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Original references from Timothy Lee

  1. Bock DD, Lee WC, Kerlin AM, Andermann ML, Hood G, Wetzel AW, Yurgenson S, Soucy ER, Kim HS, Reid RC. Network anatomy and in vivo physiology of visual cortical neurons. Nature. 2011 Mar 10;471(7337):177-82. doi: 10.1038/nature09802. PMID: 21390124; PMCID: PMC3095821.
  2. Bumbarger DJ, Riebesell M, Rödelsperger C, Sommer RJ. System-wide rewiring underlies behavioral differences in predatory and bacterial-feeding nematodes. Cell. 2013 Jan 17;152(1-2):109-19. doi: 10.1016/j.cell.2012.12.013. PMID: 23332749.
  3. Dowell, W. C. T. (1959). Unobstructed mounting of serial section. J. Ultrastruct. Res., 28,634. doi: 10.1016/S0022-5320(59)90002-4
  4. Gur M, Purple RL, Whitehead R. Ultrastructure within the lateral plexus of the Limulus eye. J Gen Physiol. 1972 Mar;59(3):285-304. doi: 10.1085/jgp.59.3.285. PMID: 5058961; PMCID: PMC2203176.
  5. Hall DH, Russell RL. The posterior nervous system of the nematode Caenorhabditis elegans: serial reconstruction of identified neurons and complete pattern of synaptic interactions. J Neurosci. 1991 Jan;11(1):1-22. doi: 10.1523/JNEUROSCI.11-01-00001.1991. PMID: 1986064; PMCID: PMC6575198.
  6. Hamos JE, Van Horn SC, Raczkowski D, Sherman SM. Synaptic circuits involving an individual retinogeniculate axon in the cat. J Comp Neurol. 1987 May 8;259(2):165-92. doi: 10.1002/cne.902590202. Erratum in: J Comp Neurol 1987 Jun 15;260(3):481. PMID: 3584556.
  7. Harris KM, Perry E, Bourne J, Feinberg M, Ostroff L, Hurlburt J. Uniform serial sectioning for transmission electron microscopy. J Neurosci. 2006 Nov 22;26(47):12101-3. doi: 10.1523/JNEUROSCI.3994-06.2006. PMID: 17122034; PMCID: PMC6675417.
  8. Hoffpauir BK, Pope BA, Spirou GA. Serial sectioning and electron microscopy of large tissue volumes for 3D analysis and reconstruction: a case study of the calyx of Held. Nat Protoc. 2007;2(1):9-22. doi: 10.1038/nprot.2007.9. PMID: 17401332.
  9. Hua Y, Laserstein P, Helmstaedter M. Large-volume en-bloc staining for electron microscopy-based connectomics. Nat Commun. 2015 Aug 3;6:7923. doi: 10.1038/ncomms8923. PMID: 26235643; PMCID: PMC4532871.
  10. Kuwajima M, Mendenhall JM, Lindsey LF, Harris KM. Automated transmission-mode scanning electron microscopy (tSEM) for large volume analysis at nanoscale resolution. PLoS One. 2013;8(3):e59573. doi: 10.1371/journal.pone.0059573. Epub 2013 Mar 26. PMID: 23555711; PMCID: PMC3608656.
  11. Lee WC, Bonin V, Reed M, Graham BJ, Hood G, Glattfelder K, Reid RC. Anatomy and function of an excitatory network in the visual cortex. Nature. 2016 Apr 21;532(7599):370-4. doi: [10.1038/nature17192]https://doi.org/10.1038/nature17192). Epub 2016 Mar 28. PMID: 27018655; PMCID: PMC4844839.
  12. Lee K, & Zung J, Li P, Jain V, Seung H. (2017). Superhuman Accuracy on the SNEMI3D Connectomics Challenge. arXiv: 1706.00120.
  13. Ryan K, Lu Z, Meinertzhagen IA. The CNS connectome of a tadpole larva of Ciona intestinalis (L.) highlights sidedness in the brain of a chordate sibling. Elife. 2016 Dec 6;5:e16962. doi: 10.7554/eLife.16962. PMID: 27921996; PMCID: PMC5140270.
  14. Spacek J, Lieberman AR. Ultrastructure and three-dimensional organization of synaptic glomeruli in rat somatosensory thalamus. J Anat. 1974 Jul;117(Pt 3):487-516. PMID: 4370696; PMCID: PMC1231457.
