draft_bib.html

</dt-appendix>
</body>
<script type="text/bibliography">
@article{januszewski_high-precision_2018,
	title = {High-precision automated reconstruction of neurons with flood-filling networks},
	volume = {15},
	issn = {1548-7105},
	doi = {10.1038/s41592-018-0049-4},
	number = {8},
	journal = {Nature Methods},
	author = {Januszewski, Michał and Kornfeld, Jörgen and Li, Peter H. and Pope, Art and Blakely, Tim and Lindsey, Larry and Maitin-Shepard, Jeremy and Tyka, Mike and Denk, Winfried and Jain, Viren},
	year = {2018},
	pages = {605},
        url = {https://www.nature.com/articles/s41592-018-0049-4}
}
@article{zheng_complete_2018,
	title = {A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster},
	volume = {174},
	issn = {1097-4172},
	doi = {10.1016/j.cell.2018.06.019},
	number = {3},
	journal = {Cell},
	author = {Zheng, Zhihao and Lauritzen, J. Scott and Perlman, Eric and Robinson, Camenzind G. and Nichols, Matthew and Milkie, Daniel and Torrens, Omar and Price, John and Fisher, Corey B. and Sharifi, Nadiya and Calle-Schuler, Steven A. and Kmecova, Lucia and Ali, Iqbal J. and Karsh, Bill and Trautman, Eric T. and Bogovic, John A. and Hanslovsky, Philipp and Jefferis, Gregory S. X. E. and Kazhdan, Michael and Khairy, Khaled and Saalfeld, Stephan and Fetter, Richard D. and Bock, Davi D.},
	year = {2018},
	pages = {730--743},
        url = {https://www.sciencedirect.com/science/article/pii/S0092867418307876}
}
@article{lee_superhuman_2017,
	title = {Superhuman Accuracy on the SNEMI3D Connectomics Challenge},
	url = {http://arxiv.org/abs/1706.00120},
	journal = {arXiv:1706.00120 [cs]},
	author = {Lee, Kisuk and Zung, Jonathan and Li, Peter and Jain, Viren and Seung, H. Sebastian},
	year = {2017},
}
@article{luther_learning_2019,
	title = {Learning Metric Graphs for Neuron Segmentation In Electron Microscopy Images},
	journal = {arXiv:1902.00100 [cs]},
	author = {Luther, Kyle and Seung, H. Sebastian},
	year = {2019},
}
@inproceedings{ronneberger_u-net:_2015,
	title = {U-Net: Convolutional Networks for Biomedical Image Segmentation},
	doi = {10.1007/978-3-319-24574-4_28},
	language = {en},
	booktitle = {Medical {Image} {Computing} and {Computer}-{Assisted} {Intervention} – {MICCAI} 2015},
	author = {Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
	year = {2015},
	pages = {234--241}
}
@article{turaga_maximin_2009,
	title = {Maximin affinity learning of image segmentation},
	url = {http://arxiv.org/abs/0911.5372},
	urldate = {2020-10-05},
	journal = {arXiv:0911.5372 [cs]},
	author = {Turaga, Srinivas C. and Briggman, Kevin L. and Helmstaedter, Moritz and Denk, Winfried and Seung, H. Sebastian},
	month = nov,
	year = {2009},
	note = {arXiv: 0911.5372},
	keywords = {Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Computer Science - Neural and Evolutionary Computing}
}
@article{beier2017multicut,
  title={Multicut brings automated neurite segmentation closer to human performance},
  author={Beier, Thorsten and Pape, Constantin and Rahaman, Nasim and Prange, Timo and Berg, Stuart and Bock, Davi D and Cardona, Albert and Knott, Graham W and Plaza, Stephen M and Scheffer, Louis K and others},
  journal={Nature methods},
  volume={14},
  number={2},
  pages={101--102},
  year={2017},
  publisher={Nature Publishing Group}
}
@inproceedings{cicek_3d_2016,
	title = {3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation},
	booktitle = {Medical {Image} {Computing} and {Computer}-{Assisted} {Intervention} – {MICCAI} 2016},
	author = {\c{C}i\c{c}ek, \"{O}zg\"{u}n and Abdulkadir, Ahmed and Lienkamp, Soeren S. and Brox, Thomas and Ronneberger, Olaf},
	year = {2016},
	pages = {424--432},
}
@article{funke_large_2019,
	title = {Large Scale Image Segmentation with Structured Loss Based Deep Learning for Connectome Reconstruction},
	volume = {41},
	number = {7},
	journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	author = {Funke, Jan and Tschopp, Fabian and Grisaitis, William and Sheridan, Arlo and Singh, Chandan and Saalfeld, Stephan and Turaga, Srinivas C.},
	year = {2019},
	pages = {1669--1680},
}
@incollection{ciresan_deep_2012,
	title = {Deep Neural Networks Segment Neuronal Membranes in Electron Microscopy Images},
	url = {http://papers.nips.cc/paper/4741-deep-neural-networks-segment-neuronal-membranes-in-electron-microscopy-images.pdf},
	urldate = {2020-06-30},
	booktitle = {Advances in {Neural} {Information} {Processing} {Systems} 25},
