What I Do

Short Version

Inventor: Vaa3D, BrainAligner, NeuronTracers, SmartScope, mRMR, 3D Virtual Finger, and more. Builder: cell and brain maps. Proponent: BioImage Informatics meetings, journal sections, and Open Interface of Bioimaging Software. Location: allen institute @ Seattle and http://penglab.com

Long Version

I am currently running a research group "computational neuroanatomy and smart imaging" at the Allen Institute for Brain Science, Seattle, with the goal to better understand the structures and potentially also some functions of brains, especially mammalian brains. Prior to my arrival at Seattle in the fall of 2012, I led a microscopic image data analysis and neuroanatomy group at Janelia Farm Research Campus, Howard Hughes Medical Institute, where I stayed for almost 7 years. Before then, I did research at a series of other interesting places, including for instance the Lawrence Berkeley National Laboratory, Johns Hopkins University Medical School, etc.

Some of my recent activities can be seen in the News and Media Reports, the Publications, or the Activities. A short BIO can be found here.

  • July 11, 2014: The Virtual Finger paper is published in Nature Communications. Virtual Finger lets you instantly get the 3D location of image objects as long as you can see [part] of it!
  • Jan 1, 2014: The Vaa3D system was featured in Nature Protocols. This long protocol paper explains 10 often used pipelines/procedures for visualizing and analyzing 3D+ biological images of a number of model systems.
  • March 12, 2013: My dragonfly-paper co-authored with Paloma T. Gonzalez-Bellido et al won the 2012 PNAS Cozzarelli Prize, which "recognizes outstanding contributions to the scientific disciplines represented by the National Academy of Sciences" (USA).

In recent years, my group focuses on understanding the structures and functioning mechanisms of biosystems using data mining techniques for bioinformatics and computational molecular biology, particularly, bioimage data mining and informatics. These bioimages include cellular and molecular images and related medical images. Several recent projects are listed below. You can check some further description of my ongoing research page at Allen Institute and my research page at HHMI's Janelia Farm.

  • Novel Algorithms for 3D/4D/5D image/video computing, including image registration, neuron/fibrous-structure tracing, cell recognition and targeting, comparison and mining of complex patterns (e.g. neuron morphology), etc. We have developed a series of methods such as Reliable Landmark Matching (RLM) and Principal Skeleton (PS) for automated image alignment, Graph-augmented Deformable model (GD) and All-Path Pruning (APP) for neuron reconstruction, Simultaneous Recognition and Segmentation (SRS) of cells for image segmentation and recognition, etc.
  • 3D Digital Atlas Modeling of Animals at the Single Cell/Neuron Level: building a 3D digital Worm Atlas for single cells in C. elegans and a 3D digital Fly Brain Atlas for fruitfly. Particularly, for the first time we have quantitatively assessed the spatial invariability of patterns in these systems, which are critical for using these atlases for new biological experiments.
  • Analysis of Gene Expression Pattern Images: high-performance image analysis and mining for different model organisms, such as fruitfly, C. elegans, and mouse;
  • Feature/Model Learning: developing algorithms and software to extract/select features and learn models from biological data (e.g. microarray data, neuronal gene expression patterns in microscopical images, etc.), such as the mRMR algorithm (minimum Redundancy Maximum Relavance) for feature selection.
  • Brain Morphometry and Neuronal Structure Analysis: developing computational tools to measure and analyze quantities of brain tissues and neurons.
  • High Performance Visualization and Analysis Tools for Large-Scale Bioimages and Their Databases: developing many tools that make it much easier to explore large scale data; particularly, we developed the Vaa3D platform, which we call a Swiss Army Knife for 3D/4D/5D image visualization and analysis.

I have also worked in the more traditional pattern recognition and artificial intelligence field. I do have continuous interest in many theoretical problems there.

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