The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
TrakEM2 Software for Neural Circuit Reconstruction
Open accessAbstract
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.
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Cites
Fiji: an open-source platform for biological-image analysis
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890
Self-citationDistinctive Image Features from Scale-Invariant Keypoints
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Computer Visualization of Three-Dimensional Image Data Using IMOD
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“The turning point in this quest occurred in 1986, when Sydney Brenner and collaborators published their monumental work, the complete wiring diagram of the nematode Caenorhabditis elegans, with only 302 neurons [24].”
BackgroundAutomated electron microscope tomography using robust prediction of specimen movements
Mastronarde, D. N. (2005) · Journal of Structural Biology · doi:10.1016/j.jsb.2005.07.007 · Cited by 5,336
A faster algorithm for betweenness centrality*
Brandes, U. (2001) · The Journal of Mathematical Sociology · doi:10.1080/0022250x.2001.9990249 · Cited by 4,936
Adaptive histogram equalization and its variations
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Globally optimal stitching of tiled 3D microscopic image acquisitions
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Self-citationAutomated molecular microscopy: The new Leginon system
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Cited by
Fiji: an open-source platform for biological-image analysis
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890
Self-citationThe ImageJ ecosystem: An open platform for biomedical image analysis
Schindelin, J., Rueden, C. T., Hiner, M. C., & Eliceiri, K. W. (2015) · Molecular Reproduction and Development · doi:10.1002/mrd.22489 · Cited by 2,636
Self-citationA Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster
Zheng, Z., Lauritzen, J. S., Perlman, E., Robinson, C. G., Nichols, M., Milkie, D., Torrens, O., Price, J., Fisher, C. B., Sharifi, N., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.019 · Cited by 1,050
Self-citationMartin, J. C., Chang, C., Boschetti, G., Ungaro, R., Giri, M., Grout, J. A., Gettler, K., Chuang, L.-S., Nayar, S., Greenstein, A. J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.008 · Cited by 872
A visual motion detection circuit suggested by Drosophila connectomics
Takemura, S.-Y., Bharioke, A., Lu, Z., Nern, A., Vitaladevuni, S., Rivlin, P. K., Katz, W. T., Olbris, D. J., Plaza, S. M., Winston, P., et al. (2013) · Nature · doi:10.1038/nature12450 · Cited by 686
Metadata
- Authors
- Cardona, A., Saalfeld, S., Schindelin, J., Arganda-Carreras, I., Preibisch, S., Longair, M., Tomancak, P., Hartenstein, V., & Douglas, R. J.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-06-19
- Volume
- 7
- Issue
- 6
- Pages
- e38011
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2147762902
- Cited by
- 1,013
- References
- 42
- FWCI
- 19.96
- Type
- journal article
- Language
- en
- Open access
- gold
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