	publisher = {Curran Associates, Inc.},
	author = {Ciresan, Dan and Giusti, Alessandro and Gambardella, Luca M. and Schmidhuber, Jürgen},
	editor = {Pereira, F. and Burges, C. J. C. and Bottou, L. and Weinberger, K. Q.},
	year = {2012},
	pages = {2843--2851}
}
@article{turaga_convolutional_2010,
	title = {Convolutional Networks Can Learn to Generate Affinity Graphs for Image Segmentation},
	volume = {22},
	issn = {0899-7667},
	doi = {10.1162/neco.2009.10-08-881},
	number = {2},
	journal = {Neural Computation},
	author = {Turaga, Srinivas C. and Murray, Joseph F. and Jain, Viren and Roth, Fabian and Helmstaedter, Moritz and Briggman, Kevin and Denk, Winfried and Seung, H. Sebastian},
	month = feb,
	year = {2010},
	note = {Conference Name: Neural Computation},
	pages = {511--538}
}
@inproceedings{bai_deep_2017,
	title = {Deep Watershed Transform for Instance Segmentation},
	url = {https://openaccess.thecvf.com/content_cvpr_2017/html/Bai_Deep_Watershed_Transform_CVPR_2017_paper.html},
	urldate = {2020-06-30},
	author = {Bai, Min and Urtasun, Raquel},
	year = {2017},
	pages = {5221--5229}
}
@article{takemura_synaptic_2015,
	title = {Synaptic circuits and their variations within different columns in the visual system of Drosophila},
	volume = {112},
	issn = {0027-8424},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640747/},
	doi = {10.1073/pnas.1509820112},
	number = {44},
	urldate = {2020-07-22},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Takemura, Shin-ya and Xu, C. Shan and Lu, Zhiyuan and Rivlin, Patricia K. and Parag, Toufiq and Olbris, Donald J. and Plaza, Stephen and Zhao, Ting and Katz, William T. and Umayam, Lowell and Weaver, Charlotte and Hess, Harald F. and Horne, Jane Anne and Nunez-Iglesias, Juan and Aniceto, Roxanne and Chang, Lei-Ann and Lauchie, Shirley and Nasca, Ashley and Ogundeyi, Omotara and Sigmund, Christopher and Takemura, Satoko and Tran, Julie and Langille, Carlie and Le Lacheur, Kelsey and McLin, Sari and Shinomiya, Aya and Chklovskii, Dmitri B. and Meinertzhagen, Ian A. and Scheffer, Louis K.},
	month = nov,
	year = {2015},
	pmid = {26483464},
	pmcid = {PMC4640747},
	pages = {13711--13716},
}
@article{lee_learning_2019,
	title = {Learning Dense Voxel Embeddings for 3D Neuron Reconstruction},
	url = {http://arxiv.org/abs/1909.09872},
	urldate = {2020-09-02},
	journal = {arXiv:1909.09872 [cs]},
	author = {Lee, Kisuk and Lu, Ran and Luther, Kyle and Seung, H. Sebastian},
	month = sep,
	year = {2019},
	note = {arXiv: 1909.09872},
	keywords = {Computer Science - Computer Vision and Pattern Recognition}
}
@article{tu_auto-context_2010,
	title = {Auto-{Context} and {Its} {Application} to {High}-{Level} {Vision} {Tasks} and {3D} {Brain} {Image} {Segmentation}},
	volume = {32},
	issn = {1939-3539},
	doi = {10.1109/TPAMI.2009.186},
	number = {10},
	journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	author = {Tu, Zhuowen and Bai, Xiang},
	month = oct,
	year = {2010},
	note = {Conference Name: IEEE Transactions on Pattern Analysis and Machine Intelligence},
	pages = {1744--1757}
}
@article{meila_comparing_2007,
	title = {Comparing clusterings—an information based distance},
	volume = {98},
	issn = {0047-259X},
	url = {http://www.sciencedirect.com/science/article/pii/S0047259X06002016},
	doi = {10.1016/j.jmva.2006.11.013},
	language = {en},
	number = {5},
	urldate = {2020-09-10},
	journal = {Journal of Multivariate Analysis},
	author = {Meilă, Marina},
	month = may,
	year = {2007},
	keywords = {Agreement measures, Clustering, Comparing partitions, Information theory, Mutual information, Similarity measures},
	pages = {873--895}
}
@incollection{ferrari_mutex_2018,
	address = {Cham},
	title = {The Mutex Watershed: Efficient, Parameter-Free Image Partitioning},
	volume = {11208},
	isbn = {978-3-030-01224-3 978-3-030-01225-0},
	shorttitle = {The {Mutex} {Watershed}},
	url = {http://link.springer.com/10.1007/978-3-030-01225-0_34},
	language = {en},
	urldate = {2020-09-15},
	booktitle = {Computer {Vision} – {ECCV} 2018},
	publisher = {Springer International Publishing},
	author = {Wolf, Steffen and Pape, Constantin and Bailoni, Alberto and Rahaman, Nasim and Kreshuk, Anna and Köthe, Ullrich and Hamprecht, Fred A.},
	editor = {Ferrari, Vittorio and Hebert, Martial and Sminchisescu, Cristian and Weiss, Yair},
	year = {2018},
	doi = {10.1007/978-3-030-01225-0_34},