  15. Shepherd GM, Harris KM. Three-dimensional structure and composition of CA3-->CA1 axons in rat hippocampal slices: implications for presynaptic connectivity and compartmentalization. J Neurosci. 1998 Oct 15;18(20):8300-10. doi: 10.1523/JNEUROSCI.18-20-08300.1998. PMID: 9763474; PMCID: PMC6792846.
  16. Takemura SY, Lu Z, Meinertzhagen IA. Synaptic circuits of the Drosophila optic lobe: the input terminals to the medulla. J Comp Neurol. 2008 Aug 10;509(5):493-513. doi: 10.1002/cne.21757. PMID: 18537121; PMCID: PMC2481516.
  17. Takemura SY, Bharioke A, Lu Z, Nern A, Vitaladevuni S, Rivlin PK, Katz WT, Olbris DJ, Plaza SM, Winston P, Zhao T, Horne JA, Fetter RD, Takemura S, Blazek K, Chang LA, Ogundeyi O, Saunders MA, Shapiro V, Sigmund C, Rubin GM, Scheffer LK, Meinertzhagen IA, Chklovskii DB. A visual motion detection circuit suggested by Drosophila connectomics. Nature. 2013 Aug 8;500(7461):175-81. doi: 10.1038/nature12450. PMID: 23925240; PMCID: PMC3799980.
  18. Fahrenbach WH. Anatomical circuitry of lateral inhibition in the eye of the horseshoe crab, Limulus polyphemus. Proc R Soc Lond B Biol Sci. 1985 Aug 22;225(1239):219-49. doi: 10.1098/rspb.1985.0060. PMID: 2864695.

New references

  1. White JG, Southgate E, Thomson JN, Brenner S. The structure of the nervous system of the nematode Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci. 1986 Nov 12;314(1165):1-340. doi: 10.1098/rstb.1986.0056. PMID: 22462104.
  2. Zheng Z, Lauritzen JS, Perlman E, Robinson CG, Nichols M, Milkie D, Torrens O, Price J, Fisher CB, Sharifi N, Calle-Schuler SA, Kmecova L, Ali IJ, Karsh B, Trautman ET, Bogovic JA, Hanslovsky P, Jefferis GSXE, Kazhdan M, Khairy K, Saalfeld S, Fetter RD, Bock DD. A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster. Cell. 2018 Jul 26;174(3):730-743.e22. doi: 10.1016/j.cell.2018.06.019. Epub 2018 Jul 19. PMID: 30033368; PMCID: PMC6063995.
  3. Kasthuri N, Hayworth KJ, Berger DR, Schalek RL, Conchello JA, Knowles-Barley S, Lee D, Vázquez-Reina A, Kaynig V, Jones TR, Roberts M, Morgan JL, Tapia JC, Seung HS, Roncal WG, Vogelstein JT, Burns R, Sussman DL, Priebe CE, Pfister H, Lichtman JW. Saturated Reconstruction of a Volume of Neocortex. Cell. 2015 Jul 30;162(3):648-61. doi: 10.1016/j.cell.2015.06.054. PMID: 26232230.
  4. Ohyama T, Schneider-Mizell CM, Fetter RD, Aleman JV, Franconville R, Rivera-Alba M, Mensh BD, Branson KM, Simpson JH, Truman JW, Cardona A, Zlatic M. A multilevel multimodal circuit enhances action selection in Drosophila. Nature. 2015 Apr 30;520(7549):633-9. doi: 10.1038/nature14297. Epub 2015 Apr 20. PMID: 25896325.
  5. Schmidt H, Gour A, Straehle J, Boergens KM, Brecht M, Helmstaedter M. Axonal synapse sorting in medial entorhinal cortex. Nature. 2017 Sep 28;549(7673):469-475. doi: 10.1038/nature24005. Epub 2017 Sep 20. PMID: 28959971.
  6. Bloss EB, Cembrowski MS, Karsh B, Colonell J, Fetter RD, Spruston N. Single excitatory axons form clustered synapses onto CA1 pyramidal cell dendrites. Nat Neurosci. 2018 Mar;21(3):353-363. doi: 10.1038/s41593-018-0084-6. Epub 2018 Feb 19. PMID: 29459763.
  7. Helmstaedter M, Briggman KL, Turaga SC, Jain V, Seung HS, Denk W. Connectomic reconstruction of the inner plexiform layer in the mouse retina. Nature. 2013 Aug 8;500(7461):168-74. doi: 10.1038/nature12346. Erratum in: Nature. 2014 Oct 16;514(7522):394. PMID: 23925239.
