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Foreword; We Live in Exciting Times; Contents; Notes from the Editors; Anatomy: High-Resolution Neuroanatomy Using Molecular-Genetic Tools; 1 The Current State of the Neuroanatomy Toolkit in the Fruit Fly Drosophila melanogaster; Abstract; 1.1 Introduction; 1.2 Binary Activation Systems; 1.2.1 The GAL4 System; 1.2.2 The LexA System; 1.2.3 The Q System; 1.3 Neurogenetic Labeling; 1.3.1 Fluorescent Protein Reporters; 1.3.2 Non-fluorescent Protein Reporters; 1.4 Regulating Binary Activators; 1.4.1 Enhancer Trapping and Bashing; 1.4.2 Promoter Bashing and Trapping; 1.4.3 Protein Trapping
1.5 Refining Genetic Targeting by Intersectional Perturbations1.5.1 OR Gates; 1.5.2 AND Gates; 1.5.3 NOT Gates; 1.5.4 Combinatorial AND/NOT Gating; 1.6 Mitotic Analysis and Multicolor Stochastic Labeling Strategies in D. melanogaster; 1.7 Conclusions and Future Directions; Acknowledgements; References; 2 Retinal Connectomics; Abstract; 2.1 Introduction; 2.2 Some Basic Retinal Anatomy; 2.3 Why Is Retinal Connectomics Difficult?; 2.4 The Long Overdue Automation of Electron Microscopy; 2.5 The Real Bottleneck-Data Analysis; 2.6 A Retinal 'Contactome'
2.7 Correlating Retinal Structure with Function2.8 Species-Dependent Differences in Retinal Wiring; 2.9 Future of Retinal Connectomics; References; 3 Recent Progress in the 3D Reconstruction of Drosophila Neural Circuits; Abstract; 3.1 Introduction; 3.1.1 The Fly CNS as a Model System of Connectomics Study; 3.1.2 Anatomy of the Drosophila CNS; 3.2 Reconstruction of Neuronal Circuits and Analysis Using CLSM Image Data; 3.2.1 Visualizing Neurons with Confocal Laser Microscopy; 3.2.2 Three-Dimensional Reconstruction of Neurons in the Fly Brain
3.2.2.1 Algorithms for Three-Dimensional Reconstruction3.2.2.2 FluoRender: A Volume Rendering Tool Optimized for CLSM Volume Data; 3.2.3 3D Registration of Brains; 3.2.4 Application of 3D Reconstruction and Registration; 3.2.4.1 Clonal Unit Analysis; 3.2.4.2 Prediction of Synaptic Partners; 3.3 Electron Microscopy-Based Reconstruction and Connectomics; 3.3.1 Ultrastructures Visualized with EM; 3.3.2 Strategies of 3D Reconstruction; 3.3.2.1 Dense (Saturated) Reconstruction/Sparse Reconstruction; 3.3.2.2 Volumetric Reconstruction/Skeletonized Reconstruction
3.3.2.3 Manual Tracing/Automatic Tracing3.3.3 3D EM Methods in Connectomics Studies of Drosophila CNS; 3.3.3.1 Serial-Section Transmission EM (ssTEM); 3.3.3.2 Serial Block-Face Scanning EM (SBF-SEM); 3.3.3.3 Focused-Ion Beam-Aided Scanning EM (FIB-SEM); 3.3.4 EM Connectomics Studies in the Fly CNS; 3.3.4.1 Connectivity Analysis in the Optic Lobe Neuropils Using ssTEM and FIB-SEM Methods; 3.3.4.2 Imaging the Blowfly Brain with SBF-SEM; 3.3.4.3 Reconstruction of the Larval CNS with ssTEM; 3.3.5 Other Imaging Techniques for Large-Scale Connectomics
1.5 Refining Genetic Targeting by Intersectional Perturbations1.5.1 OR Gates; 1.5.2 AND Gates; 1.5.3 NOT Gates; 1.5.4 Combinatorial AND/NOT Gating; 1.6 Mitotic Analysis and Multicolor Stochastic Labeling Strategies in D. melanogaster; 1.7 Conclusions and Future Directions; Acknowledgements; References; 2 Retinal Connectomics; Abstract; 2.1 Introduction; 2.2 Some Basic Retinal Anatomy; 2.3 Why Is Retinal Connectomics Difficult?; 2.4 The Long Overdue Automation of Electron Microscopy; 2.5 The Real Bottleneck-Data Analysis; 2.6 A Retinal 'Contactome'
2.7 Correlating Retinal Structure with Function2.8 Species-Dependent Differences in Retinal Wiring; 2.9 Future of Retinal Connectomics; References; 3 Recent Progress in the 3D Reconstruction of Drosophila Neural Circuits; Abstract; 3.1 Introduction; 3.1.1 The Fly CNS as a Model System of Connectomics Study; 3.1.2 Anatomy of the Drosophila CNS; 3.2 Reconstruction of Neuronal Circuits and Analysis Using CLSM Image Data; 3.2.1 Visualizing Neurons with Confocal Laser Microscopy; 3.2.2 Three-Dimensional Reconstruction of Neurons in the Fly Brain
3.2.2.1 Algorithms for Three-Dimensional Reconstruction3.2.2.2 FluoRender: A Volume Rendering Tool Optimized for CLSM Volume Data; 3.2.3 3D Registration of Brains; 3.2.4 Application of 3D Reconstruction and Registration; 3.2.4.1 Clonal Unit Analysis; 3.2.4.2 Prediction of Synaptic Partners; 3.3 Electron Microscopy-Based Reconstruction and Connectomics; 3.3.1 Ultrastructures Visualized with EM; 3.3.2 Strategies of 3D Reconstruction; 3.3.2.1 Dense (Saturated) Reconstruction/Sparse Reconstruction; 3.3.2.2 Volumetric Reconstruction/Skeletonized Reconstruction
3.3.2.3 Manual Tracing/Automatic Tracing3.3.3 3D EM Methods in Connectomics Studies of Drosophila CNS; 3.3.3.1 Serial-Section Transmission EM (ssTEM); 3.3.3.2 Serial Block-Face Scanning EM (SBF-SEM); 3.3.3.3 Focused-Ion Beam-Aided Scanning EM (FIB-SEM); 3.3.4 EM Connectomics Studies in the Fly CNS; 3.3.4.1 Connectivity Analysis in the Optic Lobe Neuropils Using ssTEM and FIB-SEM Methods; 3.3.4.2 Imaging the Blowfly Brain with SBF-SEM; 3.3.4.3 Reconstruction of the Larval CNS with ssTEM; 3.3.5 Other Imaging Techniques for Large-Scale Connectomics