Resurgent interest in synaptic circuitry and plasticity has emphasized the importance of 3D reconstruction from serial section electron microscopy (3DEM). Three volumes of hippocampal CA1 neuropil from adult rat were imaged at X-Y resolution of ~2 nm on serial sections of ~50-60 nm thickness. These are the first densely reconstructed hippocampal volumes. All axons, dendrites, glia, and synapses were reconstructed in a cube (~10 μm(3)) surrounding a large dendritic spine, a cylinder (~43 μm(3)) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm(3)) surrounding an apical dendritic segment (4.9 μm long). The data provide standards for identifying ultrastructural objects in 3DEM, realistic reconstructions for modeling biophysical properties of synaptic transmission, and a test bed for enhancing reconstruction tools. Representative synapses are quantified from varying section planes, and microtubules, polyribosomes, smooth endoplasmic reticulum, and endosomes are identified and reconstructed in a subset of dendrites. The original images, traces, and Reconstruct software and files are freely available and visualized at the Open Connectome Project (Data Citation 1).

Department of Biomedical Engineering Institute for Computational Medicine Johns Hopkins University Clark Hall Room 317C 3400 N Charles St Baltimore Maryland 21218 USA

Department of Computer Science Institute for Data Intensive Science and Engineering Johns Hopkins University 160 Malone Hall 3400 N Charles St Baltimore Maryland 21218 USA

Department of Neuroscience Center for Learning and Memory Institute for Neuroscience University of Texas at Austin 1 University Station C7000 Austin Texas 78712 USA

Department of Pathology Charles University at Prague Faculty of Medicine 500 35 Hradec Kralove Czech Republic

Zobrazit více v PubMed

Harris K. M. 2015. Open Connectome Project. http://dx.doi.org/10.7281/T11Z429Q DOI

Chiang R. G. & Govind C. K. Reorganization of synaptic ultrastructure at facilitated lobster neuromuscular terminals. J. Neurocytol. 15, 63–74 (1986). PubMed

Jarrell T. A. et al. The connectome of a decision-making neural network. Science 337, 437–444 (2012). PubMed

Bundgaard M. The three-dimensional organization of tight junctions in a capillary endothelium revealed by serial-section electron microscopy. J Ultrastruct. Res. 88, 1–17 (1984). PubMed

Keddie F. M. & Barajas L. Three-dimensional reconstruction of Pityrosporum yeast cells based on serial section electron microscopy. J. Ultrastruct. Res. 29, 260–275 (1969). PubMed

Novikoff P. M., Novikoff A. B., Quintana N. & Hauw J. J. Golgi apparatus, GERL, and lysosomes of neurons in rat dorsal root ganglia, studied by thick section and thin section cytochemistry. J. Cell Biol. 50, 859–886 (1971). PubMed PMC

Osafune T. & Schwartzbach S. D. Serial section immunoelectron microscopy of algal cells. Methods Mol. Biol. 657, 259–274 (2010). PubMed

Spacek J. & Lieberman A. R. Spine-like astrocytic protrusions into large axon terminals. Z. Zellforsch. Mikrosk. Anat. 115, 494–500 (1971). PubMed

Spacek J. & Lieberman A. R. Ultrastructure and three-dimensional organization of synaptic glomeruli in rat somatosensory thalamus. J. Anat. 117, 487–516 (1974). PubMed PMC

Starborg T., Lu Y., Huffman A., Holmes D. F. & Kadler K. E. Electron microscope 3D reconstruction of branched collagen fibrils in vivo. Scand. J Med. Sci. Sports 19, 547–552 (2009). PubMed

Thaemert J. C. Ultrastructural interrelationships of nerve processes and smooth muscle cells in three dimensions. J. Cell Biol. 28, 37–49 (1966). PubMed PMC

Mishchenko Y. et al. Ultrastructural analysis of hippocampal neuropil from the connectomics perspective. Neuron 67, 1009–1020 (2010). PubMed PMC

