PhD Projects

4D (3D+T) Pavement Cell Analysis Jan.2018 - Dec 2021

  • Accurate segmentation of cells from 3D pavement cell image stack

  • Tracking segmented cells over time

  • Build the 3D model for individual cell and extract biological features

  • Analyze the growth of those cells based on biological features

  • Propose joint segmentation/tracking deep learning method


3D Neuron Morphology Analysis Jan 2020 - Nov 2022

  • 3D cellular structure shape modeling using skeleton mesh representation

  • 3D neuron classification based on the skeleton mesh representation

  • Sub-cellular features computation from the 3D shape model

  • Applied it specifically on Ciona neurons and find that Ciona neuron functions may be closely related to neuron shapes

BisQue: Open Source Web-based Image Analysis Platform Jan.2019 - Present

  • Integrate new image analysis methods as bisque modules to make them convenient to use

  • Build an interactive 3D segmentation mask visualization tool in BisQue

  • Help promote image-based inter-disciplinary research by utilizing BisQue

  • Help update BisQue backend to make it support the latest image analysis tools such as GPU-enabled methods