Hanchuan Peng

Summary

Affiliation: Howard Hughes Medical Institute
Country: USA

Publications

  1. pmc Visualization and analysis of 3D microscopic images
    Fuhui Long
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
    PLoS Comput Biol 8:e1002519. 2012
  2. pmc A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems
    Lei Qu
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 26:1091-7. 2010
  3. pmc Simultaneous recognition and segmentation of cells: application in C.elegans
    Lei Qu
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
    Bioinformatics 27:2895-902. 2011
  4. pmc Phenotype clustering of breast epithelial cells in confocal images based on nuclear protein distribution analysis
    Fuhui Long
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    BMC Cell Biol 8:S3. 2007
  5. pmc BrainAligner: 3D registration atlases of Drosophila brains
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Nat Methods 8:493-500. 2011
  6. pmc Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 26:i38-46. 2010
  7. pmc V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Nat Biotechnol 28:348-53. 2010
  8. pmc VANO: a volume-object image annotation system
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, VA, USA
    Bioinformatics 25:695-7. 2009
  9. pmc Bioimage informatics: a new area of engineering biology
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Bioinformatics 24:1827-36. 2008
  10. pmc Straightening Caenorhabditis elegans images
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 24:234-42. 2008

Collaborators

Detail Information

Publications30

  1. pmc Visualization and analysis of 3D microscopic images
    Fuhui Long
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
    PLoS Comput Biol 8:e1002519. 2012
    ..We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain...
  2. pmc A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems
    Lei Qu
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 26:1091-7. 2010
    ..In a parallel project to build a 3D digital map of the adult fly ventral nerve cord (VNC), we are confronted with a similar problem...
  3. pmc Simultaneous recognition and segmentation of cells: application in C.elegans
    Lei Qu
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
    Bioinformatics 27:2895-902. 2011
    ..An approach that is more accurate and relies on only a single signal channel is clearly desirable...
  4. pmc Phenotype clustering of breast epithelial cells in confocal images based on nuclear protein distribution analysis
    Fuhui Long
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    BMC Cell Biol 8:S3. 2007
    ..Here we describe a method that creates a hierarchical tree of the given cell phenotypes and calculates the statistical significance between them, based on the clustering analysis of nuclear protein distributions...
  5. pmc BrainAligner: 3D registration atlases of Drosophila brains
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Nat Methods 8:493-500. 2011
    ..We used BrainAligner to generate an image pattern atlas of 2954 registered brains containing 470 different expression patterns that cover all the major compartments of the fly brain...
  6. pmc Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 26:i38-46. 2010
    ..However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low single-to-noise ratio and discontinued segments of neurite patterns...
  7. pmc V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Nat Biotechnol 28:348-53. 2010
    ..Using V3D-Neuron, we demonstrate the feasibility of building a 3D digital atlas of neurite tracts in the fruitfly brain...
  8. pmc VANO: a volume-object image annotation system
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, VA, USA
    Bioinformatics 25:695-7. 2009
    ..VANO has been used to build high-resolution digital atlases of the nuclei of Caenorhabditis elegans at the L1 stage and the nuclei of Drosophila melanogaster's ventral nerve cord at the late embryonic stage...
  9. pmc Bioimage informatics: a new area of engineering biology
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Bioinformatics 24:1827-36. 2008
    ....
  10. pmc Straightening Caenorhabditis elegans images
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 24:234-42. 2008
    ..For example, worm bodies usually curve significantly in images. Thus one must 'straighten' the worms if they are to be compared under a canonical coordinate system...
  11. pmc Automatic image analysis for gene expression patterns of fly embryos
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    BMC Cell Biol 8:S7. 2007
    ..The increasing availability of ISH image data motivates the development of automated computational approaches to the analysis of gene expression patterns...
  12. pmc Segmentation of center brains and optic lobes in 3D confocal images of adult fruit fly brains
    Shing Chun Benny Lam
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
    Methods 50:63-9. 2010
    ..We have tested this approach on simulated and real 3D fly brain image stacks and demonstrated that this method can reasonably segregate OLs from CBs despite the aforementioned difficulties...
  13. pmc Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience
    Ellie S Heckscher
    Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, OR 97403, USA
    Development 141:2524-32. 2014
    ....
  14. doi request reprint Anisotropic path searching for automatic neuron reconstruction
    Jun Xie
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
    Med Image Anal 15:680-9. 2011
    ..In all cases, the approach yielded promising results...
