Post-Defense Interview: Kate Zumach

A research project or thesis exploring a question related to the field of biomedical visualization is one aspect of completing a Masters in Biomedical Visualization here at UIC. This original investigation enables greater insight into scholarship, understanding of the research process, and emphasizes original and critical thinking. Graduate students complete a written proposal, final research or thesis paper, give a final oral presentation and defense which all enable a student to develop advanced communication skills. This year, we are sitting down with our graduate students after their final defense for a quick chat about them and their research.

Recently, Kate Zumach defended her project: “Documenting Visualization Methodology and Decision-Making in Digital Reconstruction of Norellius nyctisaurops


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Kate Zumach discussing her 3D print with 1st year student, Riley Jones

Taking a page from lolmythesis.com, how would you describe your research in one sentence?

Kate: Reconstructing, animating, and 3d printing Dr. Paul Sereno’s tiny Squamate skull

Sounds adorable, but what is it?

A Squamate is a reptile in the order Squamata, the largest extant order of reptiles that includes all lizards and snakes. With over 10,000 species what makes them unique are their scaly skin and movable quadrate bones.

How did you get involved with this research?

I became involved by taking a trip to Dr. Sereno’s Paleontology lab at University of Chicago with a fellow classmate, Andy Schulte.

How did you plan out the animation to highlight the morphological structures of importance?

The morphological traits of N. ncytisaurops skull were the most important aspects of the animation. I knew from the start that they needed to be highlighted in a way that would be beneficial for both a lay and professional audience. I went about using simple 2d animations with differing opacities to illuminate traits and structures that Dr. Sereno talked about in his research. I wanted to really make each trait visible but keep the animation simple so that the viewer didn’t get disoriented. I also used call outs to focus on the smaller traits like the primitive pterygoid teeth.

What was the 3D printing process like?

3D Printing was a real challenge. The first print I had I remember staring at it for the hour just to make sure nothing went wrong. I printed in several different places as well to test out different printing materials. Before printing, every mesh had to be watertight and the topology of the models needed to be lower than 5 mb. I also have parts that interlocked with each other so I had to keep track of the printing dimensions to make sure they were uniform for all of the different prints. I used an Afinia printer and two different Makerbot printers.

ZBrush seems to be one of your 3D sculpting programs of choice. What are some of your favorite ZBrush features? How do you use them?

ZBrush was my hero for this project along with Materialize Mimics. I used ZBrush for all of the detailed sculpting and retopology. My favorite feature that I used was “skinning” my models so that I could fill the holes of the fragmented fossil bones while keeping the integrity (shape and size) of the original fossil.

You implemented a database system to keep track of your reconstruction work. Can you talk to us more about the impetus for this portion of the project and what it is?

The database really came about through the realization during the project that there were no checks and balances systems in this sort of work. Reconstructions are often  presented as a fait accompli with little to no documentation regarding the many decisions made along the way and with limited access to these stages of the digital reconstruction itself. With the database, all of the decisions, sources, and results could be found in one organized and easily accessible place. Before the database I was trying to stay organized but I was only sending screen shots of pictures with questions in a word document and hoping that it was legible. That’s when the frustration was too much and I thought there had to be a better way to collaborate with my content expert and stay more organized.

In academia, there’s an emphasis on citing references when writing a paper but not the same requirement when creating images, even though the visual references we use do impact the final image’s scientific accuracy. Do you think that such a database could be used for housing the visual references used in creating other kinds of scientific images?

Absolutely! I feel that these sorts of checks and balances are extremely helpful for creatives who are creating images that involve scientific and medical concepts. When working with a client, it would be more streamlined and efficient to use a database form to house all of the information you need for example, all of your sketches, process work, references used, descriptions, separate files, date project was started, how much time is spent, etc. Not only do you stay organized but you have a way to show all of the work and defend decisions that were made. The database format can be customized for whatever project that is needed and is not limited to certain fields.

What are your plans for the future?

My plans for the future are exciting and fast approaching! I am touring in Ireland for now and right when I get back to the states I am heading to work as a medical illustrator and animator at Swarm Interactive in Chapel Hill, NC. I am thrilled to be joining the team at Swarm!

Post-Defense Interview: Jacqueline Mason

A research project or thesis exploring a question related to the field of biomedical visualization is one aspect of completing a Masters in Biomedical Visualization here at UIC. This original investigation enables greater insight into scholarship, understanding of the research process, and emphasizes original and critical thinking. Graduate students complete a written proposal, final research or thesis paper, give a final oral presentation and defense which all enable a student to develop advanced communication skills. This year, we are sitting down with our graduate students after their final defense for a quick chat about them and their research.

