The Visit to Brown University

Radha Varadharajan at Brown with Beth Brainerd.

Radha Varadharajan at Brown with Beth Brainerd.

After spending five valuable days at Brown University, Dr. Matthew Bonnan and I learned a great deal about C-arm fluoroscopes and with XROMM technology. The early stages involved getting accustomed to the protocols of working with the fluoroscopes. This step was pivotal for the machines emit an innocuous but not neglible amount of radiation to capture the motions of our rats: Pink, Floyd, Evan, Rudy, Harry, and Taylor.  Personally, the pinnacle of the visit to Brown can be identified as the days the rats walked across the beam. With much guidance from both me and Dr. Bonnan, our furry test subjects were cajoled across the plank or dowel. Although Dr. Bonnan was the primary coaxer of our scampering participants, I was also able to give a hand in guiding them.

Within a few days into the visit, I was amazed with the advanced technologies at Brown. Comprehending the process of how the fluoroscopes operated was especially intriguing. Because I was able to accompany Dr. Bonnan on this trip to Brown University, not only did I understand the innovational technology that is XROMM, but I was also able to contribute in the smallest way possible in understanding the evolution of forelimb posture.

Here is Radha coaxing Pink the Rat through the X-ray beams.

Here is Radha coaxing Pink the Rat through the X-ray beams.

I would like to conclude this post by expressing my utmost gratitude to numerous individuals that allowed for my collaboration. My involvement in this educational visit would not have been feasible without the generous contribution of Dr. Robert Fine; Dr. Fine’s munificent gesture solely funded my trip. I would also like to thank Dr. Elizabeth Brainerd and Dr. Angela Horner for their guidance. Finally, I would like acknowledge Dr. Bonnan for his unceasing support.  Without his patience, I would not have been able to discover the numerous benefits of researching in such a compelling field.


An old dinosaur learning new tricks

Okay, so I’m the “old dinosaur” here, although I was informed recently that I could still pass as a graduate student.

I am happy to report that I am back on the campus of Brown University this week with one of my undergraduates, Radha Varadharajan, to begin what I hope to be the first in a long series of studies on the evolution of amniote (reptile, bird, mammal) forelimb posture.  We (my “rat pack” students and I) are using the XROMM technology I have detailed here on this blog to understand how the three-dimensional movements of the forelimb bones of rats actually occur.  The long-term goal of this initial study is to document how these movements facilitate hand placement and posture, and how these details of locomotion are related to bone shape.  My ultimate goal is to use the somewhat primitive forelimb posture of rats as a template to understand how some early fossil mammals may have moved.

Today, Radha and I, under the tutelage of Dr. Elizabeth Brainerd, began the process of setting up the so-called C-arm fluoroscopes that will allow us to take calibrated X-ray movies of a number of rats as they walk, run, and perhaps do other activities that we happen to capture.  This was especially exciting and informative for me, because these are the “new tricks” this “old dinosaur” wants to learn.  Tomorrow, we begin in earnest filming the skeletal movements of the rats.

You will notice in the pictures posted here that Radha and I are suited up in lead aprons and thyroid collars because, as you might anticipate, we do not want to expose ourselves to X-ray radiation during the data capture.  In fact, she and I have participated in numerous safety trainings and tests to ensure we stay safe.

Here I am behind the two C-arm fluoroscopes.  In front of the scopes, you can spy the wooden plank walk-way for the rats, and an acrylic box that the rats will walk or run through in the vicinity of the X-ray fields.

Here I am behind the two C-arm fluoroscopes. In front of the scopes, you can spy the wooden plank walk-way for the rats, and an acrylic box that the rats will walk or run through in the vicinity of the X-ray fields.

Here is Radha learning x-ray capture at the Brown C-arms lab.

Here is Radha learning x-ray capture at the Brown C-arms lab.

We also spent time today with Dr. David Baier learning how to set up what is called a rig in the MAYA software program that will later animate the skeletons of the rats we film.  Essentially, a rig in this case means creating a joint system that can be calibrated with the X-ray films and “attached” to the 3-D bone geometry from CT-scans of the rats used in the study.  I further shook some of the rust out of my head reviewing and practicing how to import calibrated data from X-ray digital movies and syncing them with 3-D bone geometry — skills I first acquired almost one year ago during Brown’s 2012 XROMM course.

All of this setup and learning is key for me and my students, not only because we want to do the science right, but also for other reasons I shall divulge in future posts.

Everyone at Brown has once again been incredibly helpful, and I am especially indebted to Dr. Brainerd for her encouragement and help over the past year with XROMM.

