Semi-Automated Reconstruction of Neural Processes from Large Numbers of Fluorescence Images
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Semi-Automated Reconstruction of Neural Processes from Large Numbers of Fluorescence Images
| Title: | Semi-Automated Reconstruction of Neural Processes from Large Numbers of Fluorescence Images |
| Author: |
Fiala, John C.; Lu, Ju; Lichtman, Jeff
Note: Order does not necessarily reflect citation order of authors. |
| Citation: | Lu, Ju, John C. Fiala, and Jeff W. Lichtman. 2009. Semi-Automated Reconstruction of Neural Processes from Large Numbers of Fluorescence Images. PLoS ONE 4(5): e5655. |
| Full Text & Related Files: |
2682575.pdf (2.172Mb; PDF) 
|
| Abstract: | We introduce a method for large scale reconstruction of complex bundles of neural processes from fluorescent image stacks. We imaged yellow fluorescent protein labeled axons that innervated a whole muscle, as well as dendrites in cerebral cortex, in transgenic mice, at the diffraction limit with a confocal microscope. Each image stack was digitally re-sampled along an orientation such that the majority of axons appeared in cross-section. A region growing algorithm was implemented in the open-source Reconstruct software and applied to the semi-automatic tracing of individual axons in three dimensions. The progression of region growing is constrained by user-specified criteria based on pixel values and object sizes, and the user has full control over the segmentation process. A full montage of reconstructed axons was assembled from the ∼200 individually reconstructed stacks. Average reconstruction speed is ∼0.5 mm per hour. We found an error rate in the automatic tracing mode of ∼1 error per 250 um of axonal length. We demonstrated the capacity of the program by reconstructing the connectome of motor axons in a small mouse muscle. |
| Published Version: | doi:10.1371/journal.pone.0005655 |
| Other Sources: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682575/pdf/ |
| Terms of Use: | This article is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#OAP |
| Citable link to this page: | http://nrs.harvard.edu/urn-3:HUL.InstRepos:4457680 |
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Peer reviewed scholarly articles from the Faculty of Arts and Sciences of Harvard University
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