Recently, Jacqueline Mason defended her project: “Developing an Interactive 3D Learning Experience to Help Students Understand Key Regulatory Processes Associated with Glycolysis”


 

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Jacqueline Mason

lolmythesis.com, how would you describe your research in one sentence?

Jacqueline: I designed an esoteric application about enzymes that kind of, sort of works.

How did you decide on your research topic?

I have a strong interest in designing solutions for problems in science education. I spent some time interviewing biology professors at UIC, asking what their students struggle with the most. Cellular respiration was nearly unanimously reported, and so I decided to design a solution for teaching certain concepts within cellular respiration. After further discussion with my committee, I narrowed the scope of my project to address allosteric regulation within the context of glycolysis.

Why do undergraduates struggle with learning glycolysis? What was your experience when you first learned about this topic?

Glycolysis, and the rest of the pathways involved in cellular respiration, are highly complex and multifaceted. Undergraduates (including me when I took undergrad biology) see their textbook illustrations with names of enzymes, compounds, molecules, and arrows all over place and it becomes a daunting memorization task. Often, students are not taught the foundational biological principles that underlie these pathways, which could help them make sense of the chaos. In addition, students typically only learn these pathways by looking at static figures– there’s no interactivity and few animations to facilitate the learning. All of these factors not only make glycolysis difficult to learn, but there is very little knowledge retention.

Can you tell us what theoretical framework you based your project?

I used a number of design and educational frameworks to guide my project. The two main educational frameworks I used were cognitivism and constructivism. Cognitivism emphasizes the need to help scaffold student learning– so helping students slowly build understanding based on prior understanding. For my project, I introduced students to the topics of enzymes and allosteric regulation is a 2D animation. I then allowed students to build on this foundational knowledge by having them explore these same principles in a 3D space with a specific pathway (Glycolysis). Constructivism places the learner at the center of the experience. For my project, I wanted students to not just learn about allosteric regulation in an abstract way. I contextualized the experience by allowing them to explore allosteric regulation in glycolysis, and then in a specific enzyme: phosphofructokinase.

What’s your typical workflow look like for a project?

For this research project, I really dove deep into the education literature to make sure I was designing an application that incorporated effective instruction strategies. I also thoroughly researched and made sure I understood the scientific topic of my research which involved the regulatory mechanisms of glycolysis. Since I was developing a learning module that involved the use of both a 2D animation and a 3D interactive application, I then developed a storyboard and wireframes to help me plan out the learning module. Asset creation was next, developing 2D vector graphics for the animation, and 3D models and animations for the application. Finally, the animation was composited, and the models and 3D animations were imported into the gaming software Unity and scripted for interactivity. The final deliverable was an online learning module incorporating the animation and application.

What was the most challenging aspect of your project research?

The most challenging aspect of my research was determining the best way to visually represent my topic in an interactive 3D space. Glycolysis alone is a big topic, so I had to make sure I was only representing the concepts that aligned with the learning objectives of the research. Secondary to that was learning enough programming to represent this molecular space accurately and effectively. I’ve learned quite a bit from this research project and hope to make improvements on future versions of the learning module.

How did the scope/implementation of your research change over time?

Originally, I had planned to develop an application that would allow students to track energy transfer throughout all of cellular respiration. This would have been a very large and daunting project. After some research, I scaled my project way back to focus on the regulatory mechanisms of glycolysis. This allowed me to develop a very focused learning module with targeted and clear learning objectives.

What was your favorite part in that workflow?

This project was my first real experience coding using the C# programming language. Writing successful scripts and seeing my project transform into a responsive, interactive experience was very gratifying.

You have previous experience as a graduate student, what motivated you to pursue graduate school again? could you talk to us a bit more about your previous experiences and how it’s  impact on  your work here at UIC BVIS?

My previous master’s program in educational technology taught me the powerful ways we can leverage emerging technologies  to create meaningful learning experiences. I learned how important it is to use research-backed approaches when designing new tools for education. After graduating and working as an instructional designer, I realized how much I wished I could apply my knowledge specifically toward developing visualization tools for science education. I knew that the BVIS program would give me the final set of skills I would need. Throughout my time at BVIS, I have tried to be very intentional with every project I have developed, ensuring there is always a clear learning objective. Inspired by new fields like serious game design, I have focused my studies at BVIS around interactive media development. The interactivity classes at BVIS have been amazing, and have really allowed me to integrate everything I have learned from both graduate school experiences.

What excites you about a new project? Any new projects coming up on the horizon?

I love projects that attack a problem in a strategic and novel way. This past semester, some fellow classmates and I had the opportunity to develop educational experiences using augmented and virtual reality. I think there are many ways these technologies can impact health and science education, and I am excited to explore new projects using these technologies.  