Please stay tuned … this week promises to get more interesting …

The “Rat Pack” Succeeds

A lot has happened in the Bonnan Lab at Stockton these past few months.

First, the “Rat Pack” as I fondly call them (Evan Drake, Kadeisha Pinkney, and Radha Varadharajan), presented their research proposals for 3-D rat locomotion and kinematics to the Northeastern Regional Vertebrate Evolution Symposium (NERVES) on March 22nd, 2013, at the New York Institute of Technology (NYIT) College of Osteopathic Medicine.  Their talks were very well received and we had excellent suggestions from colleagues and scholars.  I was especially proud of these undergraduates because they were able to give technical talks to a scientific audience having only worked with me for a few months on their projects. Bravo!

A special thank you to the Symposium’s organizers, Drs. Brian Beatty and Matthew Mihlbachler!

You can read their NERVES talk titles below.

Next, they put their collective heads together and, with my input, created a very nice poster for the 2013 NAMS Research Symposium at Stockton.

You can read their NAMS research abstract below as well.

The "Rat Pack" presented their preliminary research on rat locomotion to the 2013 NAMS Research Symposium.  Left to right: Kadeisha Pinkney, Radha Varajharadan, and Evan Drake.

The “Rat Pack” presented their preliminary research on rat locomotion to the 2013 NAMS Research Symposium. Left to right: Kadeisha Pinkney, Radha Varadharajan, and Evan Drake.

Kadeisha (left) and Radha (right) explain the joys of rat locomotion to interested students.

The “Rat Pack” attracted quite a crowd.

Last, but not least, Radha Varadharajan received the first Robert L. Fines scholarship awarded at Stockton, April 26, 2013, for her work on this research and her future career goals in veterinary medicine.  Dr. Fines is a former Stockton alumnus (1975) and is one of the premiere M.D. researchers successfully fighting pancreatic cancer.  He is the Herbert Irving Associate Professor of Medicine in the Division of Medical Oncology at the Columbia University College of Physicians & Surgeons in New York, New York.  I am honored and proud that Radha has received this award from such a prestigious alumnus.

The scholarship will allow Radha to travel with me to Brown University the week of May 20-24, where we will work with Dr. Elizabeth Brainerd and colleagues X-ray filming the rats walking, running, and landing at their XROMM C-arms facility.  Stay tuned and we’ll keep you posted on our time and research activities while at Brown.

Finally, I must acknowledge the help of our campus veterinarians, Drs. Ralph Werner and Mary Wilkes, for their efforts in helping me with the rats, as well as our animal caretaker, John Rokita, for his constant help and suggestions on rodent protocols and biology.

I feel truly grateful to have made such a jump to a new college and to already be surrounded by supportive faculty, eager students, and the chance to pursue 3-D kinematics research.

NERVES Talk Titles

Varadharajan, Radha and Bonnan, Matthew F. 2013. Exploring 3-D long bone kinematics in the White Rat (Rattus norvegicus) as a model for inferring forelimb posture in early mammals: Contribution of the scapula.>

Pinkney, Kadeisha and Bonnan, Matthew F. 2013. Exploring 3-D long bone kinematics in the White Rat (Rattus norvegicus) as a model for inferring forelimb posture in early mammals: Contribution of the humerus.

Drake, Evan and Bonnan, Matthew F. 2013. Exploring 3-D long bone kinematics in the White Rat (Rattus norvegicus) as a model for inferring forelimb posture in early mammals: Contribution of the radius and ulna.


Forelimb movements in Rattus norvegicus (white rat) and their relationship to pronation: implications for early mammal forelimb posture

Varadharajan, Radha; Pinkney, Kadeisha; Drake, Evan; and Bonnan, Matthew F.


