Approaching the post nonlinearity of blind mixtures by hybrid neural network. - Hanchuan Peng; Zheru Chi (IJCNN, 1999)

A hierarchical distributed genetic algorithm for image segmentation. - Hanchuan Peng; Fuhui Long; Zheru Chi; Wanchi Su (CEC, 2000)

Document Image Matching Based on Component Blocks. - Hanchuan Peng; Fuhui Long; Wan-Chi Siu; Zheru Chi; David Dagan Feng (ICIP, 2000)

A Semi-Parametric Hybrid Neural Model for Nonlinear Blind Signal Separation. - Hanchuan Peng; Zheru Chi; Wan-Chi Siu (Int. J. Neural Syst., 2000)

A Bayesian Learning Algorithm of Discrete Variables for Automatically Mining Irregular Features of Pattern Images. - Hanchuan Peng; Fuhui Long (MDM/KDD, 2001)

Extracting Semantic Video Objects. - Fuhui Long; David Dagan Feng; Hanchuan Peng; Wan-Chi Siu (IEEE Computer Graphics and Applications, 2001)

Document image template matching based on component block list. - Hanchuan Peng; Fuhui Long; Zheru Chi; Wan-Chi Siu (Pattern Recognit. Lett., 2001)

Bayesian clustering methods for morphological analysis of MR images. - Hanchuan Peng; Edward Herskovits; Christos Davatzikos (ISBI, 2002)

Structure Search and Stability Enhancement of Bayesian Networks. - Hanchuan Peng; Chris H. Q. Ding (ICDM, 2003)

Document Image Recognition Based on Template Matching of Component Block Projections. - Hanchuan Peng; Fuhui Long; Zheru Chi (IEEE Trans. Pattern Anal. Mach. Intell., 2003)

Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes. - Victor Olman; Hanchuan Peng; Zhengchang Su; Ying Xu 001 (CSB, 2004)

Automatic content extraction of filled-form images based on clustering component block projection vectors. - Hanchuan Peng; Xiaofeng He; Fuhui Long (DRR, 2004)

Comparing in situ mRNA expression patterns of drosophila embryos. - Hanchuan Peng; Eugene W. Myers (RECOMB, 2004)

Image categorization based on clustering spatial frequency maps. - Fuhui Long; Hanchuan Peng; David Dagan Feng (Storage and Retrieval Methods and Applications for Multimedia, 2004)

A Bayesian morphometry algorithm. - Edward Herskovits; Hanchuan Peng; Christos Davatzikos (IEEE Trans. Medical Imaging, 2004)

Acquiring and calibrating a high-dynamic-range natural image database. - Fuhui Long; Hanchuan Peng (Color Imaging: Processing, Hardcopy, and Applications, 2005)

Cell Phenotype Classification Based on 3D Cell Image Analysis. - Fuhui Long; Hanchuan Peng; Damir Sudar; David W. Knowles; Sophie Lelièvre (CSB Workshops, 2005)

Image Data Mining of Fruitfly Gene Expression Patterns. - Hanchuan Peng (CSB Workshops, 2005)

Toward Automatic Annotation of in situ mRNA Expression Patterns of Drosophila Embryos. - Jie Zhou 023; Hanchuan Peng (CSB Workshops, 2005)

Finding cliques in protein interaction networks via transitive closure of a weighted graph. - Chris H. Q. Ding; Xiaofeng He; Hanchuan Peng (BIOKDD, 2005)

Evolving Feature Selection. - Huan Liu 001; Edward R. Dougherty; Jennifer G. Dy; Kari Torkkola; Eugene Tuv; Hanchuan Peng; Chris H. Q. Ding; Fuhui Long; Michael E. Berens; Lance Parsons; Zheng Zhao 002; Lei Yu 001; et al. (IEEE Intell. Syst., 2005)

Minimum Redundancy Feature Selection from Microarray Gene Expression Data. - Chris H. Q. Ding; Hanchuan Peng (J. Bioinform. Comput. Biol., 2005)

Feature Selection Based on Mutual Information: Criteria of Max-Dependency, Max-Relevance, and Min-Redundancy. - Hanchuan Peng; Fuhui Long; Chris H. Q. Ding (IEEE Trans. Pattern Anal. Mach. Intell., 2005)

Clustering gene expression patterns of fly embryos. - Hanchuan Peng; Fuhui Long; Michael B. Eisen; Eugene W. Myers (ISBI, 2006)

