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Headshot of Hsienchi Kuo

Hsienchi Kuo, Ph.D.

Scientist II


Hsienchi Kuo joined the Allen Institute in 2016 as a scientist member of the computational neuroanatomy group. Kuo received his B.S. from National Taiwan University (NTU), and completed his Ph.D. research in The University of Chicago where he developed a 3D breast tumor segmentation algorithm and a novel breast parenchymal pattern descriptor for automated tumor classification. Kuo also possesses industrial experience as an algorithm engineer developing software for cellular microscopic image analysis. In addition to quantitative image science field, Kuo also worked in NTU center of Genomic Medicine where he constructed a website for online DNA methylation microarray data analysis.

Research Focus:

Research interests include 3D neuron image analysis and computerized neuron cell classification. In addition to algorithm and model design, Kuo is also involved in the development and maintenance of Vaa3D – an open-source software created by the group which is dedicated to large-scaled 3D bioimage analysis and visualization.


  • Partial differential equation based image segmentation

  • Level set method

  • Pattern recognition

  • Machine learning

  • Image analysis

Research Programs

  • MAT

Science Programs at Allen Institute