Author Archives: Claire Shapleigh, Biomedical Visualization

About Claire Shapleigh, Biomedical Visualization

Hi, my name is Claire and I'm in my second year of the Biomedical Visualization MS program at UIC. It's a combination of art and science, and it's pretty fun. So far I've dissected a human body and learned how to draw in 2D using a computer AND my hand, and I'm about to learn how to 3D model. Holler at me if you have any questions about the program!

RSNA: Radiological Society of North America OR Rad Stuff of the New Age

I will now call it Rad Stuff of the New Age. RSNA is a yearly medical conference in Chicago, specifically radiological, with 60,000 + participants each year, making it the BIGGEST MEDICAL CONFERENCE IN THE WORLD. Not because Radiology is the largest field of medicine, or even the one with the most money, but because it has the most technology associated with it- the most cool stuff!

Entrance to the conference

You could walk around it forever. You could get lost in the GE booth or the Siemens booth, testing out their new, spiffy, minimally-invasive radiological equipment. (Well, you wouldn’t actually get an MRI or anything, but you can look and touch.) It’s like going to Brookstone and not really intending to buy anything more than an alarm clock, but sitting in the massage chair for half an hour.

That’s how I felt while working a booth at the conference this week, but many people come to the conference for REAL business. They are looking to invest, looking to buy new equipment, looking to merge companies, to showcase their new technology, to see what’s out there. Radiologists come to see what’s new and to watch famous people in their field present work and give lectures. Vendors come there to sell their patented products (and to spy on the competition). A lot of people come to see their friends in the field. It’s really the place to be if you’re in the field of medicine, radiology or medical sales.

I worked at the Fovia booth! Fovia, Inc. is a software company that takes huge data sets from radiological equipment like MRIs, CTs and Ultrasound, and makes it into high definition 3D images and movies in which you can see extreme detail. It’s the new wave of rendering medical data! and it’s awesome. You can see more here.

Oh, and the conference is so big that I failed to see the FLASH MOB that occurred on the second day of the conference! But I later found it on YouTube. Check it out!

Unclogging the Life Line

Today we turned in some drawings of a surgery of our choice. I chose the carotid endarterectomy, which is where a surgeon unclogs your carotid artery! I wrote about it previously- I like it because it’s very visual. Here are a few steps from the procedure. I chose the pen and ink style. I hope to render out more later! When things get less crazy.

Relevant anatomy of the neck

Step 2: Removal of the carotid sheath

Step 4: controlling the superior thyroid artery before incision

Spinning class : exercise :: semester at UIC : life

“OK class! Let’s start out slow! Just start peddling! Difficulty level should be at about a 5 out of 10!” yells the already-sweaty-because-this-is-her-third-spinning-class-today woman up front with the microphone.

It’s like the first few weeks of school, when you ease into studying after a crazy and lazy (but short if you have a summer semester) summer break.  You’re not thinking about the big projects, the papers. You’re thinking about how fun it is to learn!

“Now we’re gonna start off with a gradual hill.  We’ll take forty seconds at each level, and go all the way up to 10. It should hurt by the end, but you’re not dying!”

The first few tests and quizzes roll by. The first big assignment hits.  You pull your first all-nighter of the semester. It’s fine!  You can sleep it off the next night, because THINGS ARE UNDER CONTROL.

“Okayyyy, turn it back down to 5 and grab some water, catch your breath.”  The song switches to “You Can’t Hurry Love,” by the Supremes.

A lull in assignments, weekends are spent doing some work, catching up on The Office, baking cookies and attending the neighborhood block party.

“AlRIGHT! Consecutive 30 second sprints! Give it your all!!!”


“Keep it up at level 7, keep peddling those legs, you want it to hurt!” You look at the clock- you’re over half way through the class but you feel like you’re ready for the last five—the slowing down and stretching part.

This is like weeks 9 through 14- constant assignments due, and you’re thinking about how far away winter break seems but how vaguely excited you are for it.

“Keeeeeeeeeeep pushing! C’mon! You OWN it! You can’t improve unless you push yourself!!!” A heavy metal song pumps in the background. You usually hate heavy metal, but you’re actually enjoying the angry “De ner ner ner nerrr” sounds. It’s right for the moment.

Last two weeks of class, and things are not quite coming together yet.

And then there’s the last hill.  The one where you start to feel sick to your stomach.  Where you take the last swig of water in the water bottle, and it turns out to be just one drop.  Your mind is playing tricks on you, saying “you can’t finish” and “I’m dyyyinggg!” And right when you think you’re going to collapse…

You’re DONE!  And you can cool down, go home and eat some home cookin’.