Transitive closure and metric inequality of weighted graphs: detecting protein interaction modules using cliques. - Chris H. Q. Ding; Xiaofeng He; Hui Xiong 001; Hanchuan Peng; Stephen R. Holbrook (Int. J. Data Min. Bioinform., 2006)

Automatic Segmentation of Nuclei in 3d Microscopy Images of C.Elegans. - Fuhui Long; Hanchuan Peng; Eugene W. Myers (ISBI, 2007)

Straightening Worm Images. - Hanchuan Peng; Fuhui Long; Eugene W. Myers (ISBI, 2007)

Automatic recognition and annotation of gene expression patterns of fly embryos. - Jie Zhou 023; Hanchuan Peng (Bioinform., 2007)

Automatic Recognition of Cells (ARC) for 3D Images of C. elegans. - Fuhui Long; Hanchuan Peng; Xiao Liu; Stuart K. Kim; Gene Myers (RECOMB, 2008)

Bioimage informatics: a new area of engineering biology. - Hanchuan Peng (Bioinform., 2008)

Straightening Caenorhabditis elegans images. - Hanchuan Peng; Fuhui Long; Xiao Liu; Stuart K. Kim; Eugene W. Myers (Bioinform., 2008)

Data-driven decomposition for multi-class classification. - Jie Zhou 023; Hanchuan Peng; Ching Y. Suen (Pattern Recognit., 2008)

VANO: a volume-object image annotation system. - Hanchuan Peng; Fuhui Long; Eugene W. Myers (Bioinform., 2009)

Imaging informatics for personalised medicine: applications and challenges. - Tianming Liu 001; Hanchuan Peng; Xiaobo Zhou 001 (Int. J. Funct. Informatics Pers. Medicine, 2009)

Automatic Neuron Tracing in Volumetric Microscopy Images with Anisotropic Path Searching. - Jun Xie; Ting Zhao; Tzumin Lee; Eugene W. Myers; Hanchuan Peng (MICCAI (2), 2010)

Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model. - Hanchuan Peng; Zongcai Ruan; Deniz Atasoy; Scott Sternson (Bioinform., 2010)

A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems. - Lei Qu; Hanchuan Peng (Bioinform., 2010)

Counting cells in 3D confocal images based on discriminative models. - Jie Zhou 023; Hanchuan Peng (BCB, 2011)

3D Neuron Tip Detection in Volumetric Microscopy Images. - Min Liu 008; Hanchuan Peng; Amit K. Roy-Chowdhury; Eugene W. Myers (BIBM, 2011)

Automated high speed stitching of large 3D microscopic images. - Yang Yu; Hanchuan Peng (ISBI, 2011)

Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets. - Hanchuan Peng; Fuhui Long (RECOMB, 2011)

Automatic 3D neuron tracing using all-path pruning. - Hanchuan Peng; Fuhui Long; Gene Myers (Bioinform., 2011)

Simultaneous recognition and segmentation of cells: application in C.elegans. - Lei Qu; Fuhui Long; Xiao Liu; Stuart K. Kim; Eugene W. Myers; Hanchuan Peng (Bioinform., 2011)

Anisotropic path searching for automatic neuron reconstruction. - Jun Xie; Ting Zhao; Tzumin Lee; Eugene W. Myers; Hanchuan Peng (Medical Image Anal., 2011)

Proof-editing is the Bottleneck Of 3D Neuron Reconstruction: The Problem and Solutions. - Hanchuan Peng; Fuhui Long; Ting Zhao; Eugene W. Myers (Neuroinformatics, 2011)

Automated Reconstruction of Neuronal Morphology Based on Local Geometrical and Global Structural Models. - Ting Zhao; Jun Xie; Fernando Amat; Nathan G. Clack; Parvez Ahammad; Hanchuan Peng; Fuhui Long; Eugene W. Myers (Neuroinformatics, 2011)

Bioimage informatics: a new category in Bioinformatics. - Hanchuan Peng; Alex Bateman; Alfonso Valencia; Jonathan D. Wren (Bioinform., 2012)

Visualization and Analysis of 3D Microscopic Images. - Fuhui Long; Jianlong Zhou; Hanchuan Peng (PLoS Comput. Biol., 2012)

Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans. - Sarah J. Aerni; Xiao Liu; Chuong B. Do; Samuel S. Gross; Andy Nguyen; Stephen D. Guo; Fuhui Long; Hanchuan Peng; Stuart S. Kim; Serafim Batzoglou (Bioinform., 2013)

APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree. - Hang Xiao; Hanchuan Peng (Bioinform., 2013)

