# Hongrui Zhu

> Biomedical Informatics M.S. | Imaging Informatics & Computer Vision | Stony Brook University

Profile: https://flows.cv/hongrui

## Work Experience
### Research Internship @ Prof. Chen's Lab, Department of Biomedical Informatics, Stony Brook University
Jan 2025
Project Summary: Annotated cells in pathology images, developed algorithms to expand point annotations into region-based annotations, and trained/tested benchmark models to evaluate performance
● Annotated cells in large-scale pathology images, ensuring accurate identification of different cell types for downstream analysis
● Designed and implemented algorithms to transform point-based annotations into region-based masks, enabling richer training data for segmentation tasks
● Trained and evaluated benchmark models including CellViT, Hover-Net, and StarDist on the curated dataset, systematically analyzing performance across multiple metrics

### Research Internship @ Dormant Biology Lab, Department of Biochemistry & Cell Biology, Stony Brook University
Jan 2025 – Jan 2025
• Developed FishLEN, a deep learning model for estimating fish length from images to support biological research.  
• Built an end-to-end pipeline utilizing data preprocessing, model training, and evaluation with PyTorch.  
• Enhanced model performance through iterative experimentation, including data augmentation and model tuning.

### Research Internship @ Prof. Chen's Lab, Department of Biomedical Informatics, Stony Brook University
Jan 2024 – Jan 2024
Project Summary: Reviewed research papers in the field, analyzed experimental results from models based on provided GitHub files, and presented findings through visualizations
● Reviewed and analyzed papers to summarize cutting-edge models in cell classification and segmentation, 
deepening understanding and tracking advancements
● Ran the Hover-Net project hosted on GitHub from a published paper, thoroughly analyzed the output results, and extracted key features to facilitate deeper insights
● Visualized the extracted feature data comprehensively, generated images, and converted selected features into QuPath-compatible files to support further analysis and applications


## Education
### Master of Science - MS
Stony Brook University

### Bachelor of Engineering - BE
Dalian Jiaotong University

### Bachelor of Science - BS
Dalian Jiaotong University


## Contact & Social
- LinkedIn: https://linkedin.com/in/hongruizhu
- Portfolio: https://blog.csdn.net/BlackOrnate
- Portfolio: https://blackornate.github.io/
- GitHub: https://github.com/BlackOrnate
- Portfolio: https://blackornate.github.io
- Email: mailto:zhuhongrui0917@gmail.com

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Source: https://flows.cv/hongrui
JSON Resume: https://flows.cv/hongrui/resume.json
Last updated: 2026-04-19