 

Post-Defense Interview: Ashley Ulm

A research project or thesis exploring a question related to the field of biomedical visualization is one aspect of completing a Masters in Biomedical Visualization here at UIC. This original investigation enables greater insight into scholarship, understanding of the research process, and emphasizes original and critical thinking. Graduate students complete a written proposal, final research or thesis paper, give a final oral presentation and defense which all enable a student to develop advanced communication skills. This year, we are sitting down with our graduate students after their final defense for a quick chat about them and their research.

This past week, Ashley Ulm defended her project: “Visualizing the attachments and internal architecture of the masseter muscle in Cavia porcellus using contrast enhanced micro-CT


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Ashley Ulm

Taking a page from lolmythesis.com, how would you describe your research in one sentence?

I spent a year meticulously dissecting one muscle on a guinea pig . . . surprise! it chews.

Although quite cute critters, why a guinea pig? and why this muscle?

Guinea pigs belong to a specific group of rodents that have a unique set of masticatory muscles, or the muscles used to gnaw and chew. The ZM is the muscle that really makes this group of rodents unique, in that it passes through a hole in the skull called the infraorbital foramen and inserts on the snout. This means that it crosses over bone, which allows it to act like a pulley system when the muscle contracts. Dr. Druzinsky plans to study the biomechanics of this pulley system using the models generated in this study.

Where did your research-project come from?

Dr. Druzinsky is a faculty member of the University of Illinois at Chicago College of Dentistry. He had access to contrast-enhanced micro-CT (CE micro-CT) scans of a guinea pig, and thought that the extreme detail shown in this new type of CT scan could be utilized somehow. He reached out to the Biomedical Visualization department to find someone to help him visualize the data, and I was eager to work with him.

Can you talk a little bit more about these new CT scans? How are they being used currently? Where do you think they will go in the future?

These CT scans are called contrast-enhanced because the specimen that is scanned is first soaked in an iodine solution that penetrates the muscle fascicles but not the connective tissue between them. In traditional CT scans, bone shows up white and everything else is black. The iodine solution causes details in the soft tissue, such as the muscle fascicles, to show up as white more like the bone. This means that you can see a lot of detail in the soft tissue that traditional CT scans do not show.

This process is still fairly new, and many studies such as this one are investigating how to best utilize the information written in these scans. I am interested to see what scientists will do once they have access to 3D models of this detail that they can interact with.

Can you give us an overview of the workflow in creating your research project?

I used the CE micro-CT scans from Dr. Druzinsky and the Materialise Mimics Innovation Suite® to segment the zygomaticomandibularis portion of the guinea pig masseter muscle. This muscle starts along the snout then travels down through the skull to connect to the lower jaw. I first found the whole muscle, then segmented out each muscle fascicle, which was visible in the CE micro-CT scans. I aligned the muscle with a 3D model of the guinea pig skull. Then I embedded the models into a 3D interactive PDF. Inside here, you can rotate and pan the model, change color and transparency of the models, and toggle on and off a slice plane. This helps to view the anatomy spatially and in cross-section.

What insights have you gained from studying this technique? And do you have any advice to other visualizers looking into this methodology?

It is well established that different muscle architectures exist, such as unipennate and multipennate. The ZM is multipennate, meaning that the muscle fascicles are arranged in several directions in relation to the line of action of the muscle. Knowing this, and having the ability to interact with a 3D model of this data will help artists to think a bit more critically about muscles as they draw them. Since form begets function, knowing the muscle architecture and knowing that the fascicles that make up a muscle do not run the entire length of each muscle will help inform both 2D and 3D representations.

You recently attended the Experimental Biology conference in Chicago and met with professionals in other fields such as paleontology using this technique. What did you learn from them?

In speaking with attendees of the EB conference, I learned that this contrast technique is reversible, so it can be used on museum specimens in order to avoid dissecting rare or precious samples, and then it can be reversed and the specimen can be restored to the museum intact.

I also discovered that contrast enhanced CT scans are being used to scan “animals of today,” such as horses and rodents, and then the information harvested from the scans is used to map origins, insertions, and muscle architecture to fossilized bones. This may lead to advances in understanding dinosaurs and other prehistoric creatures.

What have you learned from the process of completing your Masters of Science?

I became very familiar with the Mimics software. With this, I learned how to re-slice image data, explored interpolation, and did extensive mask editing in 2D and 3D. I went from looking at the CE micro-CT scans in bewilderment to confidently differentiating between soft tissue structures within the image data. Finally, I got to practice low poly modeling with a high poly look to optimize my models for the 3D PDF environment.

In the BVIS program, I’ve grown as both a scientist and an artist while honing my attention to detail and critical thinking skills. I cannot wait to use this skill set to inspire learning, appreciation, and advancement of the sciences. I have had opportunities to work with people in fields such as neurosurgery, plastic surgery, evolutionary biology, nursing, and the talented BVIS faculty. These collaborations have formed a unique, once-in-a-lifetime experience that I will use as the foundation for my career as a medical artist.

