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Items: 1 to 20 of 107

1.

SynEM, automated synapse detection for connectomics.

Staffler B, Berning M, Boergens KM, Gour A, Smagt PV, Helmstaedter M.

Elife. 2017 Jul 14;6. pii: e26414. doi: 10.7554/eLife.26414.

2.

SegEM: Efficient Image Analysis for High-Resolution Connectomics.

Berning M, Boergens KM, Helmstaedter M.

Neuron. 2015 Sep 23;87(6):1193-1206. doi: 10.1016/j.neuron.2015.09.003.

3.

Large-volume en-bloc staining for electron microscopy-based connectomics.

Hua Y, Laserstein P, Helmstaedter M.

Nat Commun. 2015 Aug 3;6:7923. doi: 10.1038/ncomms8923.

4.

webKnossos: efficient online 3D data annotation for connectomics.

Boergens KM, Berning M, Bocklisch T, Bräunlein D, Drawitsch F, Frohnhofen J, Herold T, Otto P, Rzepka N, Werkmeister T, Werner D, Wiese G, Wissler H, Helmstaedter M.

Nat Methods. 2017 Jul;14(7):691-694. doi: 10.1038/nmeth.4331. Epub 2017 Jun 12.

PMID:
28604722
5.

Extracellular space preservation aids the connectomic analysis of neural circuits.

Pallotto M, Watkins PV, Fubara B, Singer JH, Briggman KL.

Elife. 2015 Dec 9;4. pii: e08206. doi: 10.7554/eLife.08206.

6.

Rapid and Semi-automated Extraction of Neuronal Cell Bodies and Nuclei from Electron Microscopy Image Stacks.

Holcomb PS, Morehead M, Doretto G, Chen P, Berg S, Plaza S, Spirou G.

Methods Mol Biol. 2016;1427:277-90. doi: 10.1007/978-1-4939-3615-1_16.

7.

Recent advancement in the challenges to connectomics.

Ohno N, Katoh M, Saitoh Y, Saitoh S.

Microscopy (Oxf). 2016 Apr;65(2):97-107. doi: 10.1093/jmicro/dfv371. Epub 2015 Dec 15. Review.

PMID:
26671942
8.

Effective automated pipeline for 3D reconstruction of synapses based on deep learning.

Xiao C, Li W, Deng H, Chen X, Yang Y, Xie Q, Han H.

BMC Bioinformatics. 2018 Jul 13;19(1):263. doi: 10.1186/s12859-018-2232-0.

9.

Three-dimensional spatial distribution of synapses in the neocortex: a dual-beam electron microscopy study.

Merchán-Pérez A, Rodríguez JR, González S, Robles V, Defelipe J, Larrañaga P, Bielza C.

Cereb Cortex. 2014 Jun;24(6):1579-88. doi: 10.1093/cercor/bht018. Epub 2013 Jan 30.

10.

Rapid method for electron tomographic reconstruction and three-dimensional modeling of the murine synapse using an automated fiducial marker-free system.

Kim HW, Oh SH, Kim N, Nakazawa E, Rhyu IJ.

Microsc Microanal. 2013 Aug;19 Suppl 5:182-7. doi: 10.1017/S1431927613012622.

PMID:
23920202
11.

Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images.

Kreshuk A, Straehle CN, Sommer C, Koethe U, Cantoni M, Knott G, Hamprecht FA.

PLoS One. 2011;6(10):e24899. doi: 10.1371/journal.pone.0024899. Epub 2011 Oct 21.

12.

The effects of aging on neuropil structure in mouse somatosensory cortex-A 3D electron microscopy analysis of layer 1.

Calì C, Wawrzyniak M, Becker C, Maco B, Cantoni M, Jorstad A, Nigro B, Grillo F, De Paola V, Fua P, Knott GW.

PLoS One. 2018 Jul 2;13(7):e0198131. doi: 10.1371/journal.pone.0198131. eCollection 2018.

13.

FluoEM, virtual labeling of axons in three-dimensional electron microscopy data for long-range connectomics.

Drawitsch F, Karimi A, Boergens KM, Helmstaedter M.

Elife. 2018 Aug 14;7. pii: e38976. doi: 10.7554/eLife.38976.

14.

VAST (Volume Annotation and Segmentation Tool): Efficient Manual and Semi-Automatic Labeling of Large 3D Image Stacks.

Berger DR, Seung HS, Lichtman JW.

Front Neural Circuits. 2018 Oct 16;12:88. doi: 10.3389/fncir.2018.00088. eCollection 2018.

15.

A multiscale parallel computing architecture for automated segmentation of the brain connectome.

Jaume S, Knobe K, Newton RR, Schlimbach F, Blower M, Reid RC.

IEEE Trans Biomed Eng. 2012 Jan;59(1):35-8. doi: 10.1109/TBME.2011.2168396. Epub 2011 Sep 15.

16.

Connectome of the fly visual circuitry.

Takemura SY.

Microscopy (Oxf). 2015 Feb;64(1):37-44. doi: 10.1093/jmicro/dfu102. Epub 2014 Dec 17. Review.

PMID:
25525121
17.

Learning context cues for synapse segmentation.

Becker C, Ali K, Knott G, Fua P.

IEEE Trans Med Imaging. 2013 Oct;32(10):1864-77. doi: 10.1109/TMI.2013.2267747. Epub 2013 Jun 11.

PMID:
23771317
18.

A modular hierarchical approach to 3D electron microscopy image segmentation.

Liu T, Jones C, Seyedhosseini M, Tasdizen T.

J Neurosci Methods. 2014 Apr 15;226:88-102. doi: 10.1016/j.jneumeth.2014.01.022. Epub 2014 Jan 31.

19.

Unbiased, High-Throughput Electron Microscopy Analysis of Experience-Dependent Synaptic Changes in the Neocortex.

Chandrasekaran S, Navlakha S, Audette NJ, McCreary DD, Suhan J, Bar-Joseph Z, Barth AL.

J Neurosci. 2015 Dec 16;35(50):16450-62. doi: 10.1523/JNEUROSCI.1573-15.2015.

20.

ConnectomeExplorer: query-guided visual analysis of large volumetric neuroscience data.

Beyer J, Al-Awami A, Kasthuri N, Lichtman JW, Pfister H, Hadwiger M.

IEEE Trans Vis Comput Graph. 2013 Dec;19(12):2868-77. doi: 10.1109/TVCG.2013.142.

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