Comprehensive high-resolution structural maps are central to functional exploration and understanding in biology. For the nervous system, in which high resolution and large spatial extent are both needed, such maps are scarce as they challenge data acquisition and analysis capabilities. Here we present for the mouse inner plexiform layer—the main computational neuropil region in the mammalian retina—the dense reconstruction of 950 neurons and their mutual contacts. This was achieved by applying a combination of crowd-sourced manual annotation and machine-learning-based volume segmentation to serial block-face electron microscopy data. We characterize a new type of retinal bipolar interneuron and show that we can subdivide a known type based on connectivity. Circuit motifs that emerge from our data indicate a functional mechanism for a known cellular response in a ganglion cell that detects localized motion, and predict that another ganglion cell is motion sensitive.
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We thank J. Diamond, T. Euler, R. Masland, M. Meister and J. Sanes for discussions, J. Kornfeld and F. Svara for programming and continually improving KNOSSOS, M. Müller and J. Tritthardt for programming and building instrumentation, C. Roome for IT support, and A. Borst, M. Fee, T. Gollisch and A. Karpova for comments on the manuscript. We especially thank F. Isensee for help with synapse identification. We thank P. Bastians, A. Biasotto, F. Drawitsch, H. Falk, A. Gable, M. Grohmann, A. Gäbelein, J. Hanne, F. Isensee, H. Jakobi, M. Kotchourko, E. Möller, J. Pollmann, C. Röhrig, A. Rommerskirchen, L. Schreiber, C. Willburger, H. Wissler and J. Youm for reconstruction management and annotator training, and N. Abazova, S. Abele, O. Aderhold, C. Altbürger, T. Amberger, K. Aninditha, A. Antunes, E. Atsiatorme, H. Augenstein, I. Bartsch, I. Barz, P. Bastians, J. Bauer, H. Bauersachs, R. Bay, J. Becker, M. Beez, S. Bender, M. Berberich, I. Bertlich, J. Bewersdorf, A. Biasotto, P. Biti, M. Bittmann, K. Bretzel, J. Briegel, E. Buckler, A. Buntjer, C. Burkhardt, S. Bühler, S. Daum, N. Demir, E. Demirel, S. Dettmer, M. Diemer, J. Dietrich, S. Dittrich, C. Domnick, F. Drawitsch, C. Eck, L. Ehm, S. Ehrhardt, T. Eliguezel, K. Ernst, O. Eryilmaz, F. Euler, H. Falk, K. Fischer, K. Foerster, R. Foitzik, A. Foltin, R. Foltin, S. Freiß, A. Gable, P. Gallandi, K. Garbe, A. Gebhardt, F. Gebhart, S. Gottwalt, A. Greis, M. Grohmann, A. Gromann, S. Gröbner, E. Grün, M. Grün, K. Guo, A. Gäbelein, K. Haase, J. Hammerich, J. Hanne, B. Hauber, M. Hensen, F. Hentzschel, M. Herberz, M. Heumannskämper, C. Hilbert, L. Hofmann, P. Hofmann, T. Hondrich, U. Häusler, M. Höreth, J. Hügle, F. Isensee, A. Ivanova, F. Jahnke, H. Jakobi, M. Joel, M. Jonczyk, A. Joschko, A. Jünger, K. Kappler, S. Kaspar, C. Kehrel, J. Kern, K. Keßler, S. Khoury, M. Kiapes, M. Kirchberger, A. Klein, C. Klein, S. Klein, J. Kratzer, C. Kraut, P. Kremer, P. Kretzer, F. Kröller, D. Krüger, M. Kuderer, S. Kull, S. Kwakman, S. Laiouar, L. Lebelt, H. Lesch, R. Lichtenberger, J. Liermann, C. Lieven, J. Lin, B. Linser, S. Lorger, J. Lott, D. Luft, L. Lust, J. Löffler, C. Marschall, B. Martin, D. Maton, B. Mayer, S. Mayorca, de. Ituarte, M. Meleux, C. Meyer, M. Moll, T. Moll, L. Mroszewski, E. Möller, M. Müller, L. Münster, N. Nasresfahani, J. Nassal, M. Neuschwanger, C. Nguyen, J. Nguyen, N. Nitsche, S. Oberrauch, F. Obitz, D. Ollech, C. Orlik, T. Otolski, S. Oumohand, A. Palfi, J. Pesch, M. Pfarr, S. Pfarr, M. Pohrath, J. Pollmann, M. Prokscha, S. Putzke, E. Rachmad, M. Reichert, J. Reinhardt, M. Reitz, J. Remus, M. Richter, M. Richter, J. Ricken, N. Rieger, F. Rodriguez. Jahnke, A. Rommerskirchen, M. Roth, I. Rummer, J. Rätzer, C. Röhrig, J. Röther, V. Saratov, E. Sauter, T. Schackel, M. Schamberger, M. Scheller, J. Schied, M. Schiedeck, J. Schiele, K. Schleich, M. Schlösser, S. Schmidt, C. Schneeweis, K. Schramm, M. Schramm, L. Schreiber, D. Schwarz, A. Schürholz, L. Schütz, A. Seitz, C. Sellmann, E. Serger, J. Sieber, L. Silbermann, I. Sonntag, T. Speck, Y. Söhngen, T. Tannig, N. Tisch, V. Tran, J. Trendel, M. Uhrig, D. Vecsei, F. Viehweger, V. Viehweger, R. Vogel, A. Vogel, J. Volz, P. Weber, K. Wegmeyer, J. Wiederspohn, E. Wiegand, R. Wiggers, C. Willburger, H. Wissler, V. Wissdorf, S. Wörner, J. Youm, A. Zegarra, J. Zeilfelder, F. Zickgraf and T. Ziegler for cell reconstruction. This work was supported by the Max-Planck Society and the DFG (Leibniz prize to W.D.). H.S.S. is grateful for support from the Gatsby Charitable Foundation.
This zipped file contains Supplementary Data files 2, 4, 5, 7 and 8 (see Supplementary Information for detailed description).
This zipped file contains Supplementary Data files 3a and b, which contain volume data samples from the conventionally stained sample (see Supplementary Information for detailed description).
This zipped file contains Supplementary Data files 3c, d and e containing volume data samples of EM data from the main data set (e2006), X-direction component of the classifier output for the same region, and segmentation before skeleton-based object collection (see Supplementary Information for detailed description).
This zipped file contains Supplementary Data 6 a and b, 6a contains a gallery of 36 Ganglion cells, 6b contains Gallery of 190 small-field Amacrine cells (see Supplementary Information for detailed description).
This zipped file contains Supplementary Data 6c, which contains a gallery of 163 medium- and wide-field Amacrine cells (see Supplementary Information for detailed description).
This zipped file contains Supplementary Data 6d which contains a gallery of 307 cone bipolar cells (see Supplementary Information for detailed description).
This zipped file contains Supplementary Data 6e and f, 6e contains a gallery of 144 rod bipolar cells and 6f contains a gallery of 110 cells from the “orphan” category (see Supplementary Information for detailed description).