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1. Full Text Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy
by Hanchuan Peng and Fuhui Long and Ding, C
IEEE Transactions on Pattern Analysis and Machine Intelligence, ISSN 0162-8828, 08/2005, Volume 27, Issue 8, pp. 1226 - 1238
Feature selection is an important problem for pattern classification systems. We study how to select good features according to the maximal statistical... 
Algorithm design and analysis | Costs | minimal redundancy | Redundancy | maximal relevance | classification | Support vector machines | Diversity reception | Pattern classification | Support vector machine classification | Index Terms- Feature selection | Performance analysis | maximal dependency | Mutual information | Cancer | Minimal redundancy | Feature selection | Maximal relevance | Classification | Maximal dependency | mutual information | WRAPPERS | CANCER | feature selection | COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE | ENGINEERING, ELECTRICAL & ELECTRONIC | Algorithms | Information Storage and Retrieval - methods | Numerical Analysis, Computer-Assisted | Artificial Intelligence | Computer Simulation | Humans | Diagnosis, Computer-Assisted - methods | Neoplasms - classification | Neoplasms - diagnosis | Models, Statistical | Pattern Recognition, Automated - methods | Cluster Analysis | Redundancy (Engineering) | Artificial intelligence | Equivalence | Intelligence | Digits | Criteria | Pattern analysis | Selectors
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2. Full Text Bioimage informatics: a new area of engineering biology
by Peng, Hanchuan
Bioinformatics, ISSN 1367-4803, 9/2008, Volume 24, Issue 17, pp. 1827 - 1836
In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has... 
ZEBRAFISH | PROTEIN | GENE-EXPRESSION PATTERNS | BIOCHEMICAL RESEARCH METHODS | SUBCELLULAR LOCATION | MICROSCOPY DATA | CELL-NUCLEI | FLUORESCENCE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | TRACKING | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SEGMENTATION | IMAGE REGISTRATION | Diagnostic Imaging - methods | Computer Graphics | User-Computer Interface | Computational Biology - methods | Models, Biological | Computer Simulation | Computational Biology - trends | Biomedical Engineering - methods | Biomedical Engineering - trends | Review Paper
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3. Minimum redundancy feature selection from microarray gene expression data
by Ding, Chris and Peng, Hanchuan
Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, 04/2005, Volume 3, Issue 2, pp. 185 - 205
How to selecting a small subset out of the thousands of genes in microarray data is important for accurate classification of phenotypes. Widely used methods... 
Gene expression analysis | Naïve Bayes | Gene selection | SVM | Cancer classification | Gene Expression Profiling - methods | Algorithms | Oligonucleotide Array Sequence Analysis - methods | Pattern Recognition, Automated - methods | Discriminant Analysis
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4. Full Text Brain Informatics and Health : 8th International Conference, BIH 2015, London, UK, August 30 - September 2, 2015. Proceedings
by Guo, Yike and Friston, Karl and Faisal, Aldo and Hill, Sean and Peng, Hanchuan
08/2015, 1st ed. 2015, Lecture Notes in Computer Science, ISBN 3319233432, Volume 9250, 464
Pattern Recognition | Computer Science | Image Processing and Computer Vision | User Interfaces and Human Computer Interaction | Information Storage and Retrieval | Artificial Intelligence (incl. Robotics) | Information Systems Applications (incl. Internet)
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5. Full Text Extensible visualization and analysis for multidimensional images using Vaa3D
by Peng, Hanchuan and Bria, Alessandro and Zhou, Zhi and Iannello, Giulio and Long, Fuhui
Nature Protocols, ISSN 1754-2189, 01/2014, Volume 9, Issue 1, pp. 193 - 208
Open-Source 3D Visualization-Assisted Analysis (Vaa3D) is a software platform for the visualization and analysis of large-scale multidimensional images. In... 
MOUSE-BRAIN | PLATFORM | BIOLOGY | BIOCHEMICAL RESEARCH METHODS | NEUROANATOMY | BIOIMAGE INFORMATICS | MICROSCOPY | QUANTITATIVE-ANALYSIS | TOOL | User-Computer Interface | Animals | Neurons - ultrastructure | Brain - anatomy & histology | Computer Simulation | Imaging, Three-Dimensional - methods | Software | Drosophila - anatomy & histology | Image processing | Innovations
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6. Full Text V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets
by Peng, Hanchuan and Ruan, Zongcai and Long, Fuhui and Simpson, Julie H and Myers, Eugene W
Nature Biotechnology, ISSN 1087-0156, 04/2010, Volume 28, Issue 4, pp. 348 - 353
The V3D system provides three-dimensional (3D) visualization of gigabyte-sized microscopy image stacks in real time on current laptops and desktops. V3D... 