	note = {Series Title: Lecture Notes in Computer Science},
	pages = {571--587}
}
@article{li_automated_2019,
	title = {Automated Reconstruction of a Serial-Section EM Drosophila Brain with Flood-Filling Networks and Local Realignment},
	copyright = {© 2019, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/605634v1},
	doi = {10.1101/605634},
	language = {en},
	urldate = {2020-09-16},
	journal = {bioRxiv},
	author = {Li, Peter H. and Lindsey, Larry F. and Januszewski, Michał and Zheng, Zhihao and Bates, Alexander Shakeel and Taisz, István and Tyka, Mike and Nichols, Matthew and Li, Feng and Perlman, Eric and Maitin-Shepard, Jeremy and Blakely, Tim and Leavitt, Laramie and Jefferis, Gregory S. X. E. and Bock, Davi and Jain, Viren},
	month = apr,
	year = {2019},
	note = {Publisher: Cold Spring Harbor Laboratory Section: New Results},
	pages = {605634}
}
@article{abbott_mind_2020,
	title = {The Mind of a Mouse},
	volume = {182},
	issn = {0092-8674},
	url = {http://www.sciencedirect.com/science/article/pii/S0092867420310011},
	doi = {10.1016/j.cell.2020.08.010},
	language = {en},
	number = {6},
	urldate = {2020-09-17},
	journal = {Cell},
	author = {Abbott, Larry F. and Bock, Davi D. and Callaway, Edward M. and Denk, Winfried and Dulac, Catherine and Fairhall, Adrienne L. and Fiete, Ila and Harris, Kristen M. and Helmstaedter, Moritz and Jain, Viren and Kasthuri, Narayanan and LeCun, Yann and Lichtman, Jeff W. and Littlewood, Peter B. and Luo, Liqun and Maunsell, John H. R. and Reid, R. Clay and Rosen, Bruce R. and Rubin, Gerald M. and Sejnowski, Terrence J. and Seung, H. Sebastian and Svoboda, Karel and Tank, David W. and Tsao, Doris and Van Essen, David C.},
	month = sep,
	year = {2020},
	pages = {1372--1376}
}
@article{turner-evans_neuroanatomical_2020,
	title = {The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor},
	volume = {0},
	issn = {0896-6273},
	url = {https://www.cell.com/neuron/abstract/S0896-6273(20)30613-9},
	doi = {10.1016/j.neuron.2020.08.006},
	language = {English},
	number = {0},
	urldate = {2020-09-17},
	journal = {Neuron},
	author = {Turner-Evans, Daniel B. and Jensen, Kristopher T. and Ali, Saba and Paterson, Tyler and Sheridan, Arlo and Ray, Robert P. and Wolff, Tanya and Lauritzen, J. Scott and Rubin, Gerald M. and Bock, Davi D. and Jayaraman, Vivek},
	month = sep,
	year = {2020},
	pmid = {32916090},
	note = {Publisher: Elsevier},
	keywords = {behavior, central complex, Drosophila, electron microscopy, head direction, navigation, network dynamics, neural circuit, RNA-seq, two-photon calcium imaging}
}
@article{bates_complete_2020,
	title = {Complete Connectomic Reconstruction of Olfactory Projection Neurons in the Fly Brain},
	volume = {30},
	issn = {0960-9822},
	url = {http://www.sciencedirect.com/science/article/pii/S0960982220308587},
	doi = {10.1016/j.cub.2020.06.042},
	language = {en},
	number = {16},
	urldate = {2020-09-17},
	journal = {Current Biology},
	author = {Bates, Alexander S. and Schlegel, Philipp and Roberts, Ruairi J. V. and Drummond, Nikolas and Tamimi, Imaan F. M. and Turnbull, Robert and Zhao, Xincheng and Marin, Elizabeth C. and Popovici, Patricia D. and Dhawan, Serene and Jamasb, Arian and Javier, Alexandre and Serratosa Capdevila, Laia and Li, Feng and Rubin, Gerald M. and Waddell, Scott and Bock, Davi D. and Costa, Marta and Jefferis, Gregory S. X. E.},
	month = aug,
        year = {2020},
	keywords = {connectomics, Drosophila, EM, memory, neuroanatomy, olfaction, synapses},
	pages = {3183--3199.e6}
}
@article{motta_dense_2019,
	title = {Dense connectomic reconstruction in layer 4 of the somatosensory cortex},
	volume = {366},
	issn = {0036-8075},
	url = {https://science.sciencemag.org/content/366/6469/eaay3134},
	doi = {10.1126/science.aay3134},
	number = {6469},
	journal = {Science},
	author = {Motta, Alessandro and Berning, Manuel and Boergens, Kevin M. and Staffler, Benedikt and Beining, Marcel and Loomba, Sahil and Hennig, Philipp and Wissler, Heiko and Helmstaedter, Moritz},
	year = {2019},
	note = {Publisher: American Association for the Advancement of Science
\_eprint: https://science.sciencemag.org/content/366/6469/eaay3134.full.pdf}
}
@article{schlegel_synaptic_2016,
	title = {Synaptic transmission parallels neuromodulation in a central food-intake circuit},
	volume = {5},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.16799},
	doi = {10.7554/eLife.16799},
	urldate = {2020-09-17},
