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!

The Ridiculous

Well, that time has come. I’m going to graduate from graduate school! I’m “walking” this Thursday (in a beautiful gown complete with tassel and hood) but technically I finish up my master’s research project in July. So I’m ALMOST done. I’m already getting sentimental about leaving UIC, while at the same time ready to start something new…

It’s been a fun (almost) two years full of illustration, molecules, modeling in 3D, undergraduate science classes, COMPUTERS, friends, good and bad time management, biking around, cheap food, occasional great food at restaurants, exploring the city, concerts (outdoors and indoors), museums, field trips, long distance phone conversations, city rendevous’ and blogging. While most of it has fallen into the realm of “normal,” I’ve done a few ridiculous things while I’ve been in grad school here in Chicago. Let me take a moment to reflect on some of those things. They might give you an idea of of what to avoid while here at UIC, or what to do for fun! (many of the items on this list are specific to my graduate program, but you get the idea.)

Some things you might have found me doing during the past few years…

  • biking with three bags- one with books and computer, one with gym clothes and shoes, and one with food.
  • bringing human bones home on the bus.
  • posting on craig’s list for a nude model.
  • Google imaging certain topics while searching for visual resources for illustrations. For example, Google imaging “obese naked woman” for a reference for a character who has diabetes.
  • drinking and drawing (generally not very effective).
  • walking through a snowstorm.
  • cooking a week’s worth of pasta in one go.
  • baking a week’s worth of cookies in one go, but eating them in two days.
  • telling people I’m a medical illustrator specializing in male anatomy- to see their reaction.
  • dissecting a body and relating all the body parts/tissues to food products.
  • pulling all nighters (occasionally a necessary evil)

Well, I think that’s it… unless you think attending a medical illustration program is IN ITSELF a little ridiculous… which it probably is :) Anyway, I had a good time here and I don’t regret most of the things on this list. If nothing else, they make for a good story…

Angiotensin in 3D

Angiotensin is a hormone in the complex renin-angiotensin system of the body. This system is involved in maintaining blood pressure through kidney function-specifically water retention- and vessel constriction among other things. The Angiotensin II receptor is found in the kidney epithelial cells. Usually, Angiotensin molecules travel through the blood, into the kidney, and bind the receptors to cause vessel constriction and water retention.

Certain drugs that lower blood pressure, like Candesartan, can bind the angiotensin II receptors and block the downstream effects of the renin-angiotensin system. (high blood pressure). Here’s my depiction of this:

The purple rectangle represents the cell membrane, because the receptor sits in the cell membrane. The red molecule is Candesartan, binding the receptor. The blue molecules are the angiotensin hormone that are being blocked. I used a technique called sub surface scattering to put a texture on the molecules. This texture allows light to pass through to make the objects look a little gummy.

Kneed a break.

I finished my knee project. (see previous post). The knees are complete. I need a break, but NO! The next assignment is due in a week and a half. Which means I have to start now. NOOOOO!!!!  This is the bane of graduate school. (or just school.) (or life.) Anyway, here are my knees:

The "realistic" knee, painted in photoshop and 3ds-max. I also scanned in some real bones to get the very bony texture.

This one is the "ink and paint" version, where I tried to make it look like a drawing. I added an aneurysm there for educational purposes.

This is supposed to look like an x-ray of the front of a knee. After creating an x-ray like texture in 3DS Max, I brought it into photoshop to add the translucent leg and the "L" for "Left"

I sure learned a lot about texturing. Oh, you want me to texture that bone? that 3D character? That entire 3D world plush with colors, ornate decoration, dogs, cats and monkeys? BRING IT ON.

(I might be getting a little ahead of myself)

Knees (pronounced “neys” like “keys” or just “neez”)

I photographed these knees at the UIC health sciences library. I’m thinking about using them for an inspiration for the textures I must place on my modeled knees, shown below. (On an unrelated note and sort of morbid note, I think it would be really cool to donate my body for science, but especially if someone could guarantee that it would be on display for thousands of people to see, like maybe an airport exhibit about anatomy… yeah, celebrity bones!)

