Home » REU2017 » Tony Sun: Dynamic 3D Visualization of Blood Flow in Brain Arteries

Tony Sun: Dynamic 3D Visualization of Blood Flow in Brain Arteries

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Clemson Visualization Division Logo

Home Institution
University of Missouri – Columbia
Columbia, MO
Contact Email: tksqk6@mail.missouri.edu

Clemson Research Mentors
Dr. Ulf D. Schiller
Department of Material Science and Engineering
Mehrdad Yousefi
Department of Material Science and Engineering

Clemson Visualization Mentor
Dr. Wole Oyekoya
Visualization Director

About me: Tony Sun

Born and raised in Columbia, MO, I elected to attend my hometown institution in the hopes of strengthening ties to the community that has raised and shaped my formative years. I study mathematics and psychology and plan on attending graduate school in a related field. I am primarily interested in how socialization in competitive environments can enhance critical skill formation in areas that require quantitative competence. I would love to find a program that utilizes my interests in a diverse range of topics.

In my free time, I enjoy the outdoors, reading, and listening to music. I am also peripherally learning about football and basketball.

Project Description

My mentor is Dr. Ulf D. Schiller who has a focus in material science and engineering. He is interested in soft tissues as a research topic and is developing a method to visualize medical diagnostic tests for use in educational and clinical settings. In particular, commonly used MRI scans can only display 2D slices of an object. There are severe limitations for laypeople and trained professionals alike for whom these images only provide a snapshot of the current state. More troubling is the lack of knowledge about volatile conditions, such as intracranial aneurysms, where little concrete evidence exists for diagnosis and subsequent treatment options.

Our hope is to interpolate the data from the scans into a more accessible model with existing patient-specific clinical parameters to improve patient prognosis. We will do this by creating a virtual reality environment where an observer can step into a model of a brain to see hemodynamic blood flow and physical wall tension and interact with it in real-time to make decisions about these volatile conditions.

To do this, we must first convert the raw data from the scans into a form that can be accessed through virtual reality capable programs. Then we need to construct a model from the data. Finally, we must then program that data to be viewed through a virtual reality headset. You will find weekly documentation of my project progress below.

Week 1 Overview

Week 1 was a tumultuous time. I arrived and immediately began familiarizing myself with the lab’s technologies and culture. We were allowed to test out various virtual reality displays (HTC Vive) using current lab programs before being introduced to our mentors and our own projects.

After our orientation, we met with other visualization affiliated professionals and were trained in IRB for social and behavioral studies. The next day we went on a tour of the campus and worked on an outline for this program. We had a couple presentations on writing research papers, screen captures, and video editing. On Friday, we were taken on a tour of the Watts Family Innovation Center, where detailed attention was placed on the union of advanced visualization technologies and interdisciplinary research in a facility designed for maximizing digital communications.

This week in the lab was spent building comfort with these technologies, many of which are new to me. I have read through the existing knowledge base and am beginning the modeling soon. I will be using Paraview and OpenVR as well as Python to complete this assignment.

In addition, I’m very excited to see how everyone’s projects end up.

Week 2 Overview

This week began with a crash course in the command line interface commonly found in Linux to access the computational strength of the Palmetto cluster. We then spent some time reviewing current scientific visualization software and resources found here at Clemson and across other academic institutions. We finished the week up with an introduction to information visualization and visual analytics. Software used include OpenRefine, Tableu, SAS Visual Analytics, Gephi, and D3. There was an optional session on GIS technologies ArcCatalog and ArcMap which I found to be quite interesting.

At the beginning of week 2, I was determined to work with the Virtual Reality headsets. Before this could be done, we needed to find a way to access the simulation data with our scientific visualization program, ParaView. We accomplished this through the use of an open source extension of the software. However, animations were not supported in this extension, proving a major roadblock to utilizing a majority of our real-time data. Next steps include importing the data set into this extension and looking for animation support. I am also beginning a literature review on the implementation of virtual reality technologies in the hospital setting.