  15. ncbi request reprint Automatic neuron tracing in volumetric microscopy images with anisotropic path searching
    Jun Xie
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Med Image Comput Comput Assist Interv 13:472-9. 2010
    ..In addition, an automated neuron comparison method is introduced for performance evaluation and structure analysis. The proposed algorithm is computationally efficient. Experiments on different types of data show promising results...
  16. pmc Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis
    Hanchuan Peng
    1 Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA 2 Allen Institute for Brain Science, 551 North 34th Street, Suite 200, Seattle, Washington 98103, USA
    Nat Commun 5:4342. 2014
    ..We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain. ..
  17. pmc APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree
    Hang Xiao
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 29:1448-54. 2013
    ..However, despite a number of existing methods, few open-source techniques are completely or sufficiently automated and at the same time are able to generate robust results for real 3D microscopy images...
  18. pmc A 3D digital atlas of C. elegans and its application to single-cell analyses
    Fuhui Long
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Nat Methods 6:667-72. 2009
    ..This computational method will allow high-throughput single-cell analyses of the post-embryonic worm, such as gene expression analysis, or ablation or stimulation of cells under computer control in a high-throughput functional screen...
  19. pmc Clonal development and organization of the adult Drosophila central brain
    Hung Hsiang Yu
    Howard Hughes Medical Institute, Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
    Curr Biol 23:633-43. 2013
    ..The Drosophila central brain develops from a fixed number of neuroblasts (NBs) that deposit neurons in regional clusters...
  20. pmc A GAL4-driver line resource for Drosophila neurobiology
    Arnim Jenett
    Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
    Cell Rep 2:991-1001. 2012
    ..The set of DNA fragments, each driving a documented expression pattern, will facilitate the generation of additional constructs for manipulating neuronal function...
  21. pmc mGRASP enables mapping mammalian synaptic connectivity with light microscopy
    Jinhyun Kim
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Nat Methods 9:96-102. 2012
    ....
  22. pmc Automatic 3D neuron tracing using all-path pruning
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    Bioinformatics 27:i239-47. 2011
    ..However, manual incorporation of such global information can be very time consuming. Thus, a completely automatic approach for these hard situations is highly desirable...
  23. pmc A distance-field based automatic neuron tracing method
    Jinzhu Yang
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
    BMC Bioinformatics 14:93. 2013
    ..Automatic 3D digital reconstruction (tracing) of neurons embedded in noisy microscopic images is challenging, especially when the cell morphology is complex...
  24. doi request reprint Extensible visualization and analysis for multidimensional images using Vaa3D
    Hanchuan Peng
    1 Allen Institute for Brain Sciences, Seattle, Washington, USA 2 Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
    Nat Protoc 9:193-208. 2014
    ..Once a user is familiar with Vaa3D, visualization usually runs in real time and analysis takes less than a few minutes for a simple data set. ..
  25. ncbi request reprint Automatic recognition and annotation of gene expression patterns of fly embryos
    Jie Zhou
    Department of Computer Science, Northern Illinois University, DeKalb, IL 60115, USA
    Bioinformatics 23:589-96. 2007
    ..So far, annotations of these images are done by manually assigning a subset of anatomy ontology terms to an image. This time-consuming process depends heavily on the consistency of experts...
  26. ncbi request reprint Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy
    Hanchuan Peng
    Lawrence Berkeley National Laboratory, University of California at Berkeley, 1 Cyclotron Road, MS 84 171, Berkeley, CA 94720, USA
    IEEE Trans Pattern Anal Mach Intell 27:1226-38. 2005
    ..The results confirm that mRMR leads to promising improvement on feature selection and classification accuracy...
  27. ncbi request reprint A Bayesian morphometry algorithm
    Edward H Herskovits
    Department of Radiology, University of Pennsylvania, 3600 Market Street, Suite 370, Room 117, Philadelphia, PA 19104, USA
    IEEE Trans Med Imaging 23:723-37. 2004
    ..e., t-test and paired t-test) fails in the nonlinear-association case...
  28. ncbi request reprint Transitive closure and metric inequality of weighted graphs: detecting protein interaction modules using cliques
    Chris Ding
    Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
    Int J Data Min Bioinform 1:162-77. 2006
    ..From this, we extend the clique concept from unweighted graph to weighted graph. We outline several applications and present results of detecting protein functional modules in a protein interaction network...
  29. ncbi request reprint Minimum redundancy feature selection from microarray gene expression data
    Chris Ding
    Computational Research Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
    J Bioinform Comput Biol 3:185-205. 2005
    ..SUPPLIMENTARY: The top 60 MRMR genes for each of the datasets are listed in http://crd.lbl.gov/~cding/MRMR/. More information related to MRMR methods can be found at http://www.hpeng.net/...