TrakEM2 software for neural circuit reconstruction
Albert Cardona,Stephan Saalfeld,Johannes Schindelin,Ignacio Arganda-Carreras,Stephan Preibisch,Mark Longair,Pavel Tomancak,Volker Hartenstein,Rodney J. Douglas +8 more
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TLDR
A software application, TrakEM2, is designed that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes and addresses the challenges of image volume composition from individual, deformed images.Abstract:
A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.read more
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Fiji: an open-source platform for biological-image analysis
Johannes Schindelin,Ignacio Arganda-Carreras,Erwin Frise,Verena Kaynig,Mark Longair,Tobias Pietzsch,Stephan Preibisch,Curtis Rueden,Stephan Saalfeld,Benjamin Schmid,Jean-Yves Tinevez,Daniel J. White,Volker Hartenstein,Kevin W. Eliceiri,Pavel Tomancak,Albert Cardona +15 more
TL;DR: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis that facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.
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A visual motion detection circuit suggested by Drosophila connectomics
Shin-ya Takemura,Arjun Bharioke,Zhiyuan Lu,Zhiyuan Lu,Aljoscha Nern,Shiv Naga Prasad Vitaladevuni,Patricia K. Rivlin,William T. Katz,Donald J. Olbris,Stephen M. Plaza,Philip Brown Winston,Ting Zhao,Jane Anne Horne,Richard D. Fetter,Satoko Takemura,Katerina Blazek,Lei-Ann Chang,Omotara Ogundeyi,Mathew A. Saunders,Victor Shapiro,Christopher Sigmund,Gerald M. Rubin,Louis K. Scheffer,Ian A. Meinertzhagen,Ian A. Meinertzhagen,Dmitri B. Chklovskii +25 more
TL;DR: A semi-automated pipeline using electron microscopy is developed to reconstruct a connectome, containing 379 neurons and 8,637 chemical synaptic contacts, within the Drosophila optic medulla, and it is demonstrated that connectomes can provide key insights into neuronal computations.
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A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster.
Zhihao Zheng,J. Scott Lauritzen,Eric Perlman,Camenzind G. Robinson,Matthew Nichols,Daniel E. Milkie,O. N. Torrens,J.H. Price,Corey B. Fisher,Nadiya Sharifi,Steven A. Calle-Schuler,Lucia Kmecova,Iqbal J. Ali,Bill Karsh,Eric T. Trautman,John A. Bogovic,Philipp Hanslovsky,Gregory S.X.E. Jefferis,Gregory S.X.E. Jefferis,Michael Kazhdan,Khaled Khairy,Stephan Saalfeld,Richard D. Fetter,Davi D. Bock +23 more
TL;DR: Recon reconstructions of the entire brain of an adult female fly show that this freely available EM volume supports mapping of brain-spanning circuits, which will significantly accelerate Drosophila neuroscience.
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Ultrafast endocytosis at mouse hippocampal synapses
Shigeki Watanabe,Benjamin R. Rost,Marcial Camacho-Perez,M. Wayne Davis,Berit Söhl-Kielczynski,Christian Rosenmund,Erik M. Jorgensen +6 more
TL;DR: Optogenetics is used to stimulate cultured hippocampal neurons with a single stimulus, rapidly freeze them after fixed intervals and examine the ultrastructure using electron microscopy—‘flash-and-freeze’ electron microscopes; it is likely that ‘ultrafast endocytosis’ is specialized to restore the surface area of the membrane rapidly.
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