Who/what are your inspirations and influences when it comes to artistic style and choices?

Since I have started graduate school, I have tried out many different styles and been influenced by many artists, especially the artists I am surrounded by daily — my teachers and fellow students. In many of our classes we have been encouraged to find inspiration in the world outside of medical illustration. I think taking inspiration from daily life, interactions, and art is something many artists do intrinsically, and because of this, are constantly growing and changing.

What are your plans for after you graduate?

I got engaged over spring break! So I am moving to Portland, Maine to be with my fiance and begin my job search. I plan to work in the healthcare industry and make 2D and 3D images and short animations for patient education and empowerment.

Post-Defense Interview: Adriana Orland

A research project or thesis exploring a question related to the field of biomedical visualization is one aspect of completing a Masters in Biomedical Visualization here at UIC. This original investigation enables greater insight into scholarship, understanding of the research process, and emphasizes original and critical thinking. Graduate students complete a written proposal, final research or thesis paper, give a final oral presentation and defense which all enable a student to develop advanced communication skills. This year, we are sitting down with our graduate students after their final defense for a quick chat about them and their research.

This past week, Adriana Orland defended her project research: “Animating External Magnetic Guidance of Intrathecally Delivered Gold-Coated Nanoparticles to Treat Intramedullary Spinal Tumors.



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Adriana Orland

Taking a page from lolmythesis.com, how would you describe your research in one sentence?

Adriana: Battling Spinal Tumors with Magnets and Gold Spheres

Wow, sounds interesting! How does that work?

Basically, it means that neurosurgeons are able to inject nanoparticles (gold spheres) into your spine that carry drugs to the tumor. The nanoparticles are directed where to go by the external magnets.

Can you explain how you came to choose this topic? What was it that first interested you about it?

Since college, the study of neuroscience has intrigued me, so I jumped at the chance of working with a neurosurgeon when my advisor mentioned the possibility. The neurosurgeon’s research was already well established, so I joined his team as the animator tasked with bringing his innovative idea to future grant committee/neurosurgery researchers in an understandable manner. The new technique that he is a part of is truly on the cutting edge of the field and knowing that my animation is taking part in guiding the future of neuroscience excites me.

Did your advisor introduce you to a neurosurgeon? Can you tell us a bit about him?

Yes, my advisor did connect me with Dr. Mehta. Dr. Mehta is a Neurosurgeon and Assistant Professor in the Neurosurgery Department at UIC. For being a neurosurgeon, he is very responsive. Any question I had, I didn’t hesitate to email Dr. Mehta. He would respond within the day. It has been quite the privilege to work with someone who is so supportive and knows what he wants.

 What theories or theoretical framework is your study based on?

The project was based on Richard Mayer’s Theory of Multimedia Learning which emphasizes the use of two channels (auditory and visual) to better commit the content to memory. Furthermore, I focused on cognitive load to make sure the animation was logical and didn’t overstimulate the viewer.

What were the results from your study?

The six participants from Dr. Mehta’s Neurosurgery Lab replied positively towards the animation comprehension, the animation pace, and the organization and effectiveness of visuals paired with narrative in the animation. Unfortunately, they found the animation to be too simple for a grant committee, which was my intended audience.

What was your favorite stage during the completion of your research project?

I loved setting up the camera motion throughout the animation. The way you move the camera is the true foundation of the new world you are creating. One wrong angle and the message may be lost. The precision and focus it takes to optimize the camera movements for the benefit of the user is thrilling.

What would you do differently if you were setting out to do it today?

I would spend more time thinking through how to develop certain scenes. What comes to mind is the last scene of my animation where gold-coated nanoparticles cross the innermost layer of the spinal cord (pia) and reach the tumor. More time could have been devoted to really getting those effects working. Also, I would choose an easier title. One that people could actually read in one breath!

What have you learned the most from your research project?

The use of nanoparticles in drug delivery and how to better navigate through 3ds Max. This project pushed me out of my comfort zone especially when it came down to modeling and animating the procedure. Prior to this all other projects, were minuscule in scale.

What would be the next step(s) for you if you were to continue with this research?

The next step would be to test this animation on more individuals who are not associated with the research. While, getting feedback from Dr. Mehta’s Neurosurgery Lab was valuable and helped to improve the study, it is necessary to see how the animation is perceived by those not familiar with the technique.

What are you most excited for after graduation from UIC BVIS?

I’m most excited to devote more time to learning and becoming more comfortable in developing content for HTC Vive and Oculus. Granted, after I have time to catch up on sleep and recuperate from this tough final semester!