CMI Lab’s HuBMAP interns Present Summer Projects during National NIH Symposium

The Computational Microscopy Imaging (CMI) Laboratory’s two NIH HuBMAP Interns, Lin Xu, an undergraduate at Virginia Tech (Blacksburg, VA), and Julio Maragal, an undergraduate at Santa Fe College (Gainesville, FL), took center stage and presented their summer research projects during HuBMAP’s 2023 Summer Internship Virtual Poster Symposium. Their engaging presentations showcased the culmination of a fruitful season of research and educational enhancement, signifying the conclusion of a highly productive summer experience.

Titled “Interactive Spatial Transcriptomics Visualization Portal,” Xu’s presentation was on her project to develop cloud-based plugins for deconvolution of spatial transcriptomics data. Through his presentation, “CODEX and H&E Imaging: Cell Type Analysis and Mapping Pipeline,” Maragal discussed the development of machine learning tools for the visualization and analysis of histological images of kidney cells and tissues.

Describing how she spent her summer, Xu said, “In my internship experience, I had the privilege of contributing to developing a spatial transcriptomics visualization portal. By integrating advanced tools like Visium Spatial Gene Expression, Seurat, Shiny, and UMAP, I gained a deeper understanding of spatial transcriptomics analysis and its potential applications in quantitative medicine. This experience has further solidified my academic and career goals, motivating me to pursue a PhD and continue exploring innovative ways to bridge computational techniques with medical research.” Xu has academic career aspirations that revolve around advancing the field of medicine. She aspires to pursue a PhD and delve deeper into the intersection of computational methods and medical research, and how she can apply nanotechnology. Her goal is to contribute to developing innovative tools and approaches that enhance our understanding of complex biological systems and ultimately lead to improved healthcare outcomes.

Of his experience, Maragal said, “I was able to multiply my scientific skills thanks to the supportive team at UF’s IC3 and the Computational Microscopy Imaging lab. They allowed me to leverage new relationships to boost my academic output and achieve unmatched personal growth.” Maragal hopes to complete his undergraduate studies at the University of Florida and go on to pursue his Ph.D. He hopes to become a Principal Investigator in the area of Quantitative Health one day. As he shared during his presentation, this unique internship experience furthered his goal to “accrue sufficient knowledge to teach a younger generation of inquisitive individuals.”

The HuBMAP summer internship program is an opportunity for under-represented undergraduate students from U.S. colleges and universities to receive mentorship and training from HuBMAP Consortium investigators over a twelve-week period during which they conduct research, attend academic enrichment lectures, and participate in lab activities. Funded by the National Institutes of Health, the HuBMAP consortium is working on developing tools for an accessible global atlas of the human body at the cellular level, with the goal of enhancing our comprehension of the connections between cell organization, tissue function, and human health. Through the creation of advanced molecular analysis technologies and computational tools, HuBMAP aims to generate three-dimensional tissue maps and an atlas depicting cell function and relationships within the human body, contributing to a deeper understanding of the impact of cell interactions on health. HuBMAP contributing sites can be found across the United States. Under the direction of Dr. Pinaki Sarder, the University of Florida serves as a HuBMAP “HIVE” (Integration, Visualization, and Engagement), which is a centralized hub that integrates diverse data and tools from multiple research teams, facilitating collaborative data analysis, visualization, and knowledge advancement.