Cells of Barney (the dinosaur) in Space

I’m trying some things out for modeling the environment in my 3-dimensional scene of the nucleus (created in Autodesk Maya), and here’s what I got:

Yes, that is a chromosome that is floating in what looks like outer space. And yes, that chromosome is purple.

I actually didn’t realize exactly how purple the background would be. I had been working on it for some hours, and you know when you’ve been working on something for so long that you can’t pass any rational judgment on it? So when we were showing our progress in class the other day, a classmate said, “it’s very purple.”

And I looked at it and I said yes. Yes it is.

So I decided that this would be the insides of not a human cell, but Barney the Dinosaur’s cell. Heyyyyyy, kids! Want to travel inside my CELLS today? Hyuck hyuck! Let’s GOOOOOOO!

How you know it’s fall in Chicago

How does one know that fall has arrived in Chicago?

Mostly you can’t know for sure, you just feel it.  The wind picks up.  The smell becomes a damp, leafy one.  People around you start bundling up, carrying umbrellas, sniffling.  Babies start crying.  You begin fighting the urge to hit the snooze button, because it’s darker than usual and your comforter is 3.5 times more comfortable in the fall than in the summer (proven fact, see Claire et. roommates, 2011)

Below are a few more reasons you know that autumn has snuck up on you as you come spinning out of summer—and then an Indian summer—with your t-shirt still on.

1)   The trees are turning! But the flowers are still blooming.  It’s an intermediate stage between one extreme and the other.

Couldn't resist adding this one- view from the train heading from Chicago to St. Louis

2)   You’re walking down the street, a gust of wind comes, and all of a sudden you can’t see.

And trash lines the streets due to high winds…

3) The shadows.

The shadows become stretched out as the sun gets lower in the sky.

4)   Pumpkins, pumpkins, everywhere!

Always a good indication of fall. I think Starbucks bring it out the same date every year- they’re pretty consistent like that.

5)   one day you wake up and everyone’s dressed strangely.

You guessed it- HALLOWEEN!

6)   You can see the Sears Tower (sorry, Willis…) when you couldn’t before.

7)   General gloominess and rain.

8)   Last but not least, you look over while doing homework and your roommate is sitting in her most comfortable outfit, under a happy lamp.

That’s right- it’s a sun lamp! Everyone should get one.  Fifteen minutes in the morning, and you’re set for the day, happy as a clam.

The Real Turkish Delight

For some time now I’ve had a real thing for Turkish coffee.

turkish coffee up close

YUM! Turkish coffee is Turkish coffee because two things. One, because of the Arabica beans used, but more importantly because of the technique to make it. You can really use any beans, as long as they are ground to a very thin powder- thinner than espresso! The reason you have to grind it to a powder is because there is no filter involved in the process (which you realize when you take the last sip from your cup and you get a mouthful of grinds.)

To make it, the powerdery coffee grinds are spooned into a turkish coffee pot filled with water, and the stove is turned on.

turkish coffee pot!
finely ground turkish coffee- set grinder to VERY fine.

The ratio is about two tablespoons of coffee for every cup- it might be less but I like a strong cup of coffee! The internet say two heaping teaspoons for every “demitasse,” (which I just learned is a tiny espresso cup.)  The grinds just sit on top of the water as it is boiled- don’t stir them in. When the water begins to boil, you turn off the stove, and it’s done! The heating of the water from below causes a turbulence in the pot which mixes the coffee into the water and makes the coffee.

Alternatively, you can use an espresso coffee pot. My roommate and I have been using this one ever since she brought it home from her study abroad trip in Europe:

You can really use any pot, but it should preferably be small so the grinds don’t spread out too far on top of the water. And voila!

turkish coffee in a demitasse

And while I usually take cream with my coffee, I have to drink this black, with a little sugar. It’s how they DO.

I was introduced to turkish coffee when I traveled to the West Balkans–Montenegro, Serbia, Macedonia and Croatia. It wasn’t Turkey, but this was the kind of coffee that everyone drank.  At the end of every cup I drank there, some elderly lady would take my cup, flip it over and tell my fortune with the pattern of the grinds. That was pretty fun, mostly because I couldn’t ever understand what she was saying, so I could just pretend that she was talking about my lavish life with my extremely successful career and beautiful family, horse farm, private beach and personal staff. ha.

Strangely, according to each of these countries (and other countries in the Balkans, and Greece too), Turkish coffee originated from their country, respectively.

In Serbia, it’s “Serbian coffee.”

In Macedonia, it’s “Macedonian coffee.”

In Greece, it’s “Greek coffee.”

In Turkey, it’s “Turkish coffee.” And I guess since they’re the biggest country, they win. Or perhaps because they thought of this delicious thing first.

So next time your buying coffee, grind those beans a little more than usual and go get yourself a Turkish coffee pot, sold in European markets all over Chicago or in Greek town. You won’t be let down by the power of Turkish coffee. It’s fantastic!!!

