Clemson Research Experiences for Undergraduates

Collaborative Data Visualization Applications Summer 2015

Home Institution

Emory University
Atlanta, GA

Clemson Research Mentor

Dr. Andrew Mount
Biological Sciences

Clemson Visualization Mentor

Dr. Vetria Byrd

About Me

  • My Interests: Chemistry, Computer Science, Philosophy
  • My Hobbies: I like trying new restaurants, traveling, puns, swimming, ballet, reading, and cinema.
  • Current Courses: Organic Chemistry II and Lab, Introduction to Computer Science, Calculus II, Basic Problems in Philosphy, Religion and Films of Miyazaki
  • Awards/Recognition: Emory Dean's List, Leadership Award, (soon to be) published author of two peer-reviewed chemistry papers, member of Phi Eta Sigma

Hi there! I'm Caroline Zhang and I will be graduating Emory University in 2018 with a degree in Chemistry and Computer Science. I am unsure which field I will be pursuing after I graduate, but I aspire to apply to graduate school and obtain a doctorate degree. Should I continue with Chemistry, I hope to continue to pursue my interest in research and become a professor. If I were to continue with Computer Science, I hope to start a company with a few classmates.

Project Description

At this year's VisREU program at Clemson University, I will be working with Dr. Andrew Mount of the Biological Sciences department. Our project consists of using scanning electron microscopy (SEM) and confocal microscopy to take detailed and high resolution images of marine animals, specifically oysters and barnacles, from a molecular and cellular perspective.

Week 1

This week I focused on getting preparing myself for the beginning of the project. In a brief review, this week:

  • I was introduced to Clemson University.
  • I was introduced to Palmetto, Linux, and HTML coding.
  • I familiarized myself with the past work of Dr. Mount's lab.
  • To elaborate on the technical aspects, the VisREU program has provided us short seminars on how to use resources provided to us by the university. We were taught HTML so we could build our websites, which is something I focused this week. The seminars on Linux and Palmetto were so we would be able to use the university's computer system for our data processing needs. To elaborate on the project specific work, Dr. Mount was away for the majority of this week, so my contribution to this project has been reading articles about his previous work, aquiring necessary software for the specific microscopy methods I'll be using, getting background knowledge of the marine animals I will be studying, attending a doctoral defense of one of his group members, and discussing the project with his current group members.

    Week 2

    This week I got the tools and software I need for continuing my project: Imaris, Matlab, and Leica (and all of these programs are new to me). Imaris is a program that will help me visualize the 3D data that is collected from the confocal microscope. Matlab is a software tool that allows the user to program whatever they need, and it is especially useful for data visualization (which is conveniently, the focus of our project). Finally, Leica is a program that allows rendering of the data collected from the scanning electron microscope.

    Other than getting situated with the software, I focused on establishing milestones for the weeks leading up to the midterm presentation on July 1st, and completing my milestone for this week: to download and familiarize myself with the software.

    Week 3

    While the first two weeks can be categorized as literature review and preparation, during this week I produced substantial work on the project. I received the raw .lif (a file type compatible with the Leica software) data files from a post-doc in the group. I converted those files into .ims file types (a file type compatible with the Imaris software), and used the Imaris software to highlight the different aspects of the images. This is only preliminary work, as the final product will need more refinement after consultation with my research mentor.

    Other than work with the software, this week we had learning modules on research design and abstract writing.

    Week 4

    In this week, I made significant revisions to the work that I did in the previous week. With meetings with my mentor, I edited the Imaris generated visualizations to look more biologically accurate and created animations to highlight the different aspects of the data. I had some spare time left over to work on some of the data that another member of Dr. Mount's group needed.

    In addition to improving my visualizations, I worked on writing an abstract for my project with help from Dr. Lori Tanner. I also had to prepare my midterm presentation that will be happening next week.

    Week 5

    This week, we had our midterm evaluations. On Monday and Tuesday, I practiced my presentation and asked for advice from both my research mentor, Dr. Andrew Mount, and my visualization mentor, Dr. Vetria Byrd. On Wednesday, we had our midterm presentations in the DRL of Clemson's Cooper Library. (Here is a link to mine. If the video demonstration is unclear, download the movie for 1080p quality.) All of our respective mentors were in attendance, and our presentations were open to everyone. On Thursday we had a celebratory lunch at The Smoking Pig (and it was oh so yummy). Afterward, Dr. Byrd revealed which 5 of the 12 of us have been selected to attend the XSEDE '15 conference in St. Louis, and I'm blessed to say that I was one of the ones chosen! For the rest of the week, I worked on the assignment Dr. Jill Gemmill assigned us.