The modeled knees below are created from MRI scans of a real person’s knee, and a program called Mimix to piece all the 1000s of scans together. Then you can bring it into 3DS Max and add your own textures and materials to it. It’s crazy.

 

This is a shot of the current state of my modeled knee. It doesn’t have final textures on it, but I set it up on a stand and all the lighting for the scene. I have it all set up to paint on it!

This is an “ink and paint” version of the knee- it’s a material in 3DS Max that you can place on your model and it sort of flattens the model and makes it looks like you drew it on a piece of paper. I like the effect- this is a simple version I hope to work on more.

You can also assign an “X-ray” material to a model, to make it look like an x-ray was taken of the model. I created this material from scratch by playing around with opacity and self-illumination (where it looks like the model emits light from itself).

More to do on this assignment, I’ll report back later!

A Taste of Grad School

Home cooked dinner.

There ain’t nothing better. (especially if your roommate cooks it for you and it’s ready when you get home :)

Yes, I’m well out of college and supposed to be cooking for myself a lot, but somehow graduate school has brought me back to the dark ages in terms of simple functions like cooking. (If you consider the dark ages complete with tv dinners and a microwave.)

To me right now, healthy, balanced, home cooked meals are like ice cream. They are not a necessity, but they are a delight, and make me feel happier inside after eating them. I think it’s important to cook for yourself at least occasionally while in school to stay balanced. This means making it a priority every once in a while. (over physics homework? yes, sometimes even that.)

Here are some ideas for cooking while in grad school:

-Go to Stanley’s. (or find another local, cheap fruit and veggie market) The veggies are so cheap that you’ll get mad at every other grocery store for overpricing you your whole life.

-beans, grains and more beans. They are not too difficult to make. Sometimes you have to soak the beans which is a pain, but you can make a lot of them at once and use them as the base for a whole week’s worth of meals! Just don’t eat too many at once.

-if you have to make nachos (and everyone HAS to make nachos sometimes), add some tomatoes, peppers, corn or other veggies on there. It makes them more delicious!

-eating fruit can be a chore. Make it a habit to eat fruit for breakfast and dessert. Always carry around a banana or apple (i like to bring almonds or other nuts and raisins along with it to make my apple more exciting). That way, you can avoid the vending machine when your tummy rumbles.

-always bring your lunch. ALWAYS bring your lunch. Not only is it cheaper, it’s usually healthier. Give sandwiches a chance. They can be formatted for your specific likes and dislikes. Sandwiches are like works of art- making them is a very personal experience and a creative experience. Use whatever is in the fridge. One thing that I’ve learned time and again in my life is that when you put avacado on a sandwich, it makes the sandwich more delicious by at least 100%.

-last but not least, find the free food on campus. There is always something there. Whether it’s a booth giving away free candy, a gallery opening serving wine and cheese, or a lecture in the library that you have to sneak into and pretend you are a big fan of the speaker (shhh, i didn’t say that), campus food is usually around. And there’s usually extra, so you don’t have to feel too guilty. In fact, you’re helping them out!

Alright, those are my tips after years of experience of being in school. I hope they help!

Ipad hysteria

Well, the Jetsons really did it. They predicted the future. Yes I’m talking about the cartoon featuring George Jetson, his wife Jane, their daughter Judy and their son Elroy.

I remember watching the Jetsons when I was a little babe and thinking how crazy and cool it was that they could talk to people- namely George’s angry boss- over video on the wall or on a computer right next to them.

Well, that’s happened. No big deal, we can video chat people all the time now- our bosses, our family, our friends. It’s amazing.

But did the Jetsons predict being able to walk around with little computers that you hold in your hands? Not exactly that. We have made a step forward, past the “Jetsons predictions” future, to the unpredicted future (well, unpredicted by the reliable source of the Jetsons at least). And the ways in which we can apply this technology are pretty freakin amazing.