	journal = {eLife},
	author = {Schlegel, Philipp and Texada, Michael J and Miroschnikow, Anton and Schoofs, Andreas and Hückesfeld, Sebastian and Peters, Marc and Schneider-Mizell, Casey M and Lacin, Haluk and Li, Feng and Fetter, Richard D and Truman, James W and Cardona, Albert and Pankratz, Michael J},
	editor = {Calabrese, Ronald L},
	month = nov,
	year = {2016},
	note = {Publisher: eLife Sciences Publications, Ltd},
	keywords = {acetylcholine, co-transmission, endocrine, hugin, neuromedin, neuropeptides},
	pages = {e16799}
}
@article{schneider-mizell_quantitative_2016,
	title = {Quantitative neuroanatomy for connectomics in Drosophila},
	volume = {5},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.12059},
	doi = {10.7554/eLife.12059},
	urldate = {2020-09-17},
	journal = {eLife},
	author = {Schneider-Mizell, Casey M and Gerhard, Stephan and Longair, Mark and Kazimiers, Tom and Li, Feng and Zwart, Maarten F and Champion, Andrew and Midgley, Frank M and Fetter, Richard D and Saalfeld, Stephan and Cardona, Albert},
	editor = {Calabrese, Ronald L},
	month = mar,
	year = {2016},
	note = {Publisher: eLife Sciences Publications, Ltd},
	keywords = {connectomics, neuroanatomy, proprioception},
	pages = {e12059}
}
@article{briggman_volume_2012,
	series = {Neurotechnology},
	title = {Volume electron microscopy for neuronal circuit reconstruction},
	volume = {22},
	issn = {0959-4388},
	url = {http://www.sciencedirect.com/science/article/pii/S0959438811001887},
	doi = {10.1016/j.conb.2011.10.022},
	language = {en},
	number = {1},
	urldate = {2020-09-17},
	journal = {Current Opinion in Neurobiology},
	author = {Briggman, Kevin L and Bock, Davi D},
	month = feb,
	year = {2012},
	pages = {154--161}
}
@article{dorkenwald_binary_2019,
	title = {Binary and analog variation of synapses between cortical pyramidal neurons},
	copyright = {© 2019, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2019.12.29.890319v1},
	doi = {10.1101/2019.12.29.890319},
	language = {en},
	urldate = {2020-09-17},
	journal = {bioRxiv},
	author = {Dorkenwald, Sven and Turner, Nicholas L. and Macrina, Thomas and Lee, Kisuk and Lu, Ran and Wu, Jingpeng and Bodor, Agnes L. and Bleckert, Adam A. and Brittain, Derrick and Kemnitz, Nico and Silversmith, William M. and Ih, Dodam and Zung, Jonathan and Zlateski, Aleksandar and Tartavull, Ignacio and Yu, Szi-Chieh and Popovych, Sergiy and Wong, William and Castro, Manuel and Jordan, Chris S. and Wilson, Alyssa M. and Froudarakis, Emmanouil and Buchanan, JoAnn and Takeno, Marc and Torres, Russel and Mahalingam, Gayathri and Collman, Forrest and Schneider-Mizell, Casey and Bumbarger, Daniel J. and Li, Yang and Becker, Lynne and Suckow, Shelby and Reimer, Jacob and Tolias, Andreas S. and Costa, Nuno Maçarico da and Reid, R. Clay and Seung, H. Sebastian},
	month = dec,
	year = {2019},
	note = {Publisher: Cold Spring Harbor Laboratory Section: New Results},
	pages = {2019.12.29.890319}
}
@article{maniates-selvin_reconstruction_2020,
	title = {Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy},
	copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2020.01.10.902478v1},
	doi = {10.1101/2020.01.10.902478},
	language = {en},
	urldate = {2020-09-17},
	journal = {bioRxiv},
	author = {Maniates-Selvin, Jasper T. and Hildebrand, David Grant Colburn and Graham, Brett J. and Kuan, Aaron T. and Thomas, Logan A. and Nguyen, Tri and Buhmann, Julia and Azevedo, Anthony W. and Shanny, Brendan L. and Funke, Jan and Tuthill, John C. and Lee, Wei-Chung Allen},
	month = jan,
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory Section: New Results},
	pages = {2020.01.10.902478}
}
@article{heinrich_synaptic_2018,
	title = {Synaptic Cleft Segmentation in Non-Isotropic Volume Electron Microscopy of the Complete Drosophila Brain},
	url = {http://arxiv.org/abs/1805.02718},
	urldate = {2020-09-17},
	journal = {arXiv:1805.02718 [cs]},
	author = {Heinrich, Larissa and Funke, Jan and Pape, Constantin and Nunez-Iglesias, Juan and Saalfeld, Stephan},
	month = may,
	year = {2018},
	note = {arXiv: 1805.02718},
	keywords = {Computer Science - Computer Vision and Pattern Recognition}
}
@article{scheffer_connectome_2020,
	title = {A Connectome and Analysis of the Adult Drosophila Central Brain},
	copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2020.04.07.030213v1},
	doi = {10.1101/2020.04.07.030213},
	language = {en},
	urldate = {2020-09-17},