NEURONS | MICROSCOPY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ELEGANS | Microscopy - methods | Computer Graphics | Radiology Information Systems | User-Computer Interface | Information Storage and Retrieval - methods | Image Interpretation, Computer-Assisted - methods | Imaging, Three-Dimensional - methods | Databases, Factual | Technology application | Usage | Image processing | Three-dimensional graphics | Imaging systems | Properties | Computational biology | Computer programs | Medical imaging | Biomedical research | Microscopy | 3-D graphics
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7. Full Text APP2: Automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree
by Xiao, Hang and Peng, Hanchuan
Bioinformatics, ISSN 1367-4803, 06/2013, Volume 29, Issue 11, pp. 1448 - 1454
Motivation: Tracing of neuron morphology is an essential technique in computational neuroscience. However, despite a number of existing methods, few... 
ASSAYS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | RECONSTRUCTION | FLUORESCENCE MICROSCOPY IMAGES | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Microscopy - methods | Algorithms | Animals | Imaging, Three-Dimensional - methods | Drosophila - cytology | Neurons - cytology | Software | Original Papers
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8. Full Text BigNeuron: Large-Scale 3D Neuron Reconstruction from Optical Microscopy Images
by Peng, Hanchuan and Hawrylycz, Michael and Roskams, Jane and Hill, Sean and Spruston, Nelson and Meijering, Erik and Ascoli, Giorgio A
Neuron, ISSN 0896-6273, 07/2015, Volume 87, Issue 2, pp. 252 - 256
Understanding the structure of single neurons is critical for understanding how they function within neural circuits. BigNeuron is a new community effort that... 
VISUALIZATION | SYSTEM | DIGITAL RECONSTRUCTIONS | NEUROSCIENCES | BRAIN | NEUROSCIENCE | Microscopy - methods | Optical Imaging | Algorithms | Animals | Humans | Computational Biology | Neurons - cytology | Models, Neurological | Imaging, Three-Dimensional | Neurons | Microscope and microscopy | Neural circuitry | Datasets | Automation | Neurosciences | Brain research | Microscopy | Morphology | Software | Data bases
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9. Full Text A mesoscale connectome of the mouse brain
by Oh, Seung Wook and Oh, Seung Wook and Harris, Julie A and Harris, Julie A and Ng, Lydia and Ng, Lydia and Winslow, Brent and Winslow, Brent and Cain, Nicholas and Cain, Nicholas and Mihalas, Stefan and Mihalas, Stefan and Wang, Quanxin and Wang, Quanxin and Lau, Chris and Lau, Chris and Kuan, Leonard and Kuan, Leonard and Henry, Alex M and Henry, Alex M and Mortrud, Marty T and Mortrud, Marty T and Ouellette, Benjamin and Ouellette, Benjamin and Nguyen, Thuc Nghi and Nguyen, Thuc Nghi and Sorensen, Staci A and Sorensen, Staci A and Slaughterbeck, Clifford R and Slaughterbeck, Clifford R and Wakeman, Wayne and Wakeman, Wayne and Li, Yang and Li, Yang and Feng, David and Feng, David and Ho, Anh and Ho, Anh and Nicholas, Eric and Nicholas, Eric and Hirokawa, Karla E and Hirokawa, Karla E and Bohn, Phillip and Bohn, Phillip and Joines, Kevin M and Joines, Kevin M and Peng, Hanchuan and Peng, Hanchuan and Hawrylycz, Michael J and Hawrylycz, Michael J and Phillips, John W and Phillips, John W and Hohmann, John G and Hohmann, John G and Wohnoutka, Paul and Wohnoutka, Paul and Gerfen, Charles R and Gerfen, Charles R and Koch, Christof and Koch, Christof and Bernard, Amy and Bernard, Amy and Dang, Chinh and Dang, Chinh and Jones, Allan R and Jones, Allan R and Zeng, Hongkui and Zeng, Hongkui
Nature, ISSN 0028-0836, 2014, Volume 508, Issue 7495, pp. 207 - 214
Comprehensive knowledge of the brain's wiring diagram is fundamental for understanding how the nervous system processes information at both local and global... 