Especially in the field I’m in. Ipads are becoming a tool for everyday use in the medical field. And biomedical visualization (if you forgot, that’s what I’m learning here) in addition to graphic design and interface design, are necessary components of the development of apps in the medical field.

The animations I’m creating for my research project explaining diabetes will be incorporated into a larger diabetes management program that can be viewed as a video on YouTube, or used as an interactive program on a computer or an Ipad. As soon as I get these little animations done (soon I hope!) they will be put together with the narration, videos and testimonials to make a comprehensive program about diabetes that targets people without much science background and with low health literacy.

A team of health care workers will bring Ipads to the homes of diabetic patients to teach them about their disease and the importance of medication. It’s effective because it brings the information to people in a very hands-on, visual way. But still personal, because the health care worker can stop the video, talk to the patient and answer questions they have. Using technology like this, in a very personable and individual way, could revolutionize (and IS revolutionizing) patient education- the way people receive information about their disease, medicine regiment, surgery, etc.

Other applications of the Ipad in biomedical visualization:

- Medical Student Education: Blair Lyons (UIC Biomedical Visualization Class of 2011) created an Ipad App about the electron chain transport to teach students learning biochemistry.

It’s interactive with quizes and games so you can test your knowledge. Here’s the link to her website: http://www.stromastudios.com/index.html

- Anatomical Education (for students or patients.) This is a review of a new application that basically is an anatomy text book in an Ipad app.

- Surgeries. Doctors in the ER can look at images of the patient’s anatomy (x-ray, mri, ct data) in real time, zooming in to see the details of certain areas of the brain or whatever they are working on.

They can also view all clinical information about the patient like EKG results, all health records and use this information before or while conducting surgeries.

Of course, there are some quirks about using an Ipad in a hospital setting- like losing it, breaking it, making sure it is sterile or in a plastic, sterile protective cover. It has the potential to be a distracting device for the health care worker in a patient care setting. But overall, visualization techniques using technology like the Ipad are going to change the doctor-patient relationship and the surgical setting, most likely for the better!

Bake Sale Bloopers

I’m 28 years old, and I just held a bake sale at school. (not just me, but I say that for dramatic effect)  It was a fundraiser for the student association of medical artists. SAMA, if you want to know. We were out of money, so why not a bake sale?

Fellow medical illustration student (April) manning the sale.

As my non-UIC friend put it- aren’t bake sales for fourth graders? (she’s really cool)

No, friend, they are not. Bake sales are for everyone. Anyone who’s everyone. All ages. Your grandma.  Your grandpa. You’re sons and daughters. You. Because who doesn’t like chocolate, sugar and carbohydrates in the morning?

Actually a lot of people, I found. Students who have places to be and a large coffee in their hand because they’re on 3 hours of sleep don’t always like the idea of stopping for a banana muffin. A lot of people are also on diets, I found, or gave up baked goods for Lent.  Note to self: don’t hold a bake sale during Lent. It drops sales by at least 20% (this is an estimate and would be an interesting study).

Some bake sale observations and helpful things I learned:

1) People who just went to dunkin donuts down the hallway don’t necessarily want homemade cookies. But I bet they regret their decision.

2) Whatever happens at a bake sale, stays at a bake sale.

(only because why would anyone gossip about a bake sale? There’s nothing to say.)

3) Yelling: “kidney cake pops!”  “brownies!”  “eyeball cookies!”

gets people’s attention but does not necessarily make them hungry.

Eyeball cookies. Really.

Kidney cake pops. Yep.

4) The most receptive and most interested people are the employees of UIC, not the students. Not sure why, but our first five customers were employees or professors.

5) There is a fine line between making money on a bake sale, and falling into further deficit.

6) When it’s 75 degrees out in mid March in Chicago, people want to be biking, talking and loitering outside. They do not hang out inside next to bake sales. No amount of sugar can replace sunshine after a long, (not so terribly cold) winter.