	journal = {bioRxiv},
	author = {Scheffer, Louis K. and Xu, C. Shan and Januszewski, Michal and Lu, Zhiyuan and Takemura, Shin-ya and Hayworth, Kenneth J. and Huang, Gary B. and Shinomiya, Kazunori and Maitin-Shepard, Jeremy and Berg, Stuart and Clements, Jody and Hubbard, Philip and Katz, William and Umayam, Lowell and Zhao, Ting and Ackerman, David and Blakely, Tim and Bogovic, John and Dolafi, Tom and Kainmueller, Dagmar and Kawase, Takashi and Khairy, Khaled A. and Leavitt, Laramie and Li, Peter H. and Lindsey, Larry and Neubarth, Nicole and Olbris, Donald J. and Otsuna, Hideo and Trautman, Eric T. and Ito, Masayoshi and Goldammer, Jens and Wolff, Tanya and Svirskas, Robert and Schlegel, Philipp and Neace, Erika R. and Knecht, Christopher J. and Alvarado, Chelsea X. and Bailey, Dennis A. and Ballinger, Samantha and Borycz, Jolanta A. and Canino, Brandon S. and Cheatham, Natasha and Cook, Michael and Dreher, Marisa and Duclos, Octave and Eubanks, Bryon and Fairbanks, Kelli and Finley, Samantha and Forknall, Nora and Francis, Audrey and Hopkins, Gary Patrick and Joyce, Emily M. and Kim, SungJin and Kirk, Nicole A. and Kovalyak, Julie and Lauchie, Shirley A. and Lohff, Alanna and Maldonado, Charli and Manley, Emily A. and McLin, Sari and Mooney, Caroline and Ndama, Miatta and Ogundeyi, Omotara and Okeoma, Nneoma and Ordish, Christopher and Padilla, Nicholas and Patrick, Christopher and Paterson, Tyler and Phillips, Elliott E. and Phillips, Emily M. and Rampally, Neha and Ribeiro, Caitlin and Robertson, Madelaine K. and Rymer, Jon Thomson and Ryan, Sean M. and Sammons, Megan and Scott, Anne K. and Scott, Ashley L. and Shinomiya, Aya and Smith, Claire and Smith, Kelsey and Smith, Natalie L. and Sobeski, Margaret A. and Suleiman, Alia and Swift, Jackie and Takemura, Satoko and Talebi, Iris and Tarnogorska, Dorota and Tenshaw, Emily and Tokhi, Temour and Walsh, John J. and Yang, Tansy and Horne, Jane Anne and Li, Feng and Parekh, Ruchi and Rivlin, Patricia K. and Jayaraman, Vivek and Ito, Kei and Saalfeld, Stephan and George, Reed and Meinertzhagen, Ian A. and Rubin, Gerald M. and Hess, Harald F. and Jain, Viren and Plaza, Stephen M.},
	month = apr,
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory
Section: New Results},
	pages = {2020.04.07.030213}
}
@inproceedings{kreshuk_who_2015,
	address = {Cham},
	series = {Lecture {Notes} in {Computer} {Science}},
	title = {Who Is Talking to Whom: Synaptic Partner Detection in Anisotropic Volumes of Insect Brain},
	isbn = {978-3-319-24553-9},
	shorttitle = {Who {Is} {Talking} to {Whom}},
	doi = {10.1007/978-3-319-24553-9_81},
	language = {en},
	booktitle = {Medical {Image} {Computing} and {Computer}-{Assisted} {Intervention} -- {MICCAI} 2015},
	publisher = {Springer International Publishing},
	author = {Kreshuk, Anna and Funke, Jan and Cardona, Albert and Hamprecht, Fred A.},
	editor = {Navab, Nassir and Hornegger, Joachim and Wells, William M. and Frangi, Alejandro},
	year = {2015},
	keywords = {Circuit reconstruction, electron microscopy, graphical model},
	pages = {661--668}
}
@article{buhmann_synaptic_2018,
	title = {Synaptic partner prediction from point annotations in insect brains},
	url = {http://arxiv.org/abs/1806.08205},
	urldate = {2020-09-17},
	journal = {arXiv:1806.08205 [cs]},
	author = {Buhmann, Julia and Krause, Renate and Lentini, Rodrigo Ceballos and Eckstein, Nils and Cook, Matthew and Turaga, Srinivas and Funke, Jan},
	month = jul,
	year = {2018},
	note = {arXiv: 1806.08205},
	keywords = {Computer Science - Computer Vision and Pattern Recognition}
}
@article{buhmann_automatic_2020,
	title = {Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset},
	copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2019.12.12.874172v2},
	doi = {10.1101/2019.12.12.874172},
	language = {en},
	urldate = {2020-09-17},
	journal = {bioRxiv},
	author = {Buhmann, Julia and Sheridan, Arlo and Gerhard, Stephan and Krause, Renate and Nguyen, Tri and Heinrich, Larissa and Schlegel, Philipp and Lee, Wei-Chung Allen and Wilson, Rachel and Saalfeld, Stephan and Jefferis, Gregory and Bock, Davi and Turaga, Srinivas and Cook, Matthew and Funke, Jan},
	month = mar,
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory
Section: New Results},
	pages = {2019.12.12.874172}
}
@article{huang_fully-automatic_2018,
	title = {Fully-Automatic Synapse Prediction and Validation on a Large Data Set},
	volume = {12},
