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Understanding Cancer with Data Visualizations of Cell Microscopy

Summer 2024

Project Background

Cancer is a notoriously difficult disease to treat. Our collaborators in the Department of Chemical Engineering and the Huntsman Cancer Institute use modern microscopy technology, such as Quantitative Phase Imaging, which shows promise in acquiring data to help understand and treat cancer. A dataset collected from a single experiment can contain tens of thousands of images and millions of data points. The large amount of data, combined with the complex details in the images, makes it challenging to analyze.

Interactive data visualization systems are well-suited to help researchers understand their data. These systems can provide high-level overviews of the data while providing access to the rich contextual information in images. Designing and developing such systems is an active area of visualization research. This is an ongoing project in our lab, and the initial work has been published. Work in this area has been published and has received an honorable mention best paper award at IEEE VIS. For more information about the work already completed on this project, see the project page.

Student Role

This project involves enhancing the cutting-edge of cancer cell microscopy visualizations. The current version of the software is built as a front-end application with modern web technologies (Typescript, Vue, Quasar). To improve the software, the student will meet with our collaborators to understand the questions they are trying to answer, design visualizations and user interfaces that can answer those questions, and write the code to implement those designs into working prototypes. Depending on the student's interest, the project can be adjusted to focus more on one of these facets.

Various skills would help make the project a success. These include strong written and verbal communication skills, familiarity with web development (TypeScript, HTML, CSS), web development frameworks (Vue, D3), version control (GitHub), and visualization design. None of these are strict requirements, but an interest and desire to learn them are.

Student Learning Outcomes and Benefits

The learning outcomes include: (i) developing the ability to communicate with domain experts about their data effectively; (ii) designing visualizations for domain experts based on these communications; and (iii) implementing these designs as web applications.

The main goal of the research will be additional features built into our lab's current cell microscopy visualization platform. This application and source code will be publicly available and can demonstrate the student's skills (e.g., on job applications). The work may also result in a recorded presentation, academic poster, or academic paper. In addition to building tools to aid in cancer research and expanding the field of data visualization, the student will gain practical experience developing modern front-end applications with a team of graduate students and staff software developers.

The skills developed in this research can be applied to industry. Many software developers have careers in front-end development. Familiarity with modern tools, experience working with a team, and experience discussing requirements/getting user feedback will make for a strong foundation in this area. Beyond front-end development, the ability to discuss data with experts and design effective visualizations for their data is a useful skill for most technical jobs.

Immersion in a research lab can also provide more insight into what graduate school or an academic career would be like and would set you on a good path for a Master's Degree, PhD, or beyond!

Alexander Lex

Associate Professor
School of Computing

As a member of our lab, the student will join an active group of researchers, including doctoral students and staff software developers. The student will be invited to our lab's weekly research meeting and our group Slack. In addition, the student will meet with the project team regularly to discuss progress and next steps. In addition to this meeting, the student is welcome to ask questions or request feedback from lab members as needed.

In general, this mentoring approach aims to provide support, structure, and guidance when needed while allowing the student freedom and flexibility to make the project their own.