But overall, it was a great experience. We did get some sales. Someone even solicited us! About a third of the people wanted to know who we were, which was nice because they were actually interested in the cause.  Talking to random people on campus is super fun, and a great sales experience. I would suggest (if you’d like to host a bake sale on campus) try to get the afternoon shift, don’t hold it during Lent or right before spring break, and don’t do it when it’s over 50 degrees outside. And don’t yell out the word “kidney” when you’re trying to sell cookies. That way, you might just make a profit!

An Innovative Day.

Yesterday, for some reason, was a really innovative day for me at grad school. Why, you ask? Well, usually I just go about my business, go to class and work, do homework, hang out, nothing out of the ordinary for a grad student. But yesterday- yesterday was a unique day that started off pretty exciting and didn’t stop until I got home. (and then it was back to the grind of homework mixed with bad tv.)

It started off when I was sitting there by my computer, harmlessly doing some 3D modeling, when a guy with a video camera asked if any students would like to be interviewed. Interviewed for what? Well he was from Medill, a media and journalism school in Chicago that broadcasts news about higher ed online. He was doing a story about the Biomedical Visualization program.

I said no, I would not like to be interviewed. It was too early in the morning, and the last time I was interviewed for a story about the marine biology job I worked out in Oregon, I said something like, “The fish are so happy!” or something stupid like that.

But the director of my program decided to pinpoint me and say that I would be a good person to interview, because I was the only second year student in the room. So I couldn’t say no. The guy brought over a camera and asked a lot of questions about 3D and its applications in medical illustration. I stumbled out some answers. While it was nerve-racking, it was also exciting. I’m gonna be on INTERNET TV!!!

Then I went on a field trip. We went over to UIC’s Innovation Center, where a serious amount of innovation is happening. The reason we were there was to see 3D printing in action. 3D printing is exactly what it sounds like- you can send a digital 3D model over to the printer (in a format called .STL –> like St. Louis) and the printer will create a real-life 3D object by reading the file, and layering thin slices of whatever material is being laid down. In this case, it was a starch powder with a layer of special glue. Here are some pictures.

Andy the innovator- who works at the center- showing us how to print.

(Andy the innovator- who works at the center- showing us how to print.)

(Z-corp printer in action! – top view. you can see the unused powder on the side)
(some printed objects- so cool.)

Basically the process is like printing a document, but layering the “ink” repeatedly to get a 3D object.

Next we went over to the Art and Architecture building on East campus, and saw yet another 3D printer. This one is newer and prints with a liquid plastic that dries so fast that it can produce a small solid object in 10 minutes. Pictures:

(The printahh- a Stratus machine.)
(the printer in action- laying down an abs plastic on top of a support material)

The support material is also printed by the printer- this step comes first, so that the printer has something to lay down the plastic onto or INto. It can only make an entire 3D object if the scaffolding to hold the object exists first.

(little printed plastic guy and support material)

Lastly, I went to a lecture at UIC’s West medical campus. The speaker was Dr. Maria Siemionow, the first physician to perform a face transplant in the US! She spoke about the nuts and bolts of facial transplants- the infrastructure, manpower, knowledge, research and judgment required to perform such a surgery. She showed us pictures of patients who had applied for a facial transplant (only the worst cases were considered) but then told us how she had to be extremely discriminate when choosing recipients of this novel and dangerous procedure.

Not only is the surgery itself invasive, the patient must be forever treated with immune-suppressants after they get the transplant. Basically the point of her lecture was to inform those surgeons at UIC how to open a facial transplant business and run it effectively and safely. I could tell this woman was compassionate, passionate, intelligent and wise. I really enjoyed hearing her speak, and it was a really interesting topic!

Model me this:

I know I keep talking about 3D modeling, and I hope you don’t think it’s BORING- but let me try to make it a little interesting. Also, it’s pretty much the future of medical illustration, so I’m going to keep talking about it! Wah!

