ATUM Reference List

Papers & Publications

This is a list of papers and other publications that mention the use of the ATUM. Although not exhaustive, we plan to update this list on a continual basis. If you see any errors  or have papers to add, feel free to contact our editor at rmcsnews(at)boeckeler(dot)com.

July 7, 2016Reconstruction of genetically identified neurons imaged by serial-section electron microscopy (eLife). (Maximilian Joesch, David Mankus, Masahito Yamagata, Ali Shahbazi, Richard Schalek, Adi Suissa-Peleg, Markus Meister, Jeff W Lichtman, Walter J Scheirer, and Joshua R Sanes) Discusses targeted reconstruction of specific neuronal types as an alternative strategy for complete circuit reconstruction. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959841/.

June 2016High-Throughput, High-Resolution Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing (Cell). — (Takayasu Mikuni, Jun Nishiyama, Ye Sun, Naomi Kamasawa, and Ryohei Yasuda) Paper discusses a scalable and high-throughput method to identify precise subcellular localization of endogenous proteins essential for integrative understanding of a cell at the molecular level. (Register for full access) http://www.cell.com/cell/abstract/S0092-8674(16)30489-5.

January 21, 2016A Role for the RMC ATUMtome & RMC Advanced Substrate Holder in CLEM and NanoSIMS Research (RMC article). — How these instruments can fulfill a role beyond connectomics, including morphological analysis in CLEM and nanoSIMS. Download the PDF.

August 2015On the Road to Large Volumes in LM and SEM: New Tools for Array Tomography  (Microscopy & Microanalysis). (Irene Wacker, Waldmar Spomer, Andreas Hofmann, Ulrich Gengenbach, Marlene Thaler, Len Ness, Pat Brey and Rasmus R. Schroder) Paper discusses the advantage of array tomography over serial blockface methods of reconstructing large volumes of samples at ultra-structural resolution.  (Pay for full access) http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9918154

August 2015Advanced Substrate Holder and Multi-Axis Tool for Ultramicrotomy (Microscopy & Microanalysis). (Waldemar Spomer, Andreas Hofmann, Irene Wacker, Lenn Ness, Pat Brey, Rasmus . Schroder and Ulrich Gengenbach). A novel, multi-axis device is now being developed to support ultramicotome users in transferring sections onto a solid substrate. (Pay for full access.)  http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9919140#

July 30, 2015 — Cell, Saturated Reconstruction of a Volume of Neocortex (Lichtman Lab). This paper describes a suite of automated technologies designed to probe the structure of neural tissue at nanometer resolution, including the ATUMtome. This approach is used to generate a “saturated” reconstruction of a 1500 cubic micron sub-volume of mouse neocortex. Several related links provided below:

Lab’s Introhttps://www.mcb.harvard.edu/mcb/news/news-detail/3821/reconstructing-the-brains-wiring-diagram-lichtman-lab/

PDF of paper at: https://www.mcb.harvard.edu/mcb_files/media/editor_uploads/2015/07/PIIS0092867415008247.pdf

Related video: http://lichtmanlab.fas.harvard.edu/files/lichtman/files/lichtman_cell_2015.mp4

April 13, 2015 — Nature Methods, High-resolution whole-brain staining for electron microscopic circuit reconstruction ( Shawn Mikula & Winfried Denk). Currently only electron microscopy provides the resolution necessary to reconstruct neuronal circuits completely and with single-synapse resolution … “Our results suggest that the BROPA method can produce a preparation suitable for the reconstruction of neural circuits spanning an entire mouse brain.” Full article may require subscription. http://www.nature.com/nmeth/journal/v12/n6/full/nmeth.3361.html

March/April 2015 — Microscopy & Analysis (Wiley), The ATUMtome for automated serial sectioning and 3-D imaging (Paul Webster, Dave Bentley, Jonelle Kearney)  Online PDF reproduced from Microscopy and Analysis ©2015 John Wiley and Sons Ltd

February 2015 — Microscopy, Oxford Journals, New Developments in Electron Microscopy for Serial Image Acquisition of Neuronal Profiles (Yoshiyuki Kubota). Covers recent developments in electron microscopy that largely automate the continuous acquisition of serial electron micrographs (EMGs). http://jmicro.oxfordjournals.org/content/64/1/27.full?sid=c6cd6532-de6e-49af-9fcb-878aa8e59cd7

October 23, 2014 — Oxford Journals, Review: Mission (im)possible — mapping the brain becomes an reality (Anna Lena Eberle, Olaf Selchow,  Marlene Thaler, Dirk Zeidler and Robert Kirmse)  http://jmicro.oxfordjournals.org/content/64/1/45.full.pdf?keytype=ref&ijkey=vzgj1nAZfGBItHz