	issn = {1662-5110},
	url = {https://www.frontiersin.org/articles/10.3389/fncir.2018.00087/full},
	doi = {10.3389/fncir.2018.00087},
	language = {English},
	urldate = {2020-09-17},
	journal = {Frontiers in Neural Circuits},
	author = {Huang, Gary B. and Scheffer, Louis K. and Plaza, Stephen M.},
	year = {2018},
	note = {Publisher: Frontiers},
	keywords = {connectomics, deep learning, Drosophila, Evaluation, synapse prediction}
}
@article{plaza_analyzing_2018,
	title = {Analyzing Image Segmentation for Connectomics},
	volume = {12},
	issn = {1662-5110},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6243088/},
	doi = {10.3389/fncir.2018.00102},
	urldate = {2020-09-23},
	journal = {Frontiers in Neural Circuits},
	author = {Plaza, Stephen M. and Funke, Jan},
	month = nov,
	year = {2018},
	pmid = {30483069},
	pmcid = {PMC6243088}
}
@article{kornfeld_em_2017,
	title = {EM connectomics reveals axonal target variation in a sequence-generating network},
	volume = {6},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.24364},
	doi = {10.7554/eLife.24364},
	urldate = {2020-10-05},
	journal = {eLife},
	author = {Kornfeld, Jörgen and Benezra, Sam E and Narayanan, Rajeevan T and Svara, Fabian and Egger, Robert and Oberlaender, Marcel and Denk, Winfried and Long, Michael A},
	editor = {Svoboda, Karel},
	month = mar,
	year = {2017},
	note = {Publisher: eLife Sciences Publications, Ltd},
	keywords = {birdsong, connectomics, neural sequences, synfire chains, zebra finch},
	pages = {e24364}
}
@article{schneider-mizell_chandelier_2020,
	title = {Chandelier cell anatomy and function reveal a variably distributed but common signal},
	copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2020.03.31.018952v1},
	doi = {10.1101/2020.03.31.018952},
	language = {en},
	urldate = {2020-10-05},
	journal = {bioRxiv},
	author = {Schneider-Mizell, Casey M. and Bodor, Agnes L. and Collman, Forrest and Brittain, Derrick and Bleckert, Adam A. and Dorkenwald, Sven and Turner, Nicholas L. and Macrina, Thomas and Lee, Kisuk and Lu, Ran and Wu, Jingpeng and Zhuang, Jun and Nandi, Anirban and Hu, Brian and Buchanan, JoAnn and Takeno, Marc M. and Torres, Russel and Mahalingam, Gayathri and Bumbarger, Daniel J. and Li, Yang and Chartrand, Tom and Kemnitz, Nico and Silversmith, William M. and Ih, Dodam and Zung, Jonathan and Zlateski, Aleksandar and Tartavull, Ignacio and Popovych, Sergiy and Wong, William and Castro, Manuel and Jordan, Chris S. and Froudarakis, Emmanouil and Becker, Lynne and Suckow, Shelby and Reimer, Jacob and Tolias, Andreas S. and Anastassiou, Costas and Seung, H. Sebastian and Reid, R. Clay and Costa, Nuno Maçarico da},
	month = apr,
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory
Section: New Results},
	pages = {2020.03.31.018952}
}
@article{yin_petascale_2020,
	title = {A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy},
	volume = {11},
	copyright = {2020 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-020-18659-3},
	doi = {10.1038/s41467-020-18659-3},
	language = {en},
	number = {1},
	urldate = {2020-10-05},
	journal = {Nature Communications},
	author = {Yin, Wenjing and Brittain, Derrick and Borseth, Jay and Scott, Marie E. and Williams, Derric and Perkins, Jedediah and Own, Christopher S. and Murfitt, Matthew and Torres, Russel M. and Kapner, Daniel and Mahalingam, Gayathri and Bleckert, Adam and Castelli, Daniel and Reid, David and Lee, Wei-Chung Allen and Graham, Brett J. and Takeno, Marc and Bumbarger, Daniel J. and Farrell, Colin and Reid, R. Clay and da Costa, Nuno Macarico},
	month = oct,
	year = {2020},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {4949}
}
@article{rand_objective_1971,
	title = {Objective Criteria for the Evaluation of Clustering Methods},
	volume = {66},
	issn = {0162-1459},
	url = {https://www.jstor.org/stable/2284239},
	doi = {10.2307/2284239},
	abstract = {Many intuitively appealing methods have been suggested for clustering data, however, interpretation of their results has been hindered by the lack of objective criteria. This article proposes several criteria which isolate specific aspects of the performance of a method, such as its retrieval of inherent structure, its sensitivity to resampling and the stability of its results in the light of new data. These criteria depend on a measure of similarity between two different clusterings of the same set of data; the measure essentially considers how each pair of data points is assigned in each clustering.},