Baby Steps

I am coming along in my Maya 3D modeling class, slowly but surely. We are to continue to fill in our “space” with more objects, environment, lighting and texture. I still feel at the beginning stages of this modeling process, because I am having trouble making my DNA look like DNA. But I have a vision, which is a good start.

DNA is a helical thing, with a repetitive pattern that looks like a ladder if you untwist it.

A cartoon by a British cartoonist named Chris Madden- check him out!

It sounds easy to model, right? Well it kindof depends on how I choose to represent it.  There are many different ways to depict DNA, including the very simplistic stick figure version seen above. There is also the “ribbon” depiction, where the sides of the dna ladder are depicted by two ribbons winding around each other, with the rungs connecting them.

Image created from Chimera, an application that visualizes chemisty

Then there is the more complicated representation of DNA, where all of the atoms are visualized but they still are shown in “ball and stick” mode:

Chimera showing all atoms

Another way to depict DNA is to take what we know about its properties, and fill out the structure based on these properties. For example, we know that the parallel “ribbons” of DNA are hydrophilic, which means they like and attract water molecules.  The interior “rungs” of the DNA are very hydrophobic and hate water. So they are hugged by the hydrophilic parts of the ladder. Interactions between atoms within DNA, and therefore DNA structure, are very dependent on these properties. Here’s an example of a space-filling model based on hydrophobic properties:

Chimera Hydrophobicity model

So I’m trying to figure out how to depict the DNA in my model. I think I prefer the last way I showed, because it’s very pretty! And gives a little thickness and substance to DNA. So I’m working on it…

Current status of my DNA. View 1.

Current status of my DNA. View 2.

Current status of my DNA. View 3.Current status of my DNA. View 4. You can see the DNA wrapped around the histone complex.

It still doesn’t look very helical at this point, so I’ll be trying some things to fix that!

Lastly, I want to show an animation created by a former student at my program, Blair Lyons, who is now working at a company out in Vancouver as an intern creating animations. I happened to come across this beautiful animation she just finished, which depicts DNA and translation.  Check it out!

Very inspiring.

Notes from a Portlander

“Dear Chicago,

I want to live in Wicker Park.

Lots of love,


So my friend Megan from Portland, city of hipsters, hippies and big mountains, came to town recently to visit the Big Apple of the Midwest. And like most people hailing from the Pac North West, she really had no idea what to expect. In fact, when I lived out there I would tell people where I was from, and they’d ask, “What’s it like on the East coast?” and I’d have to explain to them that no, there is actually a lot of land mass and culture between here and New York city. So I think if you had asked Megan to say a few descriptive words about Chicago before she came, she would have said “hot dogs, tall buildings and thugs.” That’s all she knew!

I took her around town, and she had a great time. We saw some comedy, we rode on public transport, went shopping and went to the Art Institute. After her visit, for curiosity’s sake I asked her to list the three best things about Chicago and the three worst things. Here they are, in random order:

1) The architecture. The buildings have an old brick aesthetic to them, but all the different neighborhoods have a slightly different style, making it interesting to walk around in. (in Portland they use a lot of wood to make the houses- I guess they didn’t have a massive fire last century that scared them off from doing so. Also, lumber is pretty big out there.)

2) Tweakers on the bus. Not so fun to turn to your left while riding the bus and see a guy laying across two seats and an isle, twitching slightly and completely oblivious to the world. Maybe it’s a big city thing, but Megan had not been exposed to a lot of tweakers. It’s really no fun for anyone, including the one doing the tweaking.

3) The weather. Coming from Portland, where the rainy season began a couple weeks ago, an Indian summer in Chicago was a nice surprise. “Isn’t it supposed to be cold here?” Megan asked me while sweat rolled down her face as we walked in the 75-degree sun. Yes, but this is what’s so special about Midwest weather- never know what to expect.

4) The food. It’s hard to come from a place where they serve gourmet bratwursts and organic tossed salads at the airport to a place where wieners reign. As Megan said, “They’re not even Kosher!” The food in Chicago is… different. Less fresh seafood, more grease. We’re definitely in the heartland of cows and corn, and it didn’t take long for the west-coaster to notice the meat-heavy menu. Hey, I like it- it’s just harder to be a vegetarian here, if that’s your thing.

5) People not covering their mouths when they cough on public transport. Yeah, I have to say I must be used to this little phenomenon, but ever since Megan observed this, I’ve been a little paranoid about getting the plague in Chicago. Of course it’s not everyone who does this, but that one person who chooses to cough into space instead of into their elbow is also choosing to jeopardize the whole bus. Not cool, guy, NOT COOL.

