Mark Longair PhD

Mark Longair


Publications:
2011
  Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes
Longair, M, Baker, DA & Armstrong, JD 2011, 'Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes' Bioinformatics, vol 27, no. 17, pp. 2453-2454. DOI: 10.1093/bioinformatics/btr390
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 datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer.Availability: Simple Neurite Tracer is open source software, licensed under the GNU General Public Licence (GPL) and based on the public domain image processing software ImageJ. The software and further documentation are available via http://fiji.sc/Simple_Neurite_Tracer as part of the package Fiji, and can be used on Windows, Mac OS and Linux. Documentation and introductory screencasts are available at the same URL.Contact: longair@ini.phys.ethz.ch; longair@ini.phys.ethz.ch
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Longair, Mark, Baker, Dean A. & Armstrong, J. Douglas.
Keywords: (, , . )
Number of pages: 2
Pages: 2453-2454
Publication Date: 2011
Publication Information
Category: Article
Journal: Bioinformatics
Volume: 27
Issue number: 17
Original Language: English
DOIs: 10.1093/bioinformatics/btr390
2010
  BrainTrap: a database of 3D protein expression patterns in the Drosophila brain
Knowles-Barley, S, Longair, M & Armstrong, JD 2010, 'BrainTrap: a database of 3D protein expression patterns in the Drosophila brain' Database: The Journal of Biological Databases and Curation, vol 2010, baq005, pp. 1-9. DOI: 10.1093/database/baq005
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 online database of 3D confocal datasets showing reporter gene expression and protein localization in the adult brain of Drosophila. Full size images throughout the volume of the entire brain can be viewed interactively in a web browser. The database includes searchable annotations linked to the FlyBase Drosophila anatomy ontology. Anatomical search criteria can be specified using automatic completion and a hierarchical browser for the ontology. The provenance of all annotation is retained and the location where the annotator made the conclusion can be highlighted.Database URL: http://fruitfly.inf.ed.ac.uk/braintrap
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Knowles-Barley, Seymour, Longair, Mark & Armstrong, J Douglas.
Number of pages: 9
Pages: 1-9
Publication Date: 2010
Publication Information
Category: Article
Journal: Database: The Journal of Biological Databases and Curation
Volume: 2010
Original Language: English
DOIs: 10.1093/database/baq005
  A high-level 3D visualization API for Java and ImageJ
Schmid, B, Schindelin, J, Cardona, A, Longair, M & Heisenberg, M 2010, 'A high-level 3D visualization API for Java and ImageJ' BMC Bioinformatics, vol 11, no. 1, pp. 274. DOI: 10.1186/1471-2105-11-274
Background
Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.

Results
Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts.

Conclusions
Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de webcite.
General Information
Organisations: Neuroinformatics DTC.
Authors: Schmid, Benjamin, Schindelin, Johannes, Cardona, Albert, Longair, Mark & Heisenberg, Martin.
Pages: 274
Publication Date: 1 Jan 2010
Publication Information
Category: Article
Journal: BMC Bioinformatics
Volume: 11
Issue number: 1
ISSN: 1471-2105
Original Language: English
DOIs: 10.1186/1471-2105-11-274
2009
  BrainTrap: The Fly Brain Protein Trap Database
Knowles-Barley, S, Longair, M & Armstrong, D 2009, 'BrainTrap: The Fly Brain Protein Trap Database' Neurobiology of Drosophila, Cold Spring Harbor , United States, 29/09/09 - 3/10/09, .
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 BrainTrap is an online database of 3D confocal datasets showing reporter gene expression and protein localisation in the adult brain of Drosophila; it provides a valuable resource for further Drosophila neurobiology and protein research.
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Knowles-Barley, Seymour, Longair, Mark & Armstrong, Douglas.
Publication Date: 2009
Publication Information
Category: Poster
Original Language: English
2008
  Sub-mm observations of the HDF (Serjeant+, 2003)
Serjeant, S, Dunlop, JS, Mann, RG, Rowan-Robinson, M, Hughes, D, Efstathiou, A, Blain, A, Fox, M, Ivison, RJ, Jenness, T, Lawrence, A, Longair, M, Oliver, S & Peacock, JA 2008, 'Sub-mm observations of the HDF (Serjeant+, 2003)' VizieR On-line Data Catalog, vol 734, pp. 40887.
We present an extended analysis of the Submillimetre Common User Bolometer Array (SCUBA) observations of the Hubble Deep Field (HDF), expanding the areal coverage of the Hughes et al. (1998Natur.394..241H) study by a factor of ~1.8 and containing at least three further sources in addition to the five in that study. We also announce the public release of the reduced data products. The map is the deepest ever made in the submillimetre (submm), obtained in excellent conditions (median 850-{mu}m optical depth of 0.16). (1 data file).
General Information
Organisations: Neuroinformatics DTC.
Authors: Serjeant, S., Dunlop, J. S., Mann, R. G., Rowan-Robinson, M., Hughes, D., Efstathiou, A., Blain, A., Fox, M., Ivison, R. J., Jenness, T., Lawrence, A., Longair, Mark, Oliver, S. & Peacock, J. A..
Keywords: (Millimetric/submm sources. )
Pages: 40887
Publication Date: 1 Sep 2008
Publication Information
Category: Article
Journal: VizieR On-line Data Catalog
Volume: 734
Original Language: English

Projects:
Investigating MASC with drosophila orthologues (PhD)

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