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Toward a more accurate 3D atlas of C. elegans neurons
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12859_2022_Article_4738.pdf
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4.93 MB
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Adobe PDF
Checksum (MD5)
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Author(s)
Skuhersky, Michael
Wu, Tailin
Yemini, Eviatar
Nejatbakhsh, Amin
Boyden, Edward
Tegmark, Max
Date Issued
May 28, 2022
Publisher
BioMed Central
Citation
BMC Bioinformatics. 2022 May 28;23(1):195
Version
Final published version
Abstract
Abstract
Background
Determining cell identity in volumetric images of tagged neuronal nuclei is an ongoing challenge in contemporary neuroscience. Frequently, cell identity is determined by aligning and matching tags to an “atlas” of labeled neuronal positions and other identifying characteristics. Previous analyses of such C. elegans datasets have been hampered by the limited accuracy of such atlases, especially for neurons present in the ventral nerve cord, and also by time-consuming manual elements of the alignment process.
Results
We present a novel automated alignment method for sparse and incomplete point clouds of the sort resulting from typical C. elegans fluorescence microscopy datasets. This method involves a tunable learning parameter and a kernel that enforces biologically realistic deformation. We also present a pipeline for creating alignment atlases from datasets of the recently developed NeuroPAL transgene. In combination, these advances allow us to label neurons in volumetric images with confidence much higher than previous methods.
Conclusions
We release, to the best of our knowledge, the most complete full-body C. elegans 3D positional neuron atlas, incorporating positional variability derived from at least 7 animals per neuron, for the purposes of cell-type identity prediction for myriad applications (e.g., imaging neuronal activity, gene expression, and cell-fate).
Terms of Use
Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/s12859-022-04738-3
