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.

Rodents of usual size and their moving skeletons

Harry, one of the rats in our trials, walking through the X-ray beams.

Harry, one of the rats in our trials, walking through the X-ray beams.

The past week at Brown University’s C-arms XROMM lab was so busy I haven’t had a moment to post about our research experiences until now.  If you’re just catching up, please see my previous post on our setup.

This was certainly a new but fascinating experience both for me and my student, Radha.  With help from Dr. Beth Brainerd and Dr. Angela Horner, we learned how to coax the rats to walk a plank of wood between the two X-ray emitting “cans” of the positioned C-arm fluoroscopes.  At one end of the room is a bank of two computers connected to each high-speed camera and C-arm.  When the rats were doing what we were interested in, a push of a floor pedal turned on the X-rays and recorded the ensuing stream of images which were then converted into standard computer movies.

Walk the plank - each rat walked across this plan between the C-arm fluoroscopes to a hidey-hole box we nick-named the Rat Haven.

Walk the plank – each rat walked across this plank between the C-arm fluoroscopes to a hidey-hole box we nick-named the Rat Haven.

Dr. Brainerd helping Radha and I to capture the X-ray data.

Dr. Brainerd helping Radha and I to capture the X-ray data.

Radha Varadharajan at C-arms lab

Here is Radha Varadharajan capturing and recording the X-ray movies that will be the foundation of our study.

Angela Horner has been working with rats for years, and her experience in motivating these little mammals was a godsend — from Wednesday to Thursday, Radha and I learned from her experience and were able to collect loads of data that will allow us to begin reconstructing their locomotor and postural movements in 3-D.

Here, Dr. Angela Horner is motivating the rat Harry to walk the plank through the X-ray beams.

Here, Dr. Angela Horner is motivating the rat Harry to walk the plank through the X-ray beams.

Radha and I both had opportunities to coax the rats across the plank to the Rat Haven as well.  You will notice we named our rats.  Two of them were dubbed Pink and Floyd as a nod to one of my favorite bands who also featured cartoon rats in their backdrop movie for “Welcome to the Machine.”  Yeah, we’re geeky like that.

Here I am holding one of the rats we named Evan.  Evan was a bit "lazy," but ended up being great at walking a narrow dowel, helping us to see forearm movements in detail.

Here I am holding one of the rats we named Evan. Evan was a bit “lazy,” but ended up being great at walking a narrow dowel, helping us to see forearm movements in detail.

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

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

Want to see a sneak-peak of the end result of our labors?  Here is one clip of Harry the Rat.

We are especially grateful for all the help we had this past week, and among many others Erika Giblin and Ariel Camp were invaluable in providing access and assistance with all of our XROMM issues.  Thank you everyone!

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 …

XROMM Days 3-5: Data, data, data

Again, if you’re just tuning in to this thread on XROMM, please refer to my previous posts on what XROMM is, why I am excited about using it, and what I have done so far, including 3-D animating a chewing pig.

The past few days have seen us busy and social.  We’ve now learned to do scientific rotoscoping, or the art of properly aligning three-dimensional, anatomically-accurate models of vertebrates with two X-ray movies shot from different angles.  I have previously described the basic steps involved in making these XROMM movies and coordinating and calibrating the X-ray movies, so I refer you to my previous post on this.

Unlike the method of XROMM I described previously that uses bone markers to synch the moving images and the bones, in scientific rotoscoping you manually align bones frame by frame with x-ray movies.  It can be tedious at times, but essentially it is, to quote Steve Gatesy, quoting Ken Dial, fitting a digital key (the bones) into a visual lock (the X-ray movies).  In other words, you are posing the skeleton in three-dimensional coordinates based on the constraints imposed by X-ray movies.  Put simply, if your digital skeleton deviates from the reality of the X-ray movies, you are doing something wrong.

What is perhaps most important to emphasize in all of this is that because you are fitting bones into a virtual reality space of what happened when the animal was filmed, you can now recover data about skeletal and joint movements.  That’s right: you can actually retrieve reliable, repeatably scientific data on gait and movement from these 3-D animations.  For example, you assign joint markers and then measure how much the mouth of a pig opens, or how much rotation is happening in a bird knee, or even how parts of a fish skull move in relation to the skeleton and muscles.

So, you are not just making a nice skeleton movie — you are recovering what would normally be unrecoverable data.  The sort of data that allows you to more objectively describe what happens in living vertebrates, and hopefully, data that can be used as a baseline constraint for limiting what fossil vertebrates may or may not have been capable of.

All in all, this has been a great experience.  I wish to thank Beth Brainerd, Steve Gatesy, David Baier, Ariel Camp, Sabine Moritz, and Erika Giblin for all their help, information, and assistance this week.  It has been a pleasure.

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 …