	number = {336},
	urldate = {2020-10-05},
	journal = {Journal of the American Statistical Association},
	author = {Rand, William M.},
	year = {1971},
	note = {Publisher: [American Statistical Association, Taylor \& Francis, Ltd.]},
	pages = {846--850}
}
@article{turner-evans_insect_2016,
	title = {The insect central complex},
	volume = {26},
	issn = {09609822},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982216303232},
	doi = {10.1016/j.cub.2016.04.006},
	language = {en},
	number = {11},
	urldate = {2020-10-08},
	journal = {Current Biology},
	author = {Turner-Evans, Daniel B. and Jayaraman, Vivek},
	month = jun,
	year = {2016},
	pages = {R453--R457},
	file = {Turner-Evans and Jayaraman - 2016 - The insect central complex.pdf:/Users/ArloS/Zotero/storage/LR7BU6C3/Turner-Evans and Jayaraman - 2016 - The insect central complex.pdf:application/pdf}
}
@incollection{maitin-shepard_combinatorial_2016,
	title = {Combinatorial Energy Learning for Image Segmentation},
	url = {http://papers.nips.cc/paper/6595-combinatorial-energy-learning-for-image-segmentation.pdf},
	urldate = {2020-10-13},
	booktitle = {Advances in {Neural} {Information} {Processing} {Systems} 29},
	publisher = {Curran Associates, Inc.},
	author = {Maitin-Shepard, Jeremy B and Jain, Viren and Januszewski, Michal and Li, Peter and Abbeel, Pieter},
	editor = {Lee, D. D. and Sugiyama, M. and Luxburg, U. V. and Guyon, I. and Garnett, R.},
	year = {2016},
	pages = {1966--1974},
	file = {NIPS Full Text PDF:/Users/ArloS/Zotero/storage/VUAW9P2C/Maitin-Shepard et al. - 2016 - Combinatorial Energy Learning for Image Segmentati.pdf:application/pdf;NIPS Snapshot:/Users/ArloS/Zotero/storage/A5AP8YLR/6595-combinatorial-energy-learning-for-image-segmentation.html:text/html}
}
@article{nguyen2020daisy,
	title={Daisy: A Library for Block-Wise Task Scheduling for Large nD Volumes},
	author={Nguyen, Tri and Malin-Mayor, Caroline and Patton, William and Funke, Jan},
	journal={in preparation},
	year={2020}
}
@article{funke_ted_2017,
	series = {Image {Processing} for {Biologists}},
	title = {TED: A Tolerant Edit Distance for segmentation evaluation},
	volume = {115},
	issn = {1046-2023},
	shorttitle = {{TED}},
	url = {http://www.sciencedirect.com/science/article/pii/S1046202316305072},
	doi = {10.1016/j.ymeth.2016.12.013},
	language = {en},
	urldate = {2020-10-28},
	journal = {Methods},
	author = {Funke, Jan and Klein, Jonas and Moreno-Noguer, Francesc and Cardona, Albert and Cook, Matthew},
	month = feb,
	year = {2017},
	keywords = {Computer vision, Electron microscopy, Evaluation, Learning, Neuron segmentation, Segmentation},
	pages = {119--127},
	file = {ScienceDirect Full Text PDF:/Users/ArloS/Zotero/storage/P4UBBSN6/Funke et al. - 2017 - TED A Tolerant Edit Distance for segmentation eva.pdf:application/pdf;ScienceDirect Snapshot:/Users/ArloS/Zotero/storage/YSBFR2GJ/S1046202316305072.html:text/html}
}
@inproceedings{plaza_focused_2016,
	address = {Cham},
	series = {Lecture {Notes} in {Computer} {Science}},
	title = {Focused Proofreading to Reconstruct Neural Connectomes from EM Images at Scale},
	isbn = {978-3-319-46976-8},
	doi = {10.1007/978-3-319-46976-8_26},
	language = {en},
	booktitle = {Deep {Learning} and {Data} {Labeling} for {Medical} {Applications}},
	publisher = {Springer International Publishing},
	author = {Plaza, Stephen M.},
	editor = {Carneiro, Gustavo and Mateus, Diana and Peter, Loïc and Bradley, Andrew and Tavares, João Manuel R. S. and Belagiannis, Vasileios and Papa, João Paulo and Nascimento, Jacinto C. and Loog, Marco and Lu, Zhi and Cardoso, Jaime S. and Cornebise, Julien},
	year = {2016},
	keywords = {Automatic Segmentation, Edge Probability, Initial Segmentation, Optic Lobe, Synaptic Connection},
	pages = {249--258},
	file = {Springer Full Text PDF:/Users/ArloS/Zotero/storage/JNG5MEDQ/Plaza - 2016 - Focused Proofreading to Reconstruct Neural Connect.pdf:application/pdf}
}
@article{gallusser_2020,
  title={Deep-Learning-Based Automatic Organelle Segmentation in 3D Electron Microscopy Datasets},
  author={Gallusser, Benjamin and Vadakkan, Tegy John and Sahasrabudhe, Mihir and Di Caprio, Giuseppe and Kirchhausen, Tom},
  journal={in preparation},
  year={2020}
}
@article{hildebrand_whole-brain_2017,
	title = {Whole-brain serial-section electron microscopy in larval zebrafish},
	volume = {545},
