TrakEM2 software for neural circuit reconstruction.

Autor: Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein, Rodney J Douglas

Publikováno v: PLoS ONE, Vol 7, Iss 6, p e38011 (2012)

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

Externí odkaz: https://doaj.org/article/cb094fa841bf4fa09b6925752f8100fd

Fiji: an open-source platform for biological-image analysis

Autor: Benjamin Schmid, Daniel J. White, Curtis Rueden, Ignacio Arganda-Carreras, Volker Hartenstein, Stephan Preibisch, Verena Kaynig, Albert Cardona, Kevin W. Eliceiri, Johannes Schindelin, Erwin Frise, Pavel Tomancak, Tobias Pietzsch, Jean-Yves Tinevez, Stephan Saalfeld, Mark Longair

Publikováno v: Nature Methods
Nature Methods, 2012, 9 (7), pp.676-682. ⟨10.1038/nmeth.2019⟩
Nature Methods, Nature Publishing Group, 2012, 9 (7), pp.676-682. ⟨10.1038/nmeth.2019⟩

International audience; Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting lan

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::deba71556343eb174f8d877c59519c58
https://doi.org/10.1038/nmeth.2019

BrainTrap: a database of 3D protein expression patterns in the Drosophila brain

Autor: Mark Longair, Seymour Knowles-Barley, J. Douglas Armstrong

Publikováno v: Europe PubMed Central
Database: The Journal of Biological Databases and Curation

Protein-trap strains of Drosophila melanogaster provide a very useful tool for examining the 3D-expression patterns of proteins and purification of protein complexes. Here we present BrainTrap, available at http://fruitfly.inf.ed.ac.uk/braintrap, an

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dc1a7eef4da87f0ae4b5718088eb444b
https://doi.org/10.1093/database/baq005

Virtual Fly Brain: An ontology-linked schema of the Drosophila Brain

Autor: J. Douglas Armstrong, Mark Longair, David Osumi-Sutherland

Publikováno v: Nature Precedings.

Drosophila neuro-anatomical data is scattered across a large, diverse literature dating back over 75 years and a growing number of community databases. Lack of a standardized nomenclature for neuro-anatomy makes comparison and searching this growing

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::c3d48de35def546ecc4b24f80456d86d
https://doi.org/10.1038/npre.2009.3980.1

Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

Autor: Mark Longair, J. Douglas Armstrong, Dean A Baker

Publikováno v: Europe PubMed Central

Motivation: Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7631dfeb6be0e75b2ac4d5610e0f7f0c
http://europepmc.org/abstract/med/21727141