Automated image computing reshapes computational neuroscience. - Hanchuan Peng; Badrinath Roysam; Giorgio A. Ascoli (BMC Bioinform., 2013)

A distance-field based automatic neuron tracing method. - Jinzhu Yang; Paloma T. Gonzalez-Bellido; Hanchuan Peng (BMC Bioinform., 2013)

BIOCAT: a pattern recognition platform for customizable biological image classification and annotation. - Jie Zhou 023; Santosh Lamichhane; Gabriella Sterne; Bing Ye; Hanchuan Peng (BMC Bioinform., 2013)

A HPC infrastructure for processing and visualizing neuro-anatomical images obtained by Confocal Light Sheet Microscopy. - Alessandro Bria; Giulio Iannello; Paolo Soda; Hanchuan Peng; Giovanni Erbacci; Giuseppe Fiameni; Giacomo Mariani; Roberto Mucci; Marco Rorro; Francesco Pavone; Ludovico Silvestri; Paolo Frasconi; et al. (HPCS, 2014)

An open-source VAA3D plugin for real-time 3D visualization of terabyte-sized volumetric images. - Alessandro Bria; Giulio Iannello; Hanchuan Peng (ISBI, 2015)

Interactive exemplar-based segmentation toolkit for biomedical image analysis. - Xiang Li 001; Zhi Zhou; Philipp Keller; Hongkui Zeng; Tianming Liu 001; Hanchuan Peng (ISBI, 2015)

Neuron crawler: An automatic tracing algorithm for very large neuron images. - Zhi Zhou; Staci A. Sorensen; Hanchuan Peng (ISBI, 2015)

SmartTracing: self-learning-based Neuron reconstruction. - Hanbo Chen; Hang Xiao; Tianming Liu 001; Hanchuan Peng (Brain Informatics, 2015)

Global analysis of gene expression and projection target correlations in the mouse brain. - Ahmed Fakhry; Tao Zeng; Hanchuan Peng; Shuiwang Ji (Brain Informatics, 2015)

From DIADEM to BigNeuron. - Hanchuan Peng; Erik Meijering; Giorgio A. Ascoli (Neuroinformatics, 2015)

BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies. - Yinan Wan; Fuhui Long; Lei Qu; Hang Xiao; Michael Hawrylycz; Eugene W. Myers; Hanchuan Peng (Neuroinformatics, 2015)

Adaptive Image Enhancement for Tracing 3D Morphologies of Neurons and Brain Vasculatures. - Zhi Zhou 006; Staci A. Sorensen; Hongkui Zeng; Michael Hawrylycz; Hanchuan Peng (Neuroinformatics, 2015)

3-D Registration of Biological Images and Models: Registration of microscopic images and its uses in segmentation and annotation. - Lei Qu; Fuhui Long; Hanchuan Peng (IEEE Signal Process. Mag., 2015)

Reconstruction of 3D neuron morphology using Rivulet back-tracking. - Donghao Zhang; Siqi Liu 001; Sidong Liu; Dagan Feng 001; Hanchuan Peng; Weidong Cai 001 (ISBI, 2016)

Discover Mouse Gene Coexpression Landscape Using Dictionary Learning and Sparse Coding. - Yujie Li 004; Hanbo Chen; Xi Jiang 001; Xiang Li 001; Jinglei Lv; Hanchuan Peng; Joe Z. Tsien; Tianming Liu 001 (MICCAI (1), 2016)

Deep models for brain EM image segmentation: novel insights and improved performance. - Ahmed Fakhry; Hanchuan Peng; Shuiwang Ji (Bioinform., 2016)

Reconstructing the brain: from image stacks to neuron synthesis. - Julian C. Shillcock; Michael Hawrylycz; Sean L. Hill; Hanchuan Peng (Brain Informatics, 2016)

Rivulet: 3D Neuron Morphology Tracing with Iterative Back-Tracking. - Siqi Liu 001; Donghao Zhang; Sidong Liu; Dagan Feng 001; Hanchuan Peng; Weidong Cai 001 (Neuroinformatics, 2016)

TReMAP: Automatic 3D Neuron Reconstruction Based on Tracing, Reverse Mapping and Assembling of 2D Projections. - Zhi Zhou 006; Xiaoxiao Liu; Brian Long; Hanchuan Peng (Neuroinformatics, 2016)

Automatic 3D Single Neuron Reconstruction with Exhaustive Tracing. - Zihao Tang; Donghao Zhang; Siqi Liu 001; Yang Song 001; Hanchuan Peng; Weidong Cai 001 (ICCV Workshops, 2017)