Marc R. E., Jones B. W., Lauritzen J. S., Watt C. B. & Anderson J. R. Building retinal connectomes. Curr. Opin. Neurobiol. 22, 568–574 (2012). PubMed PMC

Bock D. D. et al. Network anatomy and in vivo physiology of visual cortical neurons. Nature 471, 177–182 (2011). PubMed PMC

Briggman K. L., Helmstaedter M. & Denk W. Wiring specificity in the direction-selectivity circuit of the retina. Nature 471, 183–188 (2011). PubMed

Helmstaedter M., Briggman K. L. & Denk W. 3D structural imaging of the brain with photons and electrons. Curr. Opin. Neurobiol. 18, 633–641 (2008). PubMed

Ostroff L. E., Fiala J. C., Allwardt B. & Harris K. M. Polyribosomes redistribute from dendritic shafts into spines with enlarged synapses during LTP in developing rat hippocampal slices. Neuron 35, 535–545 (2002). PubMed

Knott G. W., Quairiaux C., Genoud C. & Welker E. Formation of dendritic spines with GABAergic synapses induced by whisker stimulation in adult mice. Neuron 34, 265–273 (2002). PubMed

Bourne J. N. & Harris K. M. Coordination of size and number of excitatory and inhibitory synapses results in a balanced structural plasticity along mature hippocampal CA1 dendrites during LTP. Hippocampus 21, 354–373 (2011). PubMed PMC

Ostroff L. E., Cain C. K., Bedont J., Monfils M. H. & Ledoux J. E. Fear and safety learning differentially affect synapse size and dendritic translation in the lateral amygdala. Proc. Natl. Acad. Sci. USA 107, 9418–9423 (2010). PubMed PMC

Ostroff L. E., Cain C. K., Jindal N., Dar N. & Ledoux J. E. Stability of presynaptic vesicle pools and changes in synapse morphology in the amygdala following fear learning in adult rats. J. Comp Neurol. 520, 295–314 (2012). PubMed PMC

Spacek J. Ultrastructural pathology of dendritic spines in epitumorous human cerebral cortex. Acta Neuropathol. 73, 77–85 (1987). PubMed

Witcher M. R. et al. Three-dimensional relationships between perisynaptic astroglia and human hippocampal synapses. Glia 58, 572–587 (2010). PubMed PMC

Kuwajima M., Spacek J. & Harris K. M. Beyond counts and shapes: Studying pathology of dendritic spines in the context of the surrounding neuropil through serial section electron microscopy. Neurosci 251, 75–89 (2013). PubMed PMC

Fiala J. C., Feinberg M., Peters A. & Barbas H. Mitochondrial degeneration in dystrophic neurites of senile plaques may lead to extracellular deposition of fine filaments. Brain Struct. Funct. 212, 195–207 (2007). PubMed

Nuntagij P. et al. Amyloid deposits show complexity and intimate spatial relationship with dendrosomatic plasma membranes: an electron microscopic 3D reconstruction analysis in 3xTg-AD mice and aged canines. J Alzheimers. Dis. 16, 315–323 (2009). PubMed

Hara Y. et al. Synaptic characteristics of dentate gyrus axonal boutons and their relationships with aging, menopause, and memory in female rhesus monkeys. J Neurosci. 31, 7737–7744 (2011). PubMed PMC

Popov V. I., Kleschevnikov A. M., Klimenko O. A., Stewart M. G. & Belichenko P. V. Three-dimensional synaptic ultrastructure in the dentate gyrus and hippocampal area CA3 in the Ts65Dn mouse model of Down syndrome. J Comp Neurol. 519, 1338–1354 (2011). PubMed

Villalba R. M. & Smith Y. Neuroglial plasticity at striatal glutamatergic synapses in Parkinson's disease. Front Syst. Neurosci 5, 68 (2011). PubMed PMC

Burns R. et al. The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience. Sci. Stat. Database. Manag. (2013). PubMed PMC

