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FIB-SEM Technology / Selected Publications
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FIB-SEM Technology Publications
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11/20/20 | Automatic whole cell organelle segmentation in volumetric electron microscopy.

Gunes Parlakgul, Ana Paula Arruda, Erika Cagampan, Song Pang, Ekin Guney, Yankun Lee, Harald F. Hess, C. Shan Xu, Gokhan S. Hotamisligil.​​​
bioRxiv. 2020.11.18.387803.  2020  November 20  doi: 10.1101/2020.11.18.387803

11/16/20 | Automatic whole cell organelle segmentation in volumetric electron microscopy.

Larissa Heinrich, Davis Bennett, David Ackerman, Woohyun Park, John Bogovic, Nils Eckstein, Alyson Petruncio, Jody Clements, C. Shan Xu, Jan Funke, Wyatt Korff, Harald F. Hess, Jennifer Lippincott-Schwartz, Stephan Saalfeld, Aubrey V. Weigel, COSEM Project Team.​​​
bioRxiv. 2020.11.14.382143.  2020  November 16  doi: 10.1101/2020.11.14.382143

11/14/20 | Isotropic 3D electron microscopy reference library of whole cells and tissues.

C. Shan Xu, Song Pang, Gleb Shtengel, Andreas Müller, Alex T. Ritter, Huxley K. Hoffman, Shin-ya Takemura, Zhiyuan Lu, H. Amalia Pasolli, Nirmala Iyer, Jeeyun Chung, Davis Bennett, Aubrey V. Weigel, Tobias C. Walther, Robert V. Farese Jr., Schuyler B. van Engelenburg, Ira Mellman, Michele Solimena, Harald F. Hess.​​​
bioRxiv. 2020.11.13.382457.  2020  November 14  doi: 10.1101/2020.11.13.382457

10/10/20 | Three-dimensional FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse beta cells.

Andreas Müller, Deborah Schmidt, C. Shan Xu, Song Pang, Joyson Verner D’Costa, Susanne Kretschmar, Carla Münster, Thomas Kurth, Florian Jug, Martin Weigert, Harald F. Hess, Michele Solimena.​​​
bioRxiv. 2020.10.07.329268.  2020 October 10  doi: 10.1101/2020.10.07.329268

09/23/20 | Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin.

Ezequiel Miron, Roel Oldenkamp, Jill M. Brown, David M.S.Pinto, C. Shan Xu, Ana R. Faria, Haitham A. Shaban, James D. P. Rhodes, Cassandravictoria Innocent, Sara de Ornellas, Harald F. Hess, Veronica Buckle, Lothar Schermelleh​​​
Science Advances. 23 Sep 2020; Vol. 6, no. 39, eaba8811 doi: 10.1126/sciadv.aba8811

09/03/20 | A connectome and analysis of the adult Drosophila central brain.

Louis K Scheffer*, C Shan Xu*, Michal Januszewski*, Zhiyuan Lu*, Shin-ya Takemura*, Kenneth J Hayworth*, Gary B Huang*, Kazunori Shinomiya*, et al.​​​
eLife. 2020 Sep 3;9:e57443 doi: 10.7554/eLife.57443

06/30/20 | Transforming FIB-SEM Systems for Large-Volume Connectomics and Cell Biology.

C. Shan Xu‡​​​, Song Pang, Kenneth J. Hayworth, Harald F. Hess​​​
Volume Microscopy. Neuromethods, vol 155. Humana, New York, NY. 2020 June 30  doi: 10.1007/978-1-0716-0691-9_12

06/02/20 | Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas.

José G. García-Cerdán, Eva M. Schmid, Tomomi Takeuchi, Ian McRae, Kent L. McDonald, Nichakarn Yordduangjun, Ahmed M. Hassan, Patricia Grob, C. Shan Xu, Harald F. Hess, Daniel A. Fletcher, Eva Nogales, Krishna K. Niyogi
Proceedings of the National Academy of Sciences of the U S A. 2020 June 2; 117(22):1-12.  doi: 10.1073/pnas.1916948117

03/24/20 | Enhanced FIB-SEM systems for large-volume 3D Imaging.

C. Shan Xu‡, Kenneth J. Hayworth, Harald F. Hess.
US Patent.  Patent No.: 10,600,615 .  Patent Granted Date: March 24, 2020

01/21/20 | A Connectome of the Adult Drosophila Central Brain.