Triple-Crossing 2.5D Convolutional Neural Network for Detecting Neuronal Arbours in 3D Microscopic Images. - Siqi Liu 001; Donghao Zhang; Yang Song 001; Hanchuan Peng; Weidong Cai 001 (MLMI@MICCAI, 2017)

Fast assembling of neuron fragments in serial 3D sections. - Hanbo Chen; Daniel Maxim Iascone; Nuno Maçarico da Costa; Ed S. Lein; Tianming Liu 001; Hanchuan Peng (Brain Informatics, 2017)

N3DFix: an Algorithm for Automatic Removal of Swelling Artifacts in Neuronal Reconstructions. - Eduardo Conde-Sousa; Peter Szücs; Hanchuan Peng; Paulo Aguiar (Neuroinformatics, 2017)

Transcriptome Architecture of Adult Mouse Brain Revealed by Sparse Coding of Genome-Wide In Situ Hybridization Images. - Yujie Li 004; Hanbo Chen; Xi Jiang 001; Xiang Li 001; Jinglei Lv; Meng Li; Hanchuan Peng; Joe Z. Tsien; Tianming Liu 001 (Neuroinformatics, 2017)

Ensemble Neuron Tracer for 3D Neuron Reconstruction. - Ching-Wei Wang; Yu-Ching Lee; Hilmil Pradana; Zhi Zhou 006; Hanchuan Peng (Neuroinformatics, 2017)

Deep Learning Segmentation of Optical Microscopy Images Improves 3-D Neuron Reconstruction. - Rongjian Li; Tao Zeng; Hanchuan Peng; Shuiwang Ji (IEEE Trans. Medical Imaging, 2017)

Memory and Time Efficient 3D Neuron Morphology Tracing in Large-Scale Images. - Heng Wang 007; Donghao Zhang; Yang Song 001; Siqi Liu 001; Rong Gao; Hanchuan Peng; Weidong Cai 001 (DICTA, 2018)

DeepNeuron: an open deep learning toolbox for neuron tracing. - Zhi Zhou 006; Hsien-Chi Kuo; Hanchuan Peng; Fuhui Long (Brain Informatics, 2018)

Automated 3D Soma Segmentation with Morphological Surface Evolution for Neuron Reconstruction. - Donghao Zhang; Siqi Liu 001; Yang Song 001; Dagan Feng 001; Hanchuan Peng; Weidong Cai 001 (Neuroinformatics, 2018)

3D neuron tip detection in volumetric microscopy images using an adaptive ray-shooting model. - Min Liu 008; Rong Gong; Weixun Chen; Hanchuan Peng (Pattern Recognit., 2018)

Automated 3-D Neuron Tracing With Precise Branch Erasing and Confidence Controlled Back Tracking. - Siqi Liu 001; Donghao Zhang; Yang Song 001; Hanchuan Peng; Weidong Cai 001 (IEEE Trans. Medical Imaging, 2018)

Multiscale Kernels for Enhanced U-Shaped Network to Improve 3D Neuron Tracing. - Heng Wang 007; Donghao Zhang; Yang Song 001; Siqi Liu 001; Heng Huang; Mei Chen; Hanchuan Peng; Weidong Cai 001 (CVPR Workshops, 2019)

Learning Hierarchical and Shared Features for Improving 3D Neuron Reconstruction. - Hao Yuan 001; Na Zou 001; Shaoting Zhang 001; Hanchuan Peng; Shuiwang Ji (ICDM, 2019)

Segmenting Neuronal Structure in 3D Optical Microscope Images via Knowledge Distillation with Teacher-Student Network. - Heng Wang 007; Donghao Zhang; Yang Song 001; Siqi Liu 001; Yue Wang 021; Dagan Feng 001; Hanchuan Peng; Weidong Cai 001 (ISBI, 2019)

FMST: an Automatic Neuron Tracing Method Based on Fast Marching and Minimum Spanning Tree. - Jian Yang 016; Ming Hao; Xiaoyang Liu; Zhijiang Wan; Ning Zhong 001; Hanchuan Peng (Neuroinformatics, 2019)

A Multiscale Ray-Shooting Model for Termination Detection of Tree-Like Structures in Biomedical Images. - Min Liu 008; Weixun Chen; Chao Wang 072; Hanchuan Peng (IEEE Trans. Medical Imaging, 2019)

