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Labs:
Project Teams:
- Overview
- Anatomy and Histology
- Cryo-Electron Microscopy
- Electron Microscopy
- Flow Cytometry
- Fly Facility
- Gene Targeting and Transgenics
- Immortalized Cell Line Culture
- Integrative Imaging
- Janelia Experimental Technology
- Mass Spectrometry
- Media Prep
- Molecular Genomics
- Primary & iPS Cell Culture
- Project Pipeline Support
- Project Technical Resources
- Quantitative Genomics
- Scientific Computing Software
- Scientific Computing Systems
- Viral Tools
- Vivarium
Conference Paper
Long F, Peng H, Myers E.
2011. Automatic 3D neuron tracing using all-paths pruning.. Conference on Intelligent Systems for Molecular Biology.
Journal Article
Long F, Peng H, Liu X, Kim SK, Myers E.
2009. A 3D digital atlas of C. elegans and its application to single-cell analyses.. Nature Methods. 6:667-72.
Liu X, Long F, Peng H, Aerni SJ, Jiang M, Sánchez-Blanco A, Murray JI, Preston E, Mericle B, Batzoglou S et al..
2009. Analysis of cell fate from single-cell gene expression profiles in C. elegans.. Cell. 139(3):623-33.
Xie J, Zhao T, Lee T, Myers E, Peng H.
2011. Anisotropic path searching for automatic neuron reconstruction.. Medical Image Analysis. 15:680-9.
Xiao H, Peng H.
2013. APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree.. Bioinformatics (Oxford, England). 29:1448-54.
Heckscher ES, Long F, Layden MJ, Chuang C-H, Manning L, Richart J, Pearson JC, Crews ST, Peng H, Myers E et al..
2014. Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.. Development. 141(12):2524-32.
Yu Y, Peng H.
2011. Automated high speed stitching of large 3D microscopic images.. 2011 8TH IEEE International Symposium on Biomedical Imaging: From Nano to Macro. :238-41.
Zhao T, Xie J, Amat F, Clack N, Ahammad P, Peng H, Long F, Myers E.
2011. Automated reconstruction of neuronal morphology based on local geometrical and global structural models.. Neuroinformatics. 9(2-3):247-61.
Peng H, Long F, Zhou J, Leung G, Eisen MB, Myers EW.
2007. Automatic image analysis for gene expression patterns of fly embryos.. BMC Cell Biology. 8(Supplement 1):S7.
Xie J, Zhao T, Lee T, Myers E, Peng H.
2010. Automatic neuron tracing in volumetric microscopy images with anisotropic path searching.. Medical Image Computing and Computer-Assisted Intervention: MICCAI International Conference on Medical Image Computing and Computer-Assisted Intervention. 13:472-9.
Zhou J, Peng H.
2007. Automatic recognition and annotation of gene expression patterns of fly embryos.. Bioinformatics. 23(5):589-96.
Peng H, Ruan Z, Atasoy D, Sternson S.
2010. Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model.. Bioinformatics. 26:i38-46.
Long F, Peng H, Myers E.
2007. Automatic segmentation of nuclei in 3D microscopy images of C. elegans.. 2007 4TH IEEE International Symposium on Biomedical Imaging: Macro to Nano, VOLS 1-3. :536-9.
Herskovits EH, Peng H, Davatzikos C.
2004. A Bayesian morphometry algorithm.. IEEE Transactions on Medical Imaging. 23(6):723-37.
Manubens-Gil L, Zhou Z, Chen H, Ramanathan A, Liu X, Liu Y, Bria A, Gillette T, Ruan Z, Yang J et al..
2023. BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.. Nature Methods. 20(6)
Peng H, Hawrylycz M, Roskams J, Hill S, Spruston N, Meijering E, Ascoli GA.
2015. BigNeuron: Large-scale 3D neuron reconstruction from optical microscopy images.. Neuron. 87:252-6.
Peng H.
2008. Bioimage informatics: a new area of engineering biology.. Bioinformatics. 24(17):1827-36.
Peng H, Bateman A, Valencia A, Wren JD.
2012. Bioimage informatics: a new category in Bioinformatics.. Bioinformatics. 28(8):1057.
Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B et al..
2012. Biological imaging software tools.. Nature Methods. 9(7):697-710.
Wan Y, Long F, Qu L, Xiao H, Hawrylycz M, Myers EW, Peng H.
2015. BlastNeuron for automated comparison, retrieval and clustering of 3D neuron morphologies.. Neuroinformatics. 13(4):487-99.
Peng H, Chung P, Long F, Qu L, Jenett A, Seeds AM, Myers EW, Simpson JH.
2011. BrainAligner: 3D registration atlases of Drosophila brains.. Nature Methods. 8:493-500.
Yu H-H, Awasaki T, Schroeder MDavid, Long F, Yang JS, He Y, Ding P, Kao J-C, Wu GYueh-Yi, Peng H et al..
2013. Clonal development and organization of the adult Drosophila central brain.. Current biology : CB. 23:633-43.