EFFERENT PROJECTIONS | PHASEOLUS-VULGARIS-LEUKOAGGLUTININ | RAT VISUAL-CORTEX | MULTIDISCIPLINARY SCIENCES | MEDIAL PREFRONTAL CORTEX | CORTICOTHALAMIC PROJECTIONS | CORTICAL PROJECTIONS | BARREL CORTEX | PARAFASCICULAR THALAMIC NUCLEUS | THALAMOCORTICAL PROJECTIONS | AFFERENT CONNECTIONS | Brain - cytology | Brain - anatomy & histology | Atlases as Topic | Mice, Inbred C57BL | Neuroanatomical Tract-Tracing Techniques | Male | Axons - physiology | Connectome | Cerebral Cortex - cytology | Corpus Striatum - cytology | Animals | Thalamus - cytology | Mice | Models, Neurological | Brain | Usage | Computer-generated environments | Neural circuitry | Computer simulation | Physiological aspects | Research | Enhanced green fluorescent protein | Medical imaging | Neural networks | Neurons | Tomography | Genetic engineering | Methods
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10. Full Text Biological imaging software tools
by Eliceiri, Kevin W and Berthold, Michael R and Goldberg, Ilya G and Ibáñez, Luis and Manjunath, B.S and Martone, Maryann E and Murphy, Robert F and Peng, Hanchuan and Plant, Anne L and Roysam, Badrinath and Stuurmann, Nico and Swedlow, Jason R and Tomancak, Pavel and Carpenter, Anne E
Nature Methods, ISSN 1548-7091, 07/2012, Volume 9, Issue 7, pp. 697 - 710
Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing... 
VISUALIZATION | CELLS | MANAGEMENT | ELEGANS | RESOLUTION | BIOCHEMICAL RESEARCH METHODS | SUBCELLULAR LOCATION PATTERNS | ILLUMINATION MICROSCOPY | PLANE ILLUMINATION | CLASSIFICATION | MACHINE | Computational Biology - methods | Information Storage and Retrieval - methods | Computational Biology - instrumentation | Image Processing, Computer-Assisted - instrumentation | Software | Image Processing, Computer-Assisted - methods | Equipment Design | Software Design | Technology application | Usage | Microscope and microscopy | Analysis | Methods | Applications software | Biology | Image processing systems
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11. Full Text MGRASP enables mapping mammalian synaptic connectivity with light microscopy
by Kim, Jinhyun and Zhao, Ting and Petralia, Ronald S and Yu, Yang and Peng, Hanchuan and Myers, Eugene and Magee, Jeffrey C
Nature Methods, ISSN 1548-7091, 01/2012, Volume 9, Issue 1, pp. 96 - 102
The GFP reconstitution across synaptic partners (GRASP) technique, based on functional complementation between two nonfluorescent GFP fragments, can be used to... 
SINGLE | SYNAPSES | MEMBRANE | BIOCHEMICAL RESEARCH METHODS | NEUREXINS | ARCHITECTURE | PROTEINS | EXPRESSION | BRAIN | CIRCUIT | Green Fluorescent Proteins - metabolism | Ventral Thalamic Nuclei - physiology | Mutant Chimeric Proteins | Synapses - physiology | Molecular Sequence Data | Electroporation | Hippocampus - cytology | Somatosensory Cortex - physiology | Animals | Microscopy | Dendrites | Mice | Genetic Vectors | Physiological aspects | Neurons | Research | Proteins | Neurosciences | Molecular biology
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12. Full Text Imagining the future of bioimage analysis
by Meijering, Erik and Carpenter, Anne E and Peng, Hanchuan and Hamprecht, Fred A and Olivo-Marin, Jean-Christophe
Nature Biotechnology, ISSN 1087-0156, 12/2016, Volume 34, Issue 12, pp. 1250 - 1255
Modern biological research increasingly relies on image data as a primary source of information in unraveling the cellular and molecular mechanisms of life.... 
VISUALIZATION | IMAGE DATA | BIG | MODELS | MEMORY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEGMENTATION | MICROSCOPY | CHALLENGES | Diagnostic imaging | Innovations | Biotechnology | Medical imaging | Cellular biology | Molecular biology
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