  8. Briggman KL, Helmstaedter M, Denk W. Wiring specificity in the direction-selectivity circuit of the retina. Nature. 2011 Mar 10;471(7337):183-8. doi: 10.1038/nature09818. PMID: 21390125.
  9. Armer HE, Mariggi G, Png KM, Genoud C, Monteith AG, Bushby AJ, Gerhardt H, Collinson LM. Imaging transient blood vessel fusion events in zebrafish by correlative volume electron microscopy. PLoS One. 2009 Nov 6;4(11):e7716. doi: 10.1371/journal.pone.0007716. PMID: 19893745; PMCID: PMC2769265.
  10. Motta A, Berning M, Boergens KM, Staffler B, Beining M, Loomba S, Hennig P, Wissler H, Helmstaedter M. Dense connectomic reconstruction in layer 4 of the somatosensory cortex. Science. 2019 Nov 29;366(6469):eaay3134. doi: 10.1126/science.aay3134. Epub 2019 Oct 24. PMID: 31649140.
  11. Maniates-Selvin J, et al. Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy. bioRxiv 2020.01.10.902478 doi: 10.1101/2020.01.10.902478
  12. Wanner AA, Genoud C, Friedrich RW. 3-dimensional electron microscopic imaging of the zebrafish olfactory bulb and dense reconstruction of neurons. Sci Data. 2016 Nov 8;3:160100. doi: 10.1038/sdata.2016.100. PMID: 27824337; PMCID: PMC5100684.
  13. Dorkenwald S, et al. Binary and analog variation of synapses between cortical pyramidal neurons. bioRxiv 2019.12.29.890319; doi: 10.1101/2019.12.29.890319
  14. Xu CS, et al. A Connectome of the Adult Drosophila Central Brain. bioRxiv 2020.01.21.911859; doi: 10.1101/2020.01.21.911859
  15. Vishwanathan A, Daie K, Ramirez AD, Lichtman JW, Aksay ERF, Seung HS. Electron Microscopic Reconstruction of Functionally Identified Cells in a Neural Integrator. Curr Biol. 2017 Jul 24;27(14):2137-2147.e3. doi: 10.1016/j.cub.2017.06.028. Epub 2017 Jul 14. PMID: 28712570; PMCID: PMC5569574.
  16. Hildebrand DGC, Cicconet M, Torres RM, Choi W, Quan TM, Moon J, Wetzel AW, Scott Champion A, Graham BJ, Randlett O, Plummer GS, Portugues R, Bianco IH, Saalfeld S, Baden AD, Lillaney K, Burns R, Vogelstein JT, Schier AF, Lee WA, Jeong WK, Lichtman JW, Engert F. Whole-brain serial-section electron microscopy in larval zebrafish. Nature. 2017 May 18;545(7654):345-349. doi: 10.1038/nature22356. Epub 2017 May 10. PMID: 28489821; PMCID: PMC5594570.
  17. Morgan JL, Berger DR, Wetzel AW, Lichtman JW. The Fuzzy Logic of Network Connectivity in Mouse Visual Thalamus. Cell. 2016 Mar 24;165(1):192-206. doi: 10.1016/j.cell.2016.02.033. PMID: 27015312; PMCID: PMC4808248.
  18. Svara FN, Kornfeld J, Denk W, Bollmann JH. Volume EM Reconstruction of Spinal Cord Reveals Wiring Specificity in Speed-Related Motor Circuits. Cell Rep. 2018 Jun 5;23(10):2942-2954. doi: 10.1016/j.celrep.2018.05.023. PMID: 29874581.
  19. Calì C, Agus M, Kare K, Boges DJ, Lehväslaiho H, Hadwiger M, Magistretti PJ. 3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat. Prog Neurobiol. 2019 Dec;183:101696. doi: 10.1016/j.pneurobio.2019.101696. Epub 2019 Sep 21. PMID: 31550514.
  20. Schneider-Mizell CM, et al. Chandelier cell anatomy and function reveal a variably distributed but common signal. bioRxiv 2020.03.31.018952; doi:10.1101/2020.03.31.018952

References that have an entry in PubMed are saved to the collection "volume-em-pubs" located at: https://www.ncbi.nlm.nih.gov/sites/myncbi/1N1tanm0-kk/collections/59211574/public/