October 20, 2014 — Microscopy & Microanalysis, Positional correlative anatomy of invertebrate model organisms increases efficiency of TEM data production. (Kolotuev) Includes some interesting approaches to specimen preparation. http://www.ncbi.nlm.nih.gov/pubmed/25180638

October 3, 2014 – Biorxiv.org, Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics (Adam H. Marblestone,
Evan R. Daugharthy, Reza Kalhor, Ian D. Peikon, Justus M. Kebschull, Seth L. Shipman, Yuriy Mishchenko, Jehyuk Lee, David A. Dalrymple, Bradley M. Zamft, Konrad P. Kording, Edward S. Boyden, Anthony M. Zador and George M. Church)  http://biorxiv.org/content/biorxiv/early/2014/04/20/001214.full.pdf

June 27, 2014 – Frontiers in Neural Circuits, Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits  ( Kenneth J. Hayworth, Josh L. Morgan, Richard Schalek, Daniel R. Berger,David G. C. Hildebrand and Jeff W. Lichtman)  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073626/

July 18, 2013 — Cell, Stacked endoplasmic reticulum sheets are connected by helicoidal membrane motifs (Mark Terasaki, Tom Shemesh, Narayanan Kasthuri,Robin W. Klemm,Richard Schalek, Kenneth J. Hayworth,Arthur R. Hand,Maya Yankova,Greg Huber,Jeff W. Lichtman,Tom A. Rapoport,and Michael M. Kozlov) http://www.cell.com/cell/abstract/S0092-8674%2813%2900770-8?_returnURL=http%3A%2%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867413007708%3Fshowall%3Dtrue

2014 – University of Heidelberg, Dissertation: Learning-based Segmentation for ConnectomicsDissertation (Diplom-Physiker Thorben Kroger) http://archiv.ub.uni-heidelberg.de/volltextserver/16834/1/diss.pdf

2014 – University of California at Berkley, Optimization-Based Artifact Correction for Electron Microscopy Image Stacks (Samaneh Azadi,
Jeremy Maitin-Shepard and Pieter Abbeel) http://link.springer.com/chapter/10.1007/978-3-319-10605-2_15#page-1

May 2013 – Nature Methods, Focus on Mapping the Brain (Erika Pastrana)   http://www.nature.com/nmeth/journal/v10/n6/full/nmeth.2509.html

2013 – Journal of Cell Science, Commentary: Is EM dead? (Graham Knott and Christel Genoud)   http://jcs.biologists.org/content/126/20/4545.full

2013 – Stanford University, On the Technology Prospects and Investment Opportunities for Scalable Neuroscience (Thomas Dean, Biafra Ahanonu, Mainak Chowdhury, Anjali Datta, Andre Esteva, Daniel Eth, Nobie Redmon, Oleg Rumyantsev, Ysis Tarter)  http://web.stanford.edu/class/cs379c/course_projects_topics/report/

July 2012 — Microscopy & Analysis, ATUM-based SEM for High-Speed Large-Volume Biological Reconstructions  ($$) (R. Schalek, A. Wilson, J. Lichtman, M. Josh, N. Kasthuri, D. Berger, S. Seung, P. Anger, K. Hayworth and D. Aderhold)   http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8758526

April 16, 2012 – PLOS One, Serial Section Scanning Electron Microscopy (S3EM) on Silicon Wafers for Ultra-Structural Volume Imaging of Cells and Tissues (Heinz Horstmann, Christoph Körber, Kurt Sätzler, Daniel Aydin, Thomas Kune) http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035172

January 12, 2012 — Nature Protocols, FESEM images of adult Drosophila brain ultrathin section mounted on Kapton tape. ( Juan Carlos Tapia, Narayanan Kasthuri, Kenneth J Hayworth, Richard Schalek, Jeff W Lichtman, Stephen J Smith & JoAnn Buchanan) http://www.nature.com/nprot/journal/v7/n2/fig_tab/nprot.2011.439_F7.html

November 24, 2011 — Science Direct, Volume electron microscopy for neuronal circuit reconstruction (Kevin L Briggman and Davi D Bock)  https://archive.org/stream/pdfy-jFNzCxKoDhqFxdNq/2012-briggman_djvu.txt

2011 — Microscopy & Microanalysis, Development of High Throughput, High Resolution 3D Reconstruction of Large Volume Biological Tissue Using Automated Tape Collection Ultramicrotomy and Scanning Electron Microscopy (R Schalek, N Kasthuri, K Hayworth, D Berger, J Tapia, J Morgan, S Turaga, E Fagerholm, H Seung and J Lichtman) http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8396995&fileId=S1431927611005708

 

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