.

Then, at long last, science will know how a greyhound stands up! Wahoo! Waise the woof! Stay tuned as we hound you with more progress on this research-as-it-happens. Rich just finished the above thigh model this week, and the rest of the leg will be done soon.

Many thanks to Rich Ellis for providing images used here. And thank you for persevering my puns; they will now be cur tailed.

Happy Freezermas! Sing it: “On the fifth day of Freezermas, this blo-og gave to me: one tibiotarsus, two silly Darwins, three muscle layers, four gory hearts, a-and five stages modelling a doggie!” ♪

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I’m not sure if this is a new tradition at this blog or not (probably not), but hey let’s give it a name: an Anatomy Vignette. Just something curious I notice during my research that deserves more than just a tweet. I borrowed some bones from the University of Cambridge Museum of Zoology (whom I love, because they have great exhibits and are very research-friendly) to CT scan for some projects. I noticed this:

femur-path

And I thought “Ouch! That’s nasty, dude.” (the holes in the bone just above the knee joint– these should just be a roughened area where the adductor muscles and other leg muscles attach)

So I was interested to see the CT scan images to find out how these possibly osteomyelitic lesions continued into the bone. They’re really pervasive, continuing into the marrow cavity quite far up the femur, as this shows (good CT-viewing practice to match up what you are seeing in the photo above with this movie):

I would be surprised if this was not the reason this animal died (presumably being euthanased at a UK zoo). There would have been extensive infection and pain resulting from this bony disease. How did it originate? Who knows. Maybe the animal strained a muscle and bacteria got inside, or maybe there was a fall or other injury. Hard to tell.

Oh, and also note the lack of a true marrow cavity in hippos, which is true for all the long bones. The “cavity” is filled in with cancellous bone. Same with rhinos, elephants, and many other species… science doesn’t entirely know why but this feature surely does help support the body on land, and grants at least some extra negative buoyancy in water; at a cost of some extra weight to lug around, of course.

And so ends this Anatomy Vignette.

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More mysterious morphology for you

I hope that you like it too

But there is a trick

The bone here is thick

And the beast might be rude, it’s true!

(What is it and what from? Answers must be in limerick form to count. Pilot scans explained in this post.)

This post is dedicated in memory of the late, great Professor Farish Jenkins, Jr; one of the best anatomists and functional morphologists ever. Excellent retrospectives here and here and here.

Aaaaaand here is the current scoreboard, as promised last time; starting from this post onwards–

RULES: 5 pts for correct, spot-on and FIRST right answer, 4 pts for very close or second, 3 pts for partly right or third in line with right answer, 2 pts for a good try, 1 pt consolation prize for just trying, or for a good joke!

If you post as “anonymous” name then it all goes into the same tomb of the unknown anatomist.

If you change your answer, you lose ~1 pt. Answers posted via Twitter, Facebook, email or whatever do not count! No appeals. I am a frigid dictator. :-)

(more…)

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I stumbled across some old pics, which I thought I’d lost, from the filming/preparations of 4 episodes of Inside Nature’s Giants (Jan-Feb 2009) at the RVC. They form a nice accompaniment to my previous post reflecting on my experience with the show, and the timing is great because I’m about to head to Raleigh, NC to talk about this research at the Society for Vertebrate Paleontology conference.

Stomach-Churning Rating: 4 at first (just a dead animal; and a rather clean one at that), then about halfway through the dissections start and it edges up to a 7 or so.

These pictures are sadly some of the few I have of the whole, intact body of a gorgeous adult Nile crocodile (Crocodylus niloticus) that the Windfall Films team managed to get to the RVC from La Ferme Aux Crocodiles in Pierrelatte, France. (I have scores of pics of the dissected limbs, shown further below) As the title indicates, it was a nice big croc. And as you’d expect, CT scanning and then dissecting it was no tiny feat, and makes a fun story. Story time, then, after an introductory pic!

Dr Samuel Martin, vet from La Ferme Aux Crocodiles, brought the crocodile (and some smaller specimens) over to our Hawkshead campus in late January 2009, and we quickly moved to run the specimen through our CT scanner to preserve some details of its anatomy (example shown at the end of this post) and for potential usage in the show. As the photos below illustrate, this was hard work for several people.

And then, as we were finishing the last CT scans of the specimen, our ageing medical scanner stopped working. And could not be resuscitated. R.I.P., Picker PQ5000 (buy one or two here!). The crocodile, “WCROC” as my team came to designate it, had claimed its final victim. It took about a year for us to get a new one, and that year sucked. It made me appreciate how lucky we are to have a CT scanner just across the parking lot from my office!

