What I Do: Brain Big Data and more
Inventor: Vaa3D, BrainAligner, NeuronTracers, SmartScope, mRMR, 3D Virtual Finger, and more. Builder: cell and brain maps. Proponent: BioImage Informatics meetings, Brain Informatics conferences, journals (Bioinformatics, BMC Bioinformatics, and Brain Informatics), and BigNeuron and Open Interface of Bioimaging Software. Location: allen institute @ Seattle and http://penglab.com
I am currently leading a Brain Big Data research group at the Allen Institute for Brain Science, Seattle, with the goal to develop revolutionary technologies to generate, manage, visualize, analyze, and understand massive-scale structure and function data related to brains, especially human brains. I am also an affiliate/adjunct faculty member (professor) with the University of Washington (USA) and the University of Georgia (USA), etc. Prior to my arrival at Seattle in the fall of 2012, I led a Big Image Mining research group at Janelia 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.
We develop and use many cutting-edge machine learning, artificial intelligence, data mining, and imaging methods to handle the very complex and very large scale brain data, gene expression data, and many other types of data. We welcome collaborations especially the large scale data challenges. Our group has been a world-leader in massive scale multi-dimensional imaging and visualization, very large scale brain mapping, neuron- and cell-phenotyping, feature extraction and Bayesian inferencing for general applications, as demonstrated in a number of high-profile, well-recognized publications and widely-used open-source software packages.
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.
- March, 2017: The Our UltraTracer software was published in Nature Methods. Read here.
- Dec, 2016: The Our new Perspective on bioimage analysis and beyond was published in Nature Biotechnology. Read here.
- March, 2016: The Vaa3D-TeraFly was published in Nature Methods. Read here.
- Dec, 2015: The SmartACT The automated 3D single cell targeting system was published. Read this Allen Institute News piece.
- March, 2015: The BigNeuron project is formally announced. This major international collaborative project is sponsored by more than 10 organizations and featured in Nature, Science, NPR, NBC, GeekWire, etc.
- July, 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, 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, 2013: My dragonfly-paper co-authored with Paloma T. Gonzalez-Bellido et al won the 2012 Cozzarelli Prize (USA).