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NeuroPAL: A Neuronal Polychromatic Atlas of Landmarks for Whole-Brain Imaging in C. elegans

Eviatar Yemini, Albert Lin, Amin Nejatbakhsh, Erdem Varol, Ruoxi Sun, Gonzalo E. Mena, Aravinthan D.T. Samuel, Liam Paninski, Vivek Venkatachalam, View ORCID ProfileOliver Hobert
doi: https://doi.org/10.1101/676312
Eviatar Yemini
1Department of Biological Sciences, Columbia University, New York
2Howard Hughes Medical Institute
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Albert Lin
3Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA
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Amin Nejatbakhsh
4Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York
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Erdem Varol
4Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York
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Ruoxi Sun
1Department of Biological Sciences, Columbia University, New York
4Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York
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Gonzalo E. Mena
5Department of Statistics and Data Science Initiative, Harvard University, Cambridge, MA
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Aravinthan D.T. Samuel
3Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA
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Liam Paninski
4Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York
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Vivek Venkatachalam
6Department of Physics, Northeastern University, Boston, MA
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Oliver Hobert
1Department of Biological Sciences, Columbia University, New York
2Howard Hughes Medical Institute
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  • ORCID record for Oliver Hobert
  • For correspondence: or38@columbia.edu
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ABSTRACT

Comprehensively resolving single neurons and their cellular identities from whole-brain fluorescent images is a major challenge. We achieve this in C. elegans through the engineering and use of a multicolor transgene called NeuroPAL (a Neuronal Polychromatic Atlas of Landmarks). NeuroPAL worms share a stereotypical multicolor fluorescence map for the entire hermaphrodite nervous system that allows comprehensive determination of neuronal identities. Neurons labeled with NeuroPAL do not exhibit fluorescence in the green, cyan, or yellow emission channels, allowing the transgene to be used with numerous reporters of gene expression or neuronal dynamics. Here we showcase three studies that leverage NeuroPAL for nervous-system-wide neuronal identification. First, we determine the brainwide expression patterns of all metabotropic receptors for acetylcholine, GABA, and glutamate, completing a map of this communication network. Second, we uncover novel changes in cell fate caused by transcription factor mutations. Third, we record brainwide activity in response to attractive and repulsive chemosensory cues, characterizing multimodal coding and novel neuronal asymmetries for these stimuli. We present a software package that enables semi-automated determination of all neuronal identities based on color and positional information. The NeuroPAL framework and software provide a means to design landmark atlases for other tissues and organisms. In conclusion, we expect NeuroPAL to serve as an invaluable tool for gene expression analysis, neuronal fate studies, and for mapping whole-brain activity patterns.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted July 03, 2020.
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NeuroPAL: A Neuronal Polychromatic Atlas of Landmarks for Whole-Brain Imaging in C. elegans
Eviatar Yemini, Albert Lin, Amin Nejatbakhsh, Erdem Varol, Ruoxi Sun, Gonzalo E. Mena, Aravinthan D.T. Samuel, Liam Paninski, Vivek Venkatachalam, Oliver Hobert
bioRxiv 676312; doi: https://doi.org/10.1101/676312
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NeuroPAL: A Neuronal Polychromatic Atlas of Landmarks for Whole-Brain Imaging in C. elegans
Eviatar Yemini, Albert Lin, Amin Nejatbakhsh, Erdem Varol, Ruoxi Sun, Gonzalo E. Mena, Aravinthan D.T. Samuel, Liam Paninski, Vivek Venkatachalam, Oliver Hobert
bioRxiv 676312; doi: https://doi.org/10.1101/676312

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