C. Shan Xu‡, Michal Januszewski, Zhiyuan Lu, Shin-ya Takemura, Kenneth Hayworth, Gary Huang, Kazunori Shinomiya, et al.
bioRxiv 2020.01.21.911859. 2020 January 21  doi: 10.1101/2020.01.21.911859 

01/16/20 | Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Click to free download [Full text or Reprint]

David P. Hoffman, Gleb Shtengel, C. Shan Xu, Kirby R. Campbell, Melanie Freeman, Lei Wang, Daniel E. Milkie, H. Amalia Pasolli, Nirmala Iyer, John A. Bogovic, Daniel R. Stabley, Abbas Shirinifard, Song Pang, David Peale, Kathy Schaefer, Wim Pomp, Chi-Lun Chang, Jennifer Lippincott-Schwartz, Tom Kirchhausen, David J. Solecki, Eric Betzig, Harald F. Hess​​​
Science. 2020, Jan 17; 367(6475):eaaz5357  doi: 10.1126/science.aaz5357  [Cover Page]

11/27/19 | En bloc preparation of Drosophila brains enables high-throughput FIB-SEM connectomics.

Zhiyuan Lu, C. Shan Xu, Kenneth J. Hayworth, Patricia Rivlin, Stephen M. Plaza, Louis Scheffer, Gerald M. Rubin, Harald F. Hess, Ian A. Meinertzhagen​​​
bioRxiv 855130. 2019 November 27  doi: 10.1101/855130

6/21/19 | Spastin tethers lipid droplets to peroxisomes and directs fatty acid trafficking through ESCRT-III.

Chi-Lun Chang, Aubrey V. Weigel, Maria S. Ioannou, H. Amalia Pasolli, C. Shan Xu, David R. Peale, Gleb Shtengel, Melanie Freeman, Harald F. Hess, Craig Blackstone, Jennifer Lippincott-Schwartz​​​
Journal of Cell Biology. 2019 June 21;218 (8): 2583. doi: 10.1083/jcb.201902061

5/30/19 | Neuron-astrocyte metabolic coupling protects against activity-induced fatty acid toxicity.

Ioannou MS, Jackson J, Sheu S, Chang C, Weigel AV, Liu H, Pasolli HA, Xu CS, Pang S, Matthies D, Hess HF, Lippincott-Schwartz J, Liu Z​​​
Cell. 2019 May 30;177(6):1522-1535.e14. doi: 10.1016/j.cell.2019.04.001

1/18/19 | Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.

Ruixuan Gao, Shoh M. Asano1, Srigokul Upadhyayula, Igor Pisarev, Daniel E. Milkie, Tsung-Li Liu, Ved Singh, Austin Graves, Grace H. Huynh, Yongxin Zhao, John Bogovic, Jennifer Colonell, Carolyn M. Ott, Christopher Zugates, Susan Tappan, Alfredo Rodriguez, Kishore R. Mosaliganti, Shu-Hsien Sheu, H. Amalia Pasolli, Song Pang, C. Shan Xu, Sean G. Megason, Harald Hess, Jennifer Lippincott-Schwartz, Adam Hantman, Gerald M. Rubin, Tom Kirchhausen, Stephan Saalfeld, Yoshinori Aso, Edward S. Boyden, Eric Betzig​​​
Science. 2019 Jan 18; 363(6424):eaau8302. doi: 10.1126/science.aau8302   [Cover Page]

11/09/18 | Comparisons between the ON- and OFF-edge motion pathways in the brain.

Shinomiya K, Huang G, Lu Z, Parag T, Xu C.Shan, Aniceto R, Ansari N, Cheatham N, Lauchie S, Neace E, Ogundeyi O, Ordish C, Peel D, Shinomiya A, Smith C, Takemura S, Talebi I, Rivlin PK, Nern A, Scheffer LK, Plaza SM, Meinertzhagen IA​
eLife. 2019 Jan 09;8:. doi:10.7554/eLife.40025

11/01/18 | A Resource for the antennal lobe provided by the connectome of glomerulus VA1v.

Home JA, Langille C, McLin S, Wiederman M, Lu Z, Xu C.Shan, Plaza SM, Scheffer LK, Hess HF, Meinertzhagen IA​
eLife. 2018 Nov 01;7:. doi:10.7554/eLife.37550

07/24/18 | The ESCRT-III Protein CHMP1A Mediates Secretion of Sonic Hedgehog on a Distinctive Subtype of Extracellular Vesicles.

