Research experience

研究经历

Presidential Fellow in Data Science 校长奖学金研究员
Investigate the Dynamic of 4D bacterial biofilms

In this project, I collaborated with Dr. Zhang from the Department of Chemistry to analyze bio-informatics of bacterial biofilms, such as the biofilm density, cell size, and orientation. I developed graph-based toolkit for bacterial cell segmentation and extended to incorporating with deep neural networks to boost the performance of single-cell identification.

Research Assistant 研究助理

Under the supervision of Prof. Scott T. Acton, I developed algorithms to solve real-world problems for collaborators in medical, biological, and chemical departments.

Select Projects:

Segmentation and Machine Learning for the Analysis of Bacterial Biofilm Images

As my dissertation topic, my work assisted in promoting the single-cell and population-level studies by combining super-resolution imaging with computational image advances. This research proposed automated analysis toolkit to perform graph-based 3D single-cell segmentation, GAN-based biofilm image synthesis and evaluation, and shape-based biofilm reconstruction and analysis. The developed algorithms are Bact-3D, LCuts, refined LCuts, Shapefilter, m-LCuts, 3D Cyclic GAN with unbalanced loss, and SSQA.

Cell analysis: calcium imaging of neuron, FLIM imaging of cancer cells

To resolve the difficulties in extracting single cell bioinformatics of other types of cells, I mainly conducted statistical shape analysis, level set segmentation method, and morphological processing. A Shapefilter was presented to repair segmentation results obtained in calcium imaging of neurons in vivo. Level set segmentation and morphological processing techniques are investigated to monitor the metabolism of Prostate cancer cells imaged by FLIM. Besides, I also collborated with Dr. Tabbasum on image segmentation for lymphatic cells, and with Dr. Ly on 3D microglial cell analysis.

Select publication

代表性论文

J. Wang, M. Zhang, J. Zhang, Y. Wang, Andreas Gahlmann, and S. T. Acton, “Graph-theoretic Post-processing of Segmentation with Application to Dense Biofilms.” IEEE Transaction on Image Processing. (2021)


J. Wang, N. Tabassum, T. T. Toma, Y. Wang, A. Gahlmann, and S. T. Acton. “3D GAN Image Synthesis and Dataset Quality Assessment for Bacterial Biofilm”. In Submission. (2021)


M. Zhang†, J. Zhang†, Y. Wang†, J. Wang, A. Achimovich, S. T. Acton, and Andreas Gahlmann, “Non-Invasive Single-Cell Morphometry and Tracking in Living Bacterial Biofilms.” Nature Communications, 11(1), pp.1-13. (2020) †: Equal contribution. My major contribution: post-processing with refined LCuts.


J. Wang, T. Batabyal, M. Zhang, J. Zhang, A. Aziz, A. Gahlmann, and S.T. Acton. “LCuts: Linear Clustering of Bacteria Using Recursive Graph Cuts.” In 2019 IEEE International Conference on Image Processing (ICIP), pp. 1575-1579. (2019) Listed in the Top 10% of papers in ICIP 2019.


J. Wang, Z. Fu, N. Sadeghzadehyazdi, J. Kipnis, and S. T. Acton. “Nonlinear shape regression for filtering segmentation results from calcium imaging.” In 2018 25th IEEE International Conference on Image Processing (ICIP), pp. 738-742. (2018)


J. Wang, R. Sarkar, A. Aziz, A. Vaccari, A. Gahlmann, and S. T. Acton. “Bact-3D: A level set segmentation approach for dense multi-layered 3D bacterial biofilms.” In 2017 IEEE International Conference on Image Processing (ICIP), pp. 330-334. (2017)