Anyway, the day of filming I was hoping to make it in to watch my colleague and friend Dr Greg Erickson help lead the dissection team, but a wicked blizzard blew up, and as I was starting the 31 mile drive south from my home to the RVC I realized, from the queue of cars that seemed to be 31 miles long (and train lines shut down), that this was going to be a snow day. So I turned around and came home. Another victory for WCROC!

The filming proceeded despite heavy snow delaying many of the key players’ arrivals. I got filmed a day or two later for a little section of the show on the limbs and locomotion of crocodiles but sadly this got cut from the main ING show (but did air in the National Geographic version “Raw Anatomy“, in the USA at least).

The limbs had been left largely intact, although some of the dissectors who didn’t know croc anatomy very well had slashed through parts of the pelvis and, in eagerness to reach key parts to demonstrate in the show, some major muscles got shredded. This is no big surprise; crocodiles have a lot of bones all over the place: in their skin (scutes; bony armour), in their bellies (the belly ribs called gastralia), and almost everywhere else, so some brute force is required to get to the gooey bits. Apparently there had been 6 or so people dissecting at once and things got a little carried away. The curse of WCROC continues?

Oh well; that’s just how documentaries go sometimes, especially with a pioneering show like this and the intensely compressed timescales of filming (time is ££!). There can be pulses of chaos. And the show turned out GREAT! (alternative link if latter does not work outside UK)

Let’s have more photos tell the story of the scanning, which also shows off this beautiful animal’s external anatomy:

Anyway, things turned out fine overall for our research. A week or so later (maybe longer; I forget if the specimen was frozen and thawed out for us) we came in to start dissections. We were really excited to measure the limb muscles of such a big crocodile, for comparison to a growth series (babies to adults) of alligators that my former PhD student (now postdoc; Dr.) Vivian Allen had dissected back in 2008. Here he is with a masked co-dissector, displaying their joy for the task at hand:

And let’s not leave out the exhuberance of visiting research fellow Dr. Shin-Ichi Fujiwara! He wanted to inspect the forelimbs for his ongoing studies of limb posture, joint cartilages and locomotor mechanics.

The remaining images show progressive stages of dissection of WCROC, starting from the pectoral (fore-) limbs with a view of the belly (and the giant jaw-closing muscles visible on the left side of image):

Isolated right forelimb, with coracoid (part of shoulder girdle) sticking through:

Assorted forelimb/upper arm (brachial) muscles:

And the triceps (elbow-straightening) muscles; not that big in such a big animal:

…and on to the pelvic limbs and the huge tail:

With a closer look at the HUGE thigh muscle, the famed M. caudofemoralis longus:

And then an isolated right hindlimb:

Thigh muscles, with which I have a peculiar fascination that stems from my PhD research:

And last, the great, paddle-like hind foot!

What a great experience that was! We have fond memories of WCROC, a great documentary from Windfall Films, some nice data– and a lovely skeleton. Perhaps the curse of WCROC is not so bad. Nothing can go wrong now!

Soon Mieke Roth, scientific illustrator from the Netherlands, is coming here to do a similar dissection on more Nile crocodiles at the RVC. As with the octopus she wrote about in September, she will make a 3D model, but with much more detail and with an emphasis on accuracy and accessibility. The end products will be really cool; think of the visible body, 3d models that can be used in teaching, animations, a book and lots more but also a “how did she do that?” blog. To finance this project (that probably will take a year or more) she will use crowd funding. In several weeks there will be more info on how to participate in her fantastic endeavour. For now, see her video with the initial pitch for “Nile Crocodile 2.0“!

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Hi folks, as my birthday present to you, and big thanks for racking up 70,000 blog views in 7 months (and my 50th post!), here is a new installment of Mystery CT Slice!

This time with a pilot (or scout) scan of an odd object. A pilot/scout scan is a quick, low exposure scan used to plan a series of CT slices, which shows a a larger area that is then narrowed down to focus just on the object of interest and a bit of buffer room for those slices. It generally isn’t used for much else, but sometimes can make a neat picture. As you can see here, the pilot scan area was excessively massive relative to the object. The two odd objects below the primary object of interest are scanning phantoms, used to calibrate density from Hounsfield units to actual real-world density (one is water at 1 g/cm3; the other is “cortical bone” at 1.69 g/cm3). Ignore them.

But what is this object and from what taxon? Be as specific as you can, but pinning it down to genus/species level will be bloody hard!

Stomach Churning Rating: 1/10; it doesn’t get much tamer than a pilot scan.

Difficulty Level: small image, hazy, not a lot of diagnostic traits visible, 1 main element.

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