Rattus norvegicus (the white rat) is a therian mammal with a forelimb morphology similar to that of early non-cursorial mammals. Currently, early mammal limb posture is controversial, with reconstructions ranging from sprawling to parasagittal. With this current ambiguity, the study of forelimb shape and movements in R. norvegicus may provide a model to infer the locomotor patterns of earlier mammals.  Previous research, most notably by Jenkins (1971, 1974), indicates that the forelimb posture of rats does not follow simple, pendulum-like mechanics but rather a more complex, less-upright range of movement. For the first time, we will study the 3-D morphology and kinematics of the forelimb in R. norvegicus by utilizing three-dimensional moving X-ray animations generated through the XROMM (X-ray Reconstruction of Moving Morphology) technique.  Specifically, we will focus on the three-dimensional movements of the scapula, humerus, and antebrachium (radius and ulna), and their combined contribution to pronation (placing the hand palm-side down).  To this end, we will test three interdependent hypotheses on the contribution of each of these limb segments to pronation. For the scapula, we examined the serratus anterior, supraspinatous, infraspinatous, spinotrapezius, acromiotrapezius, and rhomboids major and minor. Data gathered on the rat scapula through literature and dissection lead to the hypothesis that this element contributes in a significant way to pronation. Specific features of the humerus distinguish the parasagittal from the sprawling stance in early fossil mammals: degree of torsion, condylar structures of the elbow joint, width of the intertubercular groove, and the relative sizes of the lesser and greater tubercles.  These features are associated with major locomotor muscles such as the pectoralis major and minor, deltoids, and pronator teres. We hypothesize that the humerus will contribute in a significant way to the pronation of the hand in the white rat. In humans, the radius can rotate about the ulna to pronate the hand because these elements are bowed, creating the space necessary to allow such movements. The pronator teres and pronator quadratus pull on the radius and rotate it about the ulna, whereas the supinator and biceps brachii act as antagonists to return the bones to a parallel position. Unlike humans, the radius and ulna of Rattus norvegicus fit tightly together like two spoons stacked together, with little, if any, space available in which the radius can rotate about the ulna.  Moreover, the pronator quadratus has not yet been described or identified in our rat dissections. Instead, the radius and ulna appear “fused” by the interosseous membrane and rendered incapable of supination. Rats have little need to supinate the forelimb because the forelimbs are primarily used in locomotion. It is therefore hypothesized that all pronation and supination occur in the humerus and scapula in rats because the radius and ulna are in such close proximity to each other that we infer they participate little, if any, to pronation.  After we capture the three-dimensional movements of these bones with XROMM, we will test our hypotheses and perhaps gain insight into the posture of early mammals.

XROMM Day 2: This little piggy bites … in 3-D

Again, if you missed previous posts on XROMM, please read those first for better context of the discussion that follows: see what XROMM is all about, why I’m excited to be learning it, and what I’ve already done.

On our second day in the course, we took the next step to synch two different, simultaneous X-ray movies of a mini-pig eating with a three-dimensional model of its skull in the MAYA program.  These X-ray films were taken on the C-arm x-ray machines I mentioned in my previous post by Dr. Beth Brainerd and colleagues, and we were essentially learning by replicating their process.

Dr. B. and the Mini-Pig

Me and mini-pig’s skull. The original movie was filmed back in 2006, so the mini-pig that stars in the X-rays has since passed on to piggy heaven. Here I am holding the actual skull of the animal that you will see in the animation.

In XROMM, you essentially have a work-flow like this:

  1. Film an animal behavior from two directions using calibrated X-ray cameras.  The animal usually has tiny, spherical beads implanted surgically into a few of the bones of interest prior to the filming.  As an important note here, all such films and surgeries are done under strict animal welfare protocols and the animals are not harmed: the X-ray dosages are as low or lower than that of humans exposed to x-rays for diagnosis, and the beads are tiny and biologically inert.
  2. After filming the animal’s behavior, the skeleton’s three-dimensional geometry is often CT-scanned from the animal.
  3. The CT-scan bone data are converted into geometrically-accurate 3-D representations of the bones of interest.
  4. In MAYA and MATLAB, the films from the two x-ray cameras are virtually “projected,” and the beads implanted into the animal subject show up as little dots.  These dots show up as little spheres in the CT-scanned bones you import into the MAYA program.
  5. Things then get more technical, but suffice it to say that the beads you see in the X-ray films and the spheres in the CT bones are synched.  The movements of the beads (spheres) are digitized in three-dimensions calibrated from the two camera views, and then the virtual bones are “cemented” to these spheres.  Then, as the spheres move, the bones follow, and what you get is a three-dimensional reconstruction of the 2-D x-ray films!

Here is a screen shot of the animation made in XROMM today.

Mini-Pig X-ray and Reconstruction

What you get from XROMM: to the left is one of the two X-ray films, and to the right is the 3-D skull reconstruction of the mini-pig.

Here is an animation of what you get — I still can’t believe we can do this!

Dr. B. Contemplates the Mini-Pig

Dr. B. Contemplates the mini-pig skull.

And we’re not even done yet.  Stay tuned …

Seeing through vertebrates to see through time

While waiting in the airport for my last flight (long story) to Providence, RI, and on to Brown University for the XROMM course, I obtained a good WiFi signal and so I’m writing a brief post.