Briggman K. L. & Bock D. D. Volume electron microscopy for neuronal circuit reconstruction. Curr. Opin. Neurobiol. 22, 154–161 (2012). PubMed

Tomassy G. S. et al. Distinct profiles of myelin distribution along single axons of pyramidal neurons in the neocortex. Science 344, 319–324 (2014). PubMed PMC

Lichtman J. W., Pfister H. & Shavit N. The big data challenges of connectomics. Nat. Neurosci. 17, 1448–1454 (2014). PubMed PMC

Helmstaedter M. Cellular-resolution connectomics: challenges of dense neural circuit reconstruction. Nat. Methods 10, 501–507 (2013). PubMed

Burns R., Vogelstein J. T. & Szalay A. S. From cosmos to connectomes: the evolution of data-intensive science. Neuron 83, 1249–1252 (2014). PubMed

Fiala J. C. & Harris K. M. Computer-Based Alignment and Reconstruction of Serial Sections. Microscopy and Analysis 87, 5–8 (2002).

Fiala J. C. & Harris K. M. Extending unbiased stereology of brain ultrastructure to three-dimensional volumes. J. Am. Med. Inform. Assoc 8, 1–16 (2001). PubMed PMC

Harris K. M. & Stevens J. K. Dendritic spines of CA1 pyramidal cells in the rat hippocampus: serial electron microscopy with reference to their biophysical characteristics. J. Neurosci. 9, 2982–2997 (1989). PubMed PMC

Sorra K. E. & Harris K. M. Occurrence and three-dimensional structure of multiple synapses between individual radiatum axons and their target pyramidal cells in hippocampal area CA1. J. Neurosci. 13, 3736–3748 (1993). PubMed PMC

Shepherd G. M. & Harris K. M. Three-dimensional structure and composition of CA3-->CA1 axons in rat hippocampal slices: implications for presynaptic connectivity and compartmentalization. J. Neurosci. 18, 8300–8310 (1998). PubMed PMC

Lisman J. & Harris K. M. Quantal analysis and synaptic anatomy—integrating two views of hippocampal plasticity. Trends Neurosci. 16, 141–147 (1993). PubMed

Bourne J. N., Chirillo M. A. & Harris K. M. Presynaptic ultrastructural plasticity along CA3-->CA1 axons during long-term potentiation in mature hippocampus. J Comp Neurol. 521, 3898–3912 (2013). PubMed PMC

Harris K. M. & Stevens J. K. Dendritic spines of rat cerebellar Purkinje cells: serial electron microscopy with reference to their biophysical characteristics. J. Neurosci. 8, 4455–4469 (1988). PubMed PMC

Spacek J. & Harris K. M. Three-dimensional organization of smooth endoplasmic reticulum in hippocampal CA1 dendrites and dendritic spines of the immature and mature rat. J. Neurosci. 17, 190–203 (1997). PubMed PMC

Cooney J. R., Hurlburt J. L., Selig D. K., Harris K. M. & Fiala J. C. Endosomal compartments serve multiple hippocampal dendritic spines from a widespread rather than a local store of recycling membrane. J. Neurosci. 22, 2215–2224 (2002). PubMed PMC

Park M. et al. Plasticity-induced growth of dendritic spines by exocytic trafficking from recycling endosomes. Neuron 52, 817–830 (2006). PubMed PMC

Cui-Wang T. et al. Local zones of endoplasmic reticulum complexity confine cargo in neuronal dendrites. Cell 148, 309–321 (2012). PubMed PMC

Bourne J. N., Sorra K. E., Hurlburt J. & Harris K. M. Polyribosomes are increased in spines of CA1 dendrites 2 h after the induction of LTP in mature rat hippocampal slices. Hippocampus 17, 1–4 (2007). PubMed

Spacek J. & Harris K. M. Three-dimensional organization of cell adhesion junctions at synapses and dendritic spines in area CA1 of the rat hippocampus. J. Comp Neurol. 393, 58–68 (1998). PubMed