My first big project was due on Monday. The assignment: choose a medical instrument, really anything you want (our prof gave us a big box of instruments) and create a 3D model of it. To give you an idea of what this entails, let me break down how to model something on a compooter:

1) pick an object to model. Maybe it’s something that already exists, maybe it’s something imaginary, maybe anatomy (like your own face), maybe it’s the boyfriend of your dreams. Pick something that’s slightly interesting to you because you will be working with this object for a long, long time. I picked an endotracheal tube because they save people’s lives by letting them BREATHE.

a real life endotracheal tube

2) Use a 3D modeling program (in my case, 3DS Max) to “model” the instrument.  This means to create the basic shape of everything- all the individual pieces of the thing. In my case, I had the main tube, the bubble of air at the end of the tube, the mouthpiece, and the tailpiece where  you inject air into the air bubble at the end of the tube.

If you were making a model of your own face, you’d make a basic sphere as your head and then add modifiers on the sphere to look like the shape of your head. Then you would model the nose, eyes, mouth, ears and hair separately, then attach them to the head. You can do all of this in one 3D workspace. Here’s my basic model of the tube:

3) Put some materials on that thing! What does the model above look like to you? maybe you know what it is by the basic shape (if you have used one of these puppies before) but you don’t get a full idea of its functionality without the correct “materials” assigned to it. For example, with the face you’re modeling- you don’t want it to look plastic. You want it to look like it has skin and hair, so make some materials that look like skin and hair.

This process is a matter of experimentation. There is something called the “material editor” in 3DS Max where you can literally build a material based on its color, opacity, shinyness, transparency, translucency, texture, etc. You can build a material from scratch, or use preset materials like “rough plastic” or “chrome” that people have created and put into materials libraries available to 3DS Max users.

I had a lot of plastic material for my object. Here’s an example of an experimentation with a plastic material:

Used a clear plastic for the bubble, and added the material of a crinkled paper bag on top of that to make it look wrinkled.

I used this picture of dust to make some of my materials look rough, by plugging it into a "bump map", which takes information from a picture and applies it to a surface to make it look like a 3d texture.

4) LIGHTING! What is a world without light? You have to add lights to your scene to emphasize certain traits about your model. For example, plastic has a lot of highlights, so I wanted the lights in my scene to reflect sharply on the object. For your face model, you don’t want your nose to look too shiny (unless it’s being used in an ad for Biore) This is something that you can change in the properties of the light, or in the material of the object itself. Here is a snapshot of me experimenting with light to make the tailpiece look slightly shiny and glossy:

The light is a little too strong in the background- it looks like a spotlight is shining back there.

 

5) And voila! you must render the final scene. To do this, you have to set up a camera (sometimes as easy as clicking “command + C” to create a camera in the scene) You can play with focus, perspective and depth of field, just like you can with a real-world camera. You must make sure to set up the scene so the model isn’t floating in air. Give it a setting by making a ground plane, and applying a texture to it (in my case, surgical cloth). Then you click render. Rendering the final scene takes time because the computer has to process all the data for lighting, materials, modeling, etc. BRING A BOOK!

Here are my final renders. I did two because I changed some things for the second one. I kind of like them for different reasons, so if I ever fix this I’ll use what I like in both to make a new render.

endotracheal tube #1

Endotracheal tube #2

So I hope you understand the process of 3D modeling a little better. Anyone can do it! I hope to see your modeled faces soon.

Syringe you happy to see me?

My 3D instructor gave us a tutorial to model and texture a syringe. Here’s mine. Does it look real?

modeled and textured syringe

Ahh! it's gonna get me!

It’s funny because in this class we spend hours and hours in front of a computer, tweaking vertices and edges, lighting and various materials, only to create something that already exists! Plus, you can’t even use this syringe to draw real blood. haha. But of course there are obvious uses to model objects like this. It can be used in a commercial for syringes! It can be used as a prop in a virtual world like Second Life. Or, it can just be a way to learn how to model in 3D, which is what I use it for. Anyway, I’m getting the hang of this modeling thing.

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