Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes - PubMed (original) (raw)
Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes
Mark H Longair et al. Bioinformatics. 2011.
Abstract
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.
Similar articles
- SparseTracer: the Reconstruction of Discontinuous Neuronal Morphology in Noisy Images.
Li S, Zhou H, Quan T, Li J, Li Y, Li A, Luo Q, Gong H, Zeng S. Li S, et al. Neuroinformatics. 2017 Apr;15(2):133-149. doi: 10.1007/s12021-016-9317-6. Neuroinformatics. 2017. PMID: 27928656 - Automated tracing of neurites from light microscopy stacks of images.
Chothani P, Mehta V, Stepanyants A. Chothani P, et al. Neuroinformatics. 2011 Sep;9(2-3):263-78. doi: 10.1007/s12021-011-9121-2. Neuroinformatics. 2011. PMID: 21562803 Free PMC article. - NeuronMetrics: software for semi-automated processing of cultured neuron images.
Narro ML, Yang F, Kraft R, Wenk C, Efrat A, Restifo LL. Narro ML, et al. Brain Res. 2007 Mar 23;1138:57-75. doi: 10.1016/j.brainres.2006.10.094. Epub 2007 Jan 31. Brain Res. 2007. PMID: 17270152 Free PMC article. - The DIADEM data sets: representative light microscopy images of neuronal morphology to advance automation of digital reconstructions.
Brown KM, Barrionuevo G, Canty AJ, De Paola V, Hirsch JA, Jefferis GS, Lu J, Snippe M, Sugihara I, Ascoli GA. Brown KM, et al. Neuroinformatics. 2011 Sep;9(2-3):143-57. doi: 10.1007/s12021-010-9095-5. Neuroinformatics. 2011. PMID: 21249531 Free PMC article. Review. - A rapid and sensitive automated image-based approach for in vitro and in vivo characterization of cell morphology and quantification of cell number and neurite architecture.
Tapias V, Greenamyre JT. Tapias V, et al. Curr Protoc Cytom. 2014 Apr 1;68:12.33.1-12.33.22. doi: 10.1002/0471142956.cy1233s68. Curr Protoc Cytom. 2014. PMID: 24692056 Review.
Cited by
- Voltage-gated calcium channels act upstream of adenylyl cyclase Ac78C to promote timely initiation of dendrite regeneration.
Hertzler JI, Teng J, Bernard AR, Stone MC, Kline HL, Mahata G, Kumar N, Rolls MM. Hertzler JI, et al. PLoS Genet. 2024 Aug 26;20(8):e1011388. doi: 10.1371/journal.pgen.1011388. eCollection 2024 Aug. PLoS Genet. 2024. PMID: 39186815 Free PMC article. - Mitochondrial network reorganization and transient expansion during oligodendrocyte generation.
Bame X, Hill RA. Bame X, et al. Nat Commun. 2024 Aug 14;15(1):6979. doi: 10.1038/s41467-024-51016-2. Nat Commun. 2024. PMID: 39143079 Free PMC article. - Visualizing and Measuring Dendrite Arborization in Drosophila Somatosensory Neurons.
Xu Y, Bush I, Han C. Xu Y, et al. Methods Mol Biol. 2024;2831:59-71. doi: 10.1007/978-1-0716-3969-6_5. Methods Mol Biol. 2024. PMID: 39134843 - Analysis of Neurite and Spine Formation in Neurons In Vitro.
Diaz JR, Sadowski MJ. Diaz JR, et al. Methods Mol Biol. 2024;2831:21-37. doi: 10.1007/978-1-0716-3969-6_3. Methods Mol Biol. 2024. PMID: 39134841 - Automated Quantification of Meiotic Recombination Foci Position and Intensity.
Fozard J, Morgan C. Fozard J, et al. Methods Mol Biol. 2024;2818:239-248. doi: 10.1007/978-1-0716-3906-1_16. Methods Mol Biol. 2024. PMID: 39126479
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources
Miscellaneous