Franks K. M., Stevens C. F. & Sejnowski T. J. Independent sources of quantal variability at single glutamatergic synapses. J. Neurosci. 23, 3186–3195 (2003). PubMed PMC

Franks K. M., Bartol T. M. Jr. & Sejnowski T. J. A Monte Carlo model reveals independent signaling at central glutamatergic synapses. Biophys. J. 83, 2333–2348 (2002). PubMed PMC

Bell M. E. et al. Dynamics of nascent and active zone ultrastructure as synapses enlarge during long-term potentiation in mature hippocampus. J. Comp Neurol. 522, 3861–3884 (2014). PubMed PMC

Kinney J. P. et al. Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil. J. Comp Neurol. 521, 448–464 (2013). PubMed PMC

Ventura R. & Harris K. M. Three-dimensional relationships between hippocampal synapses and astrocytes. J. Neurosci 19, 6897–6906 (1999). PubMed PMC

Witcher M. R., Kirov S. A. & Harris K. M. Plasticity of perisynaptic astroglia during synaptogenesis in the mature rat hippocampus. Glia 55, 13–23 (2007). PubMed

Cardona A. Towards semi-automatic reconstruction of neural circuits. Neuroinformatics 11, 31–33 (2013). PubMed

Saalfeld S., Fetter R., Cardona A. & Tomancak P. Elastic volume reconstruction from series of ultra-thin microscopy sections. Nat. Methods 9, 717–720 (2012). PubMed

Harris K. M. et al. Uniform serial sectioning for transmission electron microscopy. J. Neurosci. 26, 12101–12103 (2006). PubMed PMC

Kuwajima M., Mendenhall J. M., Lindsey L. F. & Harris K. M. Automated transmission-mode scanning electron microscopy (tSEM) for large volume analysis at nanoscale resolution. PLoS. ONE. 8, e59573 (2013). PubMed PMC

Fiala J. C. Reconstruct: a free editor for serial section microscopy. J. Microsc. 218, 52–61 (2005). PubMed

Cardona A. et al. TrakEM2 software for neural circuit reconstruction. PLoS. ONE 7, e38011 (2012). PubMed PMC

Schindelin J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012). PubMed PMC

Fiala J. C. & Harris K. M. Cylindrical diameters method for calibrating section thickness in serial electron microscopy. J. Microsc. 202, 468–472 (2001). PubMed

Saalfeld S., Cardona A., Hartenstein V. & Tomancak P. CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics 25, 1984–1986 (2009). PubMed PMC

Bushong E. A., Martone M. E. & Ellisman M. H. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. International Journal of Developmental Neuroscience 22, 73–86 (2004). PubMed

Bushong E. A., Martone M. E., Jones Y. Z. & Ellisman M. H. Protoplasmic astrocytes in CA1 stratum radiatum occupy separate anatomical domains. J Neurosci 22, 183–192 (2002). PubMed PMC

Boissonnat J. D. Shape reconstruction from planar cross sections. Computer Vision, Graphics, and Image Processing 44, 1–29 (1988).

Fiala J. C. et al. Timing of neuronal and glial ultrastructure disruption during brain slice preparation and recovery in vitro . J Comp Neurol 465, 90–103 (2003). PubMed

von Bartheld C. S. & Altick A. L. Multivesicular bodies in neurons: distribution, protein content, and trafficking functions. Prog. Neurobiol. 93, 313–340 (2011). PubMed PMC

Peters A., Palay S. L. & Webster H. d. The fine structure of the nervous system: The neurons and supporting cells (W.B.Saunders, Co., 1991).

Edwards J. et al. VolRoverN: enhancing surface and volumetric reconstruction for realistic dynamical simulation of cellular and subcellular function. Neuroinformatics 12, 277–289 (2014). PubMed PMC

Thorne R. G. & Nicholson C. In vivo diffusion analysis with quantum dots and dextrans predicts the width of brain extracellular space. Proc. Natl. Acad. Sci. USA 103, 5567–5572 (2006). PubMed PMC