6) The culture. The diversity! All the different ethnicities, all the different preferences and styles in Chicago. And I will attest to this; when I lived in Portland I felt a little stifled when I’d get on the bus in the morning and everyone would be sitting quietly, head down, reading their novel. Not to get me wrong, there is a different kind of diversity in Portland. Like all the different kinds of sunglasses! Haha. But yes, the diversity and exposure to hundreds of different cultures in Chicago is a big plus for everyone who lives here.

So these are reasons why Chicago is the best but also what it might be able to improve on… in the eyes of a Portlander. So bye bye Megan, tell the beautiful North West hello but also tell them to come visit the Midwest- because it’s pretty awesome too.

D.N. izzay

DNA! Is the coolest! And I’m gonna draw it! Well, I’m gonna piece it together, in a 3D modeling fashion. I’m inspired by people like Drew Berry and David Bolinsky. They are innovators in the field of visualizing biochemistry. Which is hard to do, I’ve found. It’s one thing to takes notes in my biochemistry class and memorize stick figures that represent the elements of our body, and maybe even try to day-dream about molecular interactions, but it’s another to put it down on paper (or a screen)–to so certainly “record” something we can’t see with our eyes.

So I turned in a very rough first draft today of the scene I’m trying to create. Picture this: you’re a DNA molecule. You’re all wrapped up and cozy in a chromosome, drifting along in the nucleus. You find yourself unraveling, which is a normal occurrence during the beginning stages of replication- you have to unravel to let the enzymes work their magic and create an exact copy of you. But something’s wrong! The part of you that codes for growth and replication of the cell you’re in is being forced to unwind by these little annoying guys called “methyl groups.” The methyl groups are binding to you (and to the histones, around which you’re wrapped) and causing you to unwind to allow for unlimited replication! Being in an unwound, or relaxed state, you’re exposed to all the transcription enzymes that transcribe away- the first step in the creation of proteins and cell growth.

Next thing you know, you wake up and you’re in a tumor. Why? What happened? Well, those little methyl groups (and a few other elements that affect the structure of you and your fellow DNA molecules) have caused chaos.

Don’t get me wrong- methyl groups aren’t evil. In fact, they’re job is to regulate the structure of DNA by binding to it, and in doing so they are essential to life. But usually, cells in which the methyl groups get mixed up like this are killed immediately. This time, however, in this one specific cell, the genes that code for these regulators have been blocked by some of the same mechanisms that caused the unlimited transcription of YOU (because you’re still the DNA molecule.) It’s like a double whammy! It’s like a house party with no supervision. Things have gotten out of hand.

So this is new research. Whereas before we blamed the sequence of the gene itself on tumors, now we blame the structure- the winding and unwinding. So I’d like to try to depict an aspect of this mechanism in a 3D model. I started creating the DNA molecule and the histones in the background. You can’t really tell what’s going on yet, but you can get a sense of the scene…

That’s all for now!

Neck Time!

I went to a surgery today that I’ve wanted to see for a while now.  It’s called a “carotid endarterectomy,” and it involves a surgeon removing plaque from a person’s gigantic carotid artery (the one you can feel pulsing in your neck.) I’ve wanted to see it because it’s what I call a pretty “primitive” surgery; even though some pretty fancy tools are used, the surgery is made up of 5 basic steps: incision, finding the artery, opening the artery, removing plaque, and sewing the person back up. While the steps are basic, it probably couldn’t have been done 100 years ago because clamping a person’s major artery so that blood doesn’t run through it (so you can remove the plaque) is a very complicated thing and requires the right balance of anesthetic, surgical speed and precision.

The surgeon was the first female surgeon I’ve seen in the OR. She was amazing. Actually she seemed unnecessarily mean at first (snippy to the resident) but really she was just very precise and demanding in the preparations for the surgery. And she liked me- a lot of surgeons don’t acknowledge the medical illustrators, but this doctor asked me my name and made sure I had a prime spot, directly behind her and towering over her on a stool. It was awesome! At one point I said to myself, I better not topple forward in excitement, because something seriously bad could happen. So when she stepped in my view, I waited patiently instead of trying to lean in.

Here are my drawings, in chronological order. I waited two hours in the room before they started, so I got some time to draw the x-rays of the patient’s arterial system in the neck.

X-ray, side view of the carotid a. and its branches. You can see where the artery narrow due to plaque build up.

X-ray, front view of the left carotid artery and its branches.

The patient, anesthetized, with markings on the neck for incision.

Initial incision.

The first view of the carotid artery and its bifurcation (where it becomes the internal and external carotid arteries. The internal goes straight to the brain. It's pretty important.

Pulling back the artery with rubber band retractors.

Removal of plaque. (this is where she started working fast.)

Drew tools while I couldn't see anything.

Suturing the artery.

The plaque sample sitting in a jar. GOT IT!

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