Biomedical Informatics | Computer Vision | Medical Image Analysis

Hi, I'm Hongrui Zhu.

I'm a Master's student at Stony Brook University specializing in computer vision, computational pathology, and biomedical image analysis. I focus on building practical and research-driven solutions for real-world medical and biological applications.

I am actively seeking internships and full-time opportunities in AI, machine learning, and data analysis.

Current Position
Master Student
Institution
Stony Brook University
Research Focus
Computer Vision for Biomedical Images
Currently Open To
Internships and full-time opportunities in AI, machine learning, and and data analysis.

About Me

I am a Master's student in Biomedical Informatics at Stony Brook University, with a strong background in Applied Mathematics and Software Engineering. My research interests focus on computer vision, computational pathology, and biomedical image analysis, where I aim to develop data-driven solutions for real-world medical and biological problems.

I have experience in building deep learning models for image segmentation and classification, including nuclei segmentation on the PanNuke dataset and pathology image analysis on NYBB data. Recently, I have been working on FishLEN, a deep learning model for fish length estimation from images. I am particularly interested in applying machine learning to practical systems and continuously improving model performance through experimentation and analysis.

Research Interests

Computer Vision Deep Learning for Medical Imaging Biomedical Image Analysis Computational Pathology Image Segmentation & Classification Weakly Supervised Learning

Technical Skills

Python PyTorch Machine Learning Computer Vision Data Analysis NumPy & Pandas Linux Git Java R HTML MVC Django MySQL SQL Server

Selected Projects

Here are a few projects that reflect my interests in research, engineering, and applied machine learning.

Nuclei Segmentation on PanNuke

Deep Learning for Multi-Class Nuclei Segmentation

A deep learning project for multi-class nuclei segmentation on the PanNuke dataset using U-Net with a ResNet encoder. Conducted systematic evaluation using metrics such as Dice and IoU, and explored model improvements through architectural design and post-processing techniques.

PyTorch U-Net ResNet Hover-Net

FishLEN

Fish Length Estimation Network

A deep learning framework for estimating fish length from images, developed for research in the Dormant Biology Lab at Stony Brook University.

Python PyTorch Computer Vision Deep Learning

Education

A brief summary of my academic background.

M.S. in Biomedical Informatics
Aug 2024 – May 2026 (Expected)
  • Focus on machine learning, computer vision, and medical image analysis
  • Experience with PyTorch-based deep learning model development and evaluation
  • Developed multiple projects including FishLEN and nuclei segmentation systems
B.S. in Applied Mathematics & Software Engineering (Double Major)
Sep 2019 - May 2024
  • Strong foundation in mathematics, algorithms, and software development
  • Two thesis projects awarded as Outstanding Graduation Thesis
  • Authored 70+ technical blog posts with 36,000+ total views, demonstrating strong technical communication skills

Experience

A brief summary of my research-related experience.

Research Internship
Prof Chen's Lab, Department of Biomedical Informatics, Stony Brook University
Jun 2025 - Present
  • Annotated large-scale pathology image datasets to support training of cell segmentation models
  • Developed algorithms to convert point annotations into region masks for segmentation training
  • Trained and evaluated CellViT, Cellpose-SAM models and analyzed performance across multiple metrics
Research Internship
Dormant Biology Lab, Department of Biochemistry & Cell Biology, Stony Brook University
Jan - Jun 2025
  • Developed FishLEN, a deep learning model for estimating fish length from images, designed to support biological research applications
  • Built an end-to-end pipeline including data preprocessing, model training, and evaluation using PyTorch
  • Improved model performance through iterative experimentation, including data augmentation, model tuning, and validation strategies
Research Internship
Prof Chen's Lab, Department of Biomedical Informatics, Stony Brook University
Nov - Dec 2024
  • Reviewed and analyzed state-of-the-art cell segmentation and classification models
  • Reproduced experiments from published work by running Hover-Net GitHub implementations
  • Visualized extracted features and converted results into QuPath-compatible datasets
Research Internship
Prof Chang's Lab, Center for Innovation in Brain Science, University of Arizona
Oct - Dec 2023
  • Migrated TensorFlow v1 codebase to TensorFlow v2, improving maintainability and stability
  • Refactored training pipelines and removed ~20% redundant operations
  • Reduced runtime and memory consumption by ~10%

Contact

I’m happy to connect about research, internships, full-time opportunities, and collaborative projects.

Location
Stony Brook, New York, USA