Michael E. Coulter, Cristina M.Dorobantu, Gerrald A.Lodewijk, Francois Delalande, Sarah Cianferani, Vijay S.Ganesh, Richard S.Smith, Elaine T.Lim, C.Shan Xu, Song Pang, Eric T.Wong, Hart G.W.Lidov Monica L.Calicchio, Edward Yang, Dilenny M.Gonzalez, Thorsten M.Schlaeger, Ganeshwaran H.Mochida, Harald Hess, Christopher A.Walsh
Cell Reports. 2018 Jul 24;24(4):973-986.e8. doi:10.1016/j.celrep.2018.06.100 

04/25/18 | A novel sheet-like virus particle array is a hallmark of Zika virus infection.

Liu J, Kline BA, Kenny TA, Smith DR, Soloveva V, Beitzel B, Pang S, Lockett S, Hess HF, Palacios G, Kuhn JH, Sun MG, Zeng X 
Emerging Microbes & Infections. 2018 Apr 25;7(1):69. doi: 10.1038/s41426-018-0071-8

07/18/17 | A connectome of a learning and memory center in the adult Drosophila brain.

Takemura S, Aso Y, Hige T, Wong AM, Lu Z, Xu C.Shan, Rivlin PK, Hess HF, Zhao T, Parag T, Berg S, Huang G, Katz WT, Olbris DJ, Plaza SM, Umayam LA, Aniceto R, Chang L, Lauchie S, et al 
eLife. 2017 Jul 18;6:. doi: 10.7554/eLife: 26975

05/30/17 | Contacts between the endoplasmic reticulum and other membranes in neurons. 

Wu Y, Whiteus C, Xu C.Shan, Hayworth KJ, Weinberg RJ, Hess HF, De Camilli P
Proceedings of the National Academy of Sciences of the United States of America. 2017 May 30:. doi: 10.1073/pnas.1701078114

Xu C.Shan‡, Hayworth KJ, Lu Z, Grob P, Hassan AM, García-Cerdán JG, Niyogi KK, Nogales E, Weinberg RJ, Hess HF
eLife. 2017 May 13;6:. doi: 10.7554/eLife: 25916
Nature Methods. 2017 June 29; 14, 653 (2017):. doi: 10.1038/nmeth.4349
Jonathon Nixon-Abell
Christopher J. Obara
Aubrey V. Weigel,
Dong Li
Wesley R. Legant,  
C. Shan Xu
H. Amalia Pasolli,  
Kirsten Harvey,  
Harald F. Hess,  
Eric Betzig
Craig Blackstone,  
Jennifer Lippincott-Schwartz
Sciences (New York, N.Y.) 2016 Oct 28; 354(6311): 433-46
Takemura S, Xu C.Shan, Lu Z, Rivlin PK, Parag T, Olbris DJ, Plaza S, Zhao T, Katz WT, Umayam L, Weaver C, Hess HF, Horne JAnne, Nunez-Iglesias J, Aniceto R, Chang L, Lauchie S, Nasca A, Ogundeyi O, Sigmund C, Takemura S, Tran J, Langille C, Le Lacheur K, McLin S, Shinomiya A, Chklovskii DB, Meinertzhagen IA, Scheffer LK
Proceedings of the National Academy of Sciences of the United States of America. 2015 Nov 3;112(44):13711-6. doi: 10.1073/pnas.1509820112

02/16/15 | Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics.
Hayworth KJ, Xu C.Shan, Lu Z, Knott GW, Fetter RD, Tapia JCarlos, Lichtman JW, Hess HF
Nature Methods. 2015 Feb 16:. doi: 10.1038/nmeth.3292

08/02/13 | Electron microscopy reconstruction of brain structure using sparse representations over learned dictionaries.
Hu T, Nunez-Iglesias J, Vitaladevuni S, Scheffer L, Xu C.Shan, Bolorizadeh M, Hess H, Fetter R, Chklovskii D
IEEE Transactions on Medical Imaging. 2013 Aug 2;32(12):2179-88. doi: 10.1109/TMI.2013.2276018
10/01/12 | Super-resolution using sparse representations over learned dictionaries: reconstruction of brain structure using electron microscopy.
Hu T, Nunez-Iglesias J, Vitaladevuni S, Scheffer L, Xu C.Shan, Bolorizadeh M, Hess H, Fetter R, Chklovskii D
arXiv.org . 2012 Oct:

01/01/11 | High resolution segmentation of neuronal tissues from low depth-resolution EM imagery.   Glasner D, Hu T, Nunez-Iglesias J, Scheffer L, Xu C.Shan, Hess H, Fetter R, Chklovskii D, Basri R. 8th International Conference of Energy Minimization Methods in Computer Vision and Pattern Recognition Energy Minimization Methods in Computer Vision and Pattern Recognition. 2011;6819:261-72