	copyright = {2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature22356},
	doi = {10.1038/nature22356},
	abstract = {A complete larval zebrafish brain is examined and its myelinated axons reconstructed using serial-section electron microscopy, revealing remarkable symmetry and providing a valuable resource.},
	language = {en},
	number = {7654},
	urldate = {2020-11-11},
	journal = {Nature},
	author = {Hildebrand, David Grant Colburn and Cicconet, Marcelo and Torres, Russel Miguel and Choi, Woohyuk and Quan, Tran Minh and Moon, Jungmin and Wetzel, Arthur Willis and Scott Champion, Andrew and Graham, Brett Jesse and Randlett, Owen and Plummer, George Scott and Portugues, Ruben and Bianco, Isaac Henry and Saalfeld, Stephan and Baden, Alexander David and Lillaney, Kunal and Burns, Randal and Vogelstein, Joshua Tzvi and Schier, Alexander Franz and Lee, Wei-Chung Allen and Jeong, Won-Ki and Lichtman, Jeff William and Engert, Florian},
	month = may,
	year = {2017},
	note = {Number: 7654
Publisher: Nature Publishing Group},
	pages = {345--349},
	file = {Full Text PDF:/Users/ArloS/Zotero/storage/MXUPZ29N/Hildebrand et al. - 2017 - Whole-brain serial-section electron microscopy in .pdf:application/pdf;Snapshot:/Users/ArloS/Zotero/storage/NYCZKHWR/nature22356.html:text/html}
}
@article{saalfeld2009catmaid,
	title={CATMAID: collaborative annotation toolkit for massive amounts of image data},
	author={Saalfeld, Stephan and Cardona, Albert and Hartenstein, Volker and Toman{\v{c}}{\'a}k, Pavel},
	journal={Bioinformatics},
	volume={25},
	number={15},
	pages={1984--1986},
	year={2009},
	publisher={Oxford University Press}
}
@article{boergens_webknossos_2017,
	title = {webKnossos: efficient online {3D} data annotation for connectomics},
	volume = {14},
	copyright = {2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1548-7105},
	shorttitle = {{webKnossos}},
	url = {https://www.nature.com/articles/nmeth.4331},
	doi = {10.1038/nmeth.4331},
	language = {en},
	number = {7},
	urldate = {2020-11-16},
	journal = {Nature Methods},
	author = {Boergens, Kevin M. and Berning, Manuel and Bocklisch, Tom and Bräunlein, Dominic and Drawitsch, Florian and Frohnhofen, Johannes and Herold, Tom and Otto, Philipp and Rzepka, Norman and Werkmeister, Thomas and Werner, Daniel and Wiese, Georg and Wissler, Heiko and Helmstaedter, Moritz},
	month = jul,
	year = {2017},
	note = {Number: 7
Publisher: Nature Publishing Group},
	pages = {691--694},
	file = {Full Text PDF:/Users/ArloS/Zotero/storage/VDHQQKL2/Boergens et al. - 2017 - webKnossos efficient online 3D data annotation fo.pdf:application/pdf;Snapshot:/Users/ArloS/Zotero/storage/CQJI3QWJ/nmeth.html:text/html}
}
@article{berger_vast_2018,
	title = {VAST (Volume Annotation and Segmentation Tool): Efficient
        Manual and Semi-Automatic Labeling of Large 3D Image Stacks},
	volume = {12},
	issn = {1662-5110},
	shorttitle = {{VAST} ({Volume} {Annotation} and {Segmentation} {Tool})},
	url = {https://www.frontiersin.org/articles/10.3389/fncir.2018.00088/full},
	doi = {10.3389/fncir.2018.00088},
	language = {English},
	urldate = {2020-11-16},
	journal = {Frontiers in Neural Circuits},
	author = {Berger, Daniel R. and Seung, H. Sebastian and Lichtman, Jeff W.},
	year = {2018},
	note = {Publisher: Frontiers},
	keywords = {CLEM, connectomics, proofreading, segmentation, serial section electron microscopy, tracing, TrakEM2, visualization, Voxel},
	file = {Full Text PDF:/Users/ArloS/Zotero/storage/DBQWS7DN/Berger et al. - 2018 - VAST (Volume Annotation and Segmentation Tool) Ef.pdf:application/pdf}
}
@article{zhao_neutu_2018,
	title = {NeuTu: Software for Collaborative, Large-Scale, Segmentation-Based Connectome Reconstruction},
	volume = {12},
	issn = {1662-5110},
	shorttitle = {{NeuTu}},
	url = {https://www.frontiersin.org/articles/10.3389/fncir.2018.00101/full},
	doi = {10.3389/fncir.2018.00101},
	language = {English},
	urldate = {2020-11-16},
	journal = {Frontiers in Neural Circuits},
	author = {Zhao, Ting and Olbris, Donald J. and Yu, Yang and Plaza, Stephen M.},
	year = {2018},
	note = {Publisher: Frontiers},
	keywords = {connectome, Electron microscopy, NeuTu, proofreading, Segmentation (Image processing)},
	file = {Full Text PDF:/Users/ArloS/Zotero/storage/4WPFZEFA/Zhao et al. - 2018 - NeuTu Software for Collaborative, Large-Scale, Se.pdf:application/pdf}
}


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