Tomorrow will mark the beginning of learning new cineradiography techniques and skeletal modeling that I have jealously been wanting to do for a long time.  It is hard to convey in words how anxious and interested I am to begin learning and then using the XROMM techniques.  Perhaps this is a bit of an exaggeration, so forgive the hyperbole, but I feel somewhat like a physicist who first get access to an atom smasher or an astronomer learning for the first time how to peer into the cosmos through some technologically marvelous telescope.

For someone like myself who is interested in how the skeleton actually behaves as a machine, and how to apply this new XROMM technology to deciphering past vertebrates like dinosaurs, this is coming close to time travel.  Okay, perhaps a bit of an exaggeration again, but I believe that seeing through live vertebrates to understand quantitatively how their skeletons “tick” is seeing through time.  Conserved movement and novel functions in living relatives of dinosaurs help us realistically constrain and predict what those long-dead animals were doing when they moved, hunted, or vacuumed-up vegetation.

I’ll be updating this blog throughout the week, and of course you can follow me on twitter for up-to-the-minute thoughts and comments.

How to see the skeleton in action … in 3-D

I am interested in dinosaur locomotion.  In particular, I am interested in how the various parts of a dinosaur skeleton moved in relation to one another, especially when capped in cartilage, actuated by muscles and tendons, and ensheathed in flesh.  Of course, until time travel becomes reality or until Jack Horner brings to life his “chickenosaurus,” knowing just how dinosaurs moved is fraught with difficulties and unknown variables.

Take, for example, the recent, independent confirmations by Casey Holliday and colleagues, and that of my own group’s research, on archosaur long bone articular cartilage thickness and shape.  It turns out, frustratingly, that a good amount of joint shape and thickness are lost to time in dinosaurs.  Part of my current research focus is to develop empirical methods for reconstructing the missing cartilage shape at the ends of dinosaur long bones, but that is a long work in progress.

However, you would think that at the very least, we should be able to quite readily determine the range of movements and interactions of the living skeleton in crocodylians and birds.  Strange as it may seem, understanding how the skeleton of a vertebrate moves in real life is not easy.  An actual, physical skeleton of any given animal can only be articulated in one pose at a time, and in any case the limitations or freedom of movement resulting from soft tissues are very difficult to establish — just ask Larry Witmer and his group of dedicated students.  One could, of course, pose a dead animal in various ways and then CT-scan or take a radiograph (an X-ray photograph) of each pose, but dead animals don’t always assume natural poses.

Another technique used for a number of analyses of skeletal movement has been fluoroscopy combined with the capture of X-ray movies of live animals, called cineradiography.  Several papers have been published on various aspects of vertebrate animal movement, breathing, and other activities using cineradiography.  Whereas these previous studies have been invaluable in revealing heretofore unknown or unanticipated movements of the vertebrate skeleton (e.g., the furcula of birds acts as a flexible spring), they are limited in that they are 2-D.  All bones of the animal are compressed into a flat plane, and you have to be able to recognize and follow the movements of the bones you are interested in while they merge and pass over all the other bones in the movie.

Therefore, I am thrilled to report that I have been accepted into a 1 week course at Brown University where myself and other faculty, postdocs, and graduate students will learn a new, 3-D cineradiographic technology that enables accurate three-dimesnional animations of vertebrate skeletons!  Called XROMM (X-ray Reconstruction of Moving Morphology), this new technology uses combined, multiple fluoroscopic and standard video sequences of a moving animal in combination with three-dimensional representations of its bones to produce a scientifically accurate moving skeletal model of particular behaviors and motions.  The three-dimensional bones are obtained using standard CT-scan or laser-scanning technology.  Check out the following examples under the Movies link on the XROMM site:

  • Mini-pig feeding
  • Ray-finned fish mouth mechanics
  • Iguana breathing and rib movements
  • Bird hindlimb movements
  • Duck feeding

The advantages of XROMM over traditional fluoroscopic movies or the attachment of external markers to skin is easy to appreciate.  For the first time, you can watch the movement of bones in three dimensions from any angle and in any perspective.  Moreover, you can easily export the ranges of movements generated by the animation for further quantification and analysis of how the bones actual move in space, in time, and in relation to one another.

I will be blogging and tweeting (@MattBonnan) about my experiences in this course, which will take place Monday, June 11 through Friday, June 15, 2012.  This sort of experience will not only open new doors for the research of all those involved in the course, but it will inform projects I will conduct in the future with my students.

I wish thank the members of the XROMM course for such an amazing opportunity:

  • Beth Brainerd
  • Steve Gatesy
  • Dave Baier
  • Ariel Camp
  • Sabine Moritz

It is wonderful to be a paleontologist in the 21st century!