    Although I have completed the midterm, my work is far from over! For the rest of my few weeks here, I'll continue to work on data visualization with the Imaris software, and I will also be collecting some original data using the Scanning Electron Microscope (SEM).

    Here are some images of my data visualizations!

    Cyprid 1

    Cyprid 2


    Helpful notes: For better resolution, download the linked movie. A cyprid is the non-feeding torpedo shaped larvae stage of barnacles before they attach onto a surface and mature into adults. A hemocyte is a lukocyte that circulates in the blood stream of oysters, and have been implicated in forming crystals for oyster shell formation. The colors in the images are the result of different stains applied to the sample during imaging. The blue color represents nuclei, the green represents chitin, and the magenta/red represent lipid or cell membrane. Click here for the link to the presentation.

    Cyprid 1: The scale on the bottom left says "40 um".
    Cyprid 2: The scale on the bottom left says "10 um".
    Hemocyte: This is an image of clusters of hemocyte cells. The scale on the bottom left says "4 um".

    Week 6

    This week we started off with an enrichment lecture with Dr. Jill Gemmill on effective and analytical reading of scientific papers. On Wednesday, we had an insightful round table discussion with Jim Bottum, the Chief Information Officer for Computing and Information Technology at Clemson University. He shared his professional experiences with us, as well as some of his reflections and predictions of the computer science industry. We had two more enrichment lectures that day, one by my mentor about his research and one from Dr. Gabriel Hankins with advice about graduate school. On Thursday, I continued to work with the Imaris software on some of the upcoming projects that I mentioned in my midterm, as well as a few extra projects that my graduate student mentor asked me to look into. Throughout the week, I had also been working on condensing my midterm presentation into two slides to present at the conference we attended over the weekend, where every participant had two minutes for a lightning talk on their research.

    On Friday, we traveled to Charleston, South Carolina to attend a mini-conference at the College of Charleston, where we were joined by other REU students from North Carolina State, University of North Carolina Charlotte, and Auburn University. Leaving the conference, I had two main reflections: 1) That computer science is a field that can be applied to any kind of research - from ants to humanities to cookies. 2) The importance of the conference isn't just to present my own data, but to be exposed to the diverse research is currently happening and realize its magnitude. The slides of my 2 minute "lightning talk" below. The images are linked to a PDF of my slides. The video on my second slide is the same as the video in my Midterm Presentation.

    Slide 1

    Slide 2

    It's been a hectic week, but I'm very grateful for everything that's happened. Having a mini vacation in Charleston was great, and the mini conference broadened my horizons and left me in awe.

    Week 7

    This week we had a lecture by Dr. Bernice Rogowitz on visualization and the effect of colors on how people perceive data. After that, we had individual consultations with her for our own visualizations and webpages. For the rest of the week, I worked on improving the quality of my visualizations following Dr. Rogowitz's advice and I prepared a draft of my poster for the XSEDE '15 conference.

    Week 8

    I can't believe these two months have flown by so fast. This last week at Clemson was a blur; the first few days consisted of making and finalizing my poster (which I will include below) and then the last few days consisted of making, finalizing, and presenting my final presentation (which I will also include below).

    When all those things were said and done, it amazes me how much all of us in this VisREU has accomplished in these short 8 weeks. I'm so thankful to have had this opportunity to get such a broad education in graduate research techniques, personal branding, presentation skills, and data visualization. I am also happy to announce that I have been nominated out of my cohort to present my research at the National Science Foundation.

    Thank you to everyone who's been a part of my 8 incredible weeks at Clemson. I am eternally grateful.

    Project Summary

    This project focused on the visualization of barnacle and oyster confocal data on a cellular and molecular level to study chitin production in barnacle larvae (also known as barnacle cyprids) and shell mineralization in oyster hemocytes. I produced these visualizations using Imaris software as well as direction from Dr. Mount and his post doctorate student, Dr. Vera Chan.

    Final Presentation


    In My Own Words

    If you'd like to read about my thoughts on the VisREU experience, click here!
    If you'd like to read about my thoughts on the XSEDE '15 experience, click here!

    Last updated: 08/03/2015