TY - JOUR
T1 - NeuroPAL
T2 - A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans
AU - Yemini, Eviatar
AU - Lin, Albert
AU - Nejatbakhsh, Amin
AU - Varol, Erdem
AU - Sun, Ruoxi
AU - Mena, Gonzalo E.
AU - Samuel, Aravinthan D.T.
AU - Paninski, Liam
AU - Venkatachalam, Vivek
AU - Hobert, Oliver
N1 - Funding Information:
We thank Qi Chen for generating transgenic lines. We thank Molly Booth Reilly, Ibnul Rafi, and Emily Berghoff for alpha testing the NeuroPAL software. We thank Eduardo Leyva-Díaz for ehs-1prom7 and Michael Koelle for a gbb-2 reporter fosmid. We thank David Hall, Zeynep Altun, and Chris Crocker for use of the WormAtlas N2S/T/U EM reconstructions and Steven Cook for instruction in tracing these EM reconstructions. We thank Michael Z. Lin, Vladislav Verkhusha, and Robert E. Campbell for their considerable help in choosing fluorescent proteins. We thank Benjamin White and Wesley Grueber for their considerable help conceptualizing NeuroPAL applications in Drosophila; Guangwei Si and Jessleen Kanwal for their advice on microfluidics design and operation; Scott Linderman and Andrew Leifer for many helpful discussions regarding automated neuronal identification; and members of the Hobert, Chalfie, Paninski, and Samuel labs for comments on the manuscript. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). Microfluidics devices were manufactured using the Soft Materials Cleanroom facility of the Harvard MRSEC (DMR-1420570). O.H. was funded by the Howard Hughes Medical Institute and NSF-CRCNS Award (1912194). E.Y. was funded in part by the NIH (5T32DK7328-37, 5T32DK007328-35, 5T32MH015174-38, and 5T32MH015174-37). L.P. was funded by the NIBIB R01 (EB22913), NSF NeuroNex Award (DBI-1707398), NSF-CRCNS Award (1912194), the Simons Collaboration on the Global Brain, and the Gatsby Charitable Foundation. G.E.M. was funded by the Harvard Data Science Initiative Postdoctoral Fellowship. A.D.T.S. was funded by the NIH (1R01NS113119-01) and NSF (IOS-1452593), A.L. by the NSF Physics of Living Systems Graduate Student Research Network (1806818), and V.V. by the Burroughs Wellcome Fund Career Award at the Scientific Interface. All authors contributed in writing this manuscript. O.H. initiated the project. E.Y. designed and built NeuroPAL, designed and performed all non-stimulus behavioral phenotyping, traced the EM reconstructions, conducted all metabotropic receptor and mutant experiments, generated the panneuronal GCaMP6s strain, and performed the non-automated identification of activity traces. A.L. designed and performed all chemotactic assays. A.L. A.D.T.S. and V.V. designed and built the whole-brain imaging scope and microfluidic device then, together with E.Y. and O.H. designed the whole-brain imaging experiments that were all conducted in the A.D.T.S. lab. A.L. performed all whole-brain imaging experiments. A.N. E.V. L.P. and V.V. designed and built the software for whole-brain activity imaging that connects neurons with their identities, then extracts, de-mixes, and normalizes neuronal activity traces. A.L. E.Y. and V.V. designed and built the software to analyze the whole-brain imaging data. A.N. E.V. G.E.M. L.P. and R.S. computed the neuronal positional variability atlas, designed the semi-automated identification algorithms and software with accuracy validations, and together with E.Y. built the GUI. E.V. designed and built software to compute coloring for NeuroPAL applications and E.Y. generated the accompanying analysis. E.Y. designed the FlyPAL concept. Correspondence about calcium imaging and physiology is to be addressed to A.L. (albertlin@g.harvard.edu), V.V. (v.venkatachalam@northeastern.edu), and E.Y. (eiy1@columbia.edu). Correspondence about algorithms for semi-automated cell identification is to be addressed to A.N. (mn2822@columbia.edu), E.V. (ev2430@columbia.edu), and E.Y. (eiy1@columbia.edu). The authors declare no competing interests.
Funding Information:
We thank Qi Chen for generating transgenic lines. We thank Molly Booth Reilly, Ibnul Rafi, and Emily Berghoff for alpha testing the NeuroPAL software. We thank Eduardo Leyva-Díaz for ehs-1 prom7 and Michael Koelle for a gbb-2 reporter fosmid. We thank David Hall, Zeynep Altun, and Chris Crocker for use of the WormAtlas N2S/T/U EM reconstructions and Steven Cook for instruction in tracing these EM reconstructions. We thank Michael Z. Lin, Vladislav Verkhusha, and Robert E. Campbell for their considerable help in choosing fluorescent proteins. We thank Benjamin White and Wesley Grueber for their considerable help conceptualizing NeuroPAL applications in Drosophila; Guangwei Si and Jessleen Kanwal for their advice on microfluidics design and operation; Scott Linderman and Andrew Leifer for many helpful discussions regarding automated neuronal identification; and members of the Hobert, Chalfie, Paninski, and Samuel labs for comments on the manuscript. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs ( P40 OD010440 ). Microfluidics devices were manufactured using the Soft Materials Cleanroom facility of the Harvard MRSEC ( DMR-1420570 ). O.H. was funded by the Howard Hughes Medical Institute and NSF-CRCNS Award ( 1912194 ). E.Y. was funded in part by the NIH ( 5T32DK7328-37 , 5T32DK007328-35 , 5T32MH015174-38 , and 5T32MH015174-37 ). L.P. was funded by the NIBIB R01 ( EB22913 ), NSF NeuroNex Award ( DBI-1707398 ), NSF-CRCNS Award ( 1912194 ), the Simons Collaboration on the Global Brain , and the Gatsby Charitable Foundation . G.E.M. was funded by the Harvard Data Science Initiative Postdoctoral Fellowship . A.D.T.S. was funded by the NIH ( 1R01NS113119-01 ) and NSF ( IOS-1452593 ), A.L. by the NSF Physics of Living Systems Graduate Student Research Network ( 1806818 ), and V.V. by the Burroughs Wellcome Fund Career Award at the Scientific