Staff Profiles

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 Interests

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

Selected Publications

A multimodal cell census and atlas of the mammalian primary motor cortex

October 6, 2021

BRAIN Initiative Cell Census Network (BICCN)

Morphological diversity of single neurons in molecularly defined cell types

October 6, 2021

Peng H, Xie P, Liu L, Kuang X, Wang Y, Qu L, Gong H, Jiang S, Li A, Ruan Z, Ding L, Yao Z, Chen C, Chen M, Daigle TL, Dalley R, Ding Z, Duan Y, Feiner A, He P, Hill C, Hirokawa KE, Hong G, Huang L, Kebede S, Kuo HC, Larsen R, Lesnar P, Li L, Li Q, Li X, Li Y, Li Y, Liu A, Lu D, Mok S, Ng L, Nguyen TN, Ouyang Q, Pan J, Shen E, Song Y, Sunkin SM, Tasic B, Veldman MB, Wakeman W, Wan W, Wang P, Wang Q, Wang T, Wang Y, Xiong F, Xiong W, Xu W, Ye M, Yin L, Yu Y, Yuan J, Yuan J, Yun Z, Zeng S, Zhang S, Zhao S, Zhao Z, Zhou Z, Huang ZJ, Esposito L, Hawrylycz MJ, Sorensen SA, Yang XW, Zheng Y, Gu Z, Xie W, Koch C, Luo Q, Harris JA, Wang Y, Zeng H

Segmentation of breast masses on dedicated breast computed tomography and three-dimensional breast ultrasound images

Journal of Medical Imaging
January 7, 2014

Kuo HC, Giger ML, Reiser I, Drukker K, Boone JM, Lindfors KK, Yang K, Edwards A, Sennett CA

Impact of lesion segmentation metrics on computer-aided diagnosis/detection in breast computed tomography

Journal of Medical Imaging
October 2014

Kuo HC, Giger ML, Reiser I, Drukker K, Boone JM, Lindfors KK, Yang K, Edwards A