3D Conditional Adversarial Learning for Synthesizing Microscopic Neuron Image Using Skeleton-to-Neuron Translation. - Zihao Tang; Donghao Zhang; Yang Song 001; Heng Wang 007; Dongnan Liu; Chaoyi Zhang; Siqi Liu 001; Hanchuan Peng; Weidong Cai 001 (ISBI, 2020)

AIDE: Annotation-efficient deep learning for automatic medical image segmentation. - Cheng Li 008; Rongpin Wang; Zaiyi Liu; Meiyun Wang; Hongna Tan; Yaping Wu; Xinfeng Liu; Hui Sun; Rui Yang; Xin Liu 053; Ismail Ben Ayed; Hairong Zheng; et al. (CoRR, 2020)

DeepBranch: Deep Neural Networks for Branch Point Detection in Biomedical Images. - Yinghui Tan; Min Liu 008; Weixun Chen; Xueping Wang; Hanchuan Peng; Yaonan Wang 001 (IEEE Trans. Medical Imaging, 2020)

Single Neuron Segmentation Using Graph-Based Global Reasoning with Auxiliary Skeleton Loss from 3D Optical Microscope Images. - Heng Wang 007; Yang Song 001; Chaoyi Zhang; Jianhui Yu; Siqi Liu 001; Hanchuan Peng; Tom Weidong Cai (ISBI, 2021)

TreeMoCo: Contrastive Neuron Morphology Representation Learning. - Hanbo Chen; Jiawei Yang 002; Daniel Maxim Iascone; Lijuan Liu; Lei He 001; Hanchuan Peng; Jianhua Yao 001 (NeurIPS, 2022)

Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons. - Shuxia Guo; Xuan Zhao 004; Shengdian Jiang; Liya Ding 001; Hanchuan Peng (Bioinform., 2022)

mBrainAligner-Web: a web server for cross-modal coherent registration of whole mouse brains. - Yuanyuan Li; Jun Wu; Donghuan Lu; Chao Xu; Yefeng Zheng 001; Hanchuan Peng; Lei Qu (Bioinform., 2022)

Smart imaging to empower brain-wide neuroscience at single-cell levels. - Shuxia Guo; Jie Xue; Jian Liu; Xiangqiao Ye; Yichen Guo; Di Liu; Xuan Zhao 004; Feng Xiong; Xiaofeng Han; Hanchuan Peng (Brain Informatics, 2022)

Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains. - Shengdian Jiang; Yimin Wang; Lijuan Liu; Liya Ding 001; Zongcai Ruan; Hong-Wei Dong; Giorgio A. Ascoli; Michael Hawrylycz; Hongkui Zeng; Hanchuan Peng (Neuroinformatics, 2022)

Towards NeuroAI: Introducing Neuronal Diversity into Artificial Neural Networks. - Feng-Lei Fan; Yingxin Li; Hanchuan Peng; Tieyong Zeng; Fei Wang 001 (CoRR, 2023)

Tracing weak neuron fibers. - Yufeng Liu; Ye Zhong; Xuan Zhao 004; Lijuan Liu; Liya Ding 001; Hanchuan Peng (Bioinform., 2023)

SNAP: a structure-based neuron morphology reconstruction automatic pruning pipeline. - Liya Ding 001; Xuan Zhao 004; Shuxia Guo; Yufeng Liu; Lijuan Liu; Yimin Wang; Hanchuan Peng (Frontiers Neuroinformatics, 2023)

Boosting 3D Neuron Segmentation with 2D Vision Transformer Pre-trained on Natural Images. - Yik San Cheng; Runkai Zhao; Heng Wang 007; Hanchuan Peng; Weidong Cai 001 (CoRR, 2024)

Meet the authors: Hanchuan Peng, Peng Xie, and Feng Xiong. - Hanchuan Peng; Peng Xie; Feng Xiong (Patterns, 2024)

DSM: Deep sequential model for complete neuronal morphology representation and feature extraction. - Feng Xiong; Peng Xie; Zuohan Zhao; Yiwei Li; Sujun Zhao; Linus Manubens-Gil; Lijuan Liu; Hanchuan Peng (Patterns, 2024)

Dineuro: Distilling Knowledge from 2D Natural Images via Deformable Tubular Transferring Strategy for 3D Neuron Reconstruction. - Yik San Cheng; Runkai Zhao; Heng Wang 007; Hanchuan Peng; Yui Lo; Yuqian Chen; Lauren J. O'Donnell; Weidong Cai 001 (ISBI, 2025)