Week 3 Overview

Another week, another workshop. We covered more advanced topics today in our seminars. Monday and Tuesday were spent on learning Python. Python is a popularly used programming language for its both its accessibility and its readability. Newer programmers may have trouble with the logical flow, as with learning any language, but more experienced programmers will find the syntax relatively easy to pick up.  In addition, an emphasis is placed on limiting the exterraneous punctuation and spacing issues of older languages. I found myself to really enjoy the sessions on Python, finding it relatively easy to learn, not to mention useful. I’ve seen many applications that utilize Python scripts and a quick google search shows that it is currently and consistently ranked amongst the top 10 programming languages in use today. We also had a presentation on the capabilities of Unity as a game development platform. Unity allows one more interactive experiences with VR and AR as it supports a wide array of avatar functions. We also had a presentation on current and future uses of LiDAR technologies. LiDAR detects the returning light frequencies of various light emitting units using sensors that can be interpolated with several other pieces of data to determine the range of various scans as points. These points can then be used to map a corresponding area. Very interesting applications for UAVs.

The workshop on IPUMS ranks one of the most interesting thus far. This is a collection of international census data that is available for multidisciplinary scholarly pursuits. I would have liked to spend more time familiarizing myself with this dataset but it is beyond the scope of my current project.

Speaking of my current project, this week had slow progress. As we gear up towards our midterm presentations, I was a little disappointed in my current progress. I have spent a lot of time researching and learning new programming languages and visualization tools, yet I have still hardly anything to show for my own project. That said, we were able to demo the use of the headsets on Wednesday and are closer than ever to making Paraview compatible with the cluster. I am currently writing a draft of my paper, but the overall progress of my project, and consequently, my paper is limited. Although this may be discouraging, I look forward to beginning the next week with renewed vigor.

Week 4 Overview

Finally, something I have a foundation in! The week’s workshops were on R statistical software. I have been using R for a couple semesters now on independent research projects. Our crash course was quite useful for compiling all my experience into a cohesive whole. We learned how to use R to make graphs and write to images as well as a multitude of stylistic choices.

My project progress this week was focused on steps moving forward for the project. Ideas include the following: changing the peripherals of the clipping plane, creating a demo video, and building in real-time data visualization with the use of Unity.

Week 5 Overview

This week we had presentations. We were hosted in the Watt Family Innovation Center, which we toured earlier in the program. I must admit that I was nervous for the presentations, but I was also excited to see the progress of the rest of my program members. We all have such interesting and diverse applications united under big data visualization concepts so there are new ideas with enough overlap to be intriguing. I hope to learn from the other VizREU students during the presentations. Dr. Wole even managed to get live twitter action shots during the presentations.

We only had one workshop this week on editing 2D images. I was interested in the section on creating VR environments with 360 video through Premiere Pro. I was able to talk to Dr. Brian Adam Smith about emerging technologies regarding VR and AR, in particular, the use of AR for medical research.

Week 6 Overview

This week, I am working on implementing the Paraview Unity Plugin for Dynamic Data Visualization.

We were able to visit the ITC data center and view the Palmetto cluster. I felt like I was in a movie surrounded by the computing behemoth.

Week 7 Overview

We ran into a problem with building Paraview to communicate with Unity. We will spend the rest of this week looking for a solution.

This week’s workshops were about Leadership. The power of presence and building relationships through networking are very powerful industry skills. I’m grateful for the chance to practice them.

Week 8 Overview

This is the final week. We are presenting on Friday, so I need to finish my poster, video, and presentation before then. I am extremely stressed out but with the support of the lab, I was able to successfully complete the tasks.

This has been a tremendous experience for me. I was able to gain practical skills through the workshops and research. I was able to develop relationships with those around me and learn from their skills. I was able to take my academic research experience as an undergrad to the next level, benefiting my future academic endeavors.

I would say that this summer has been an overall positive experience. There were moments where I felt like giving up, that I would never accomplish anything I set out to do and that I was going to fail.

Thanks to Dr. Wole Oyekoya, Dr. Schiller, and Mehrdad Yousefi, I was able to complete and present at the Watt Innovation Center. Thanks again for their tireless efforts to put together the REU and for their ability to challenge, motivate, and inspire us, undergraduate students. It was a pleasure working with the Clemson Computing Division and the Visualization Lab, and it is something I would definitely consider doing again.

Final Report

Hunter College
City University of New York
695 Park Ave
New York, NY 10065

Telephone: +1 (212) 396-6837
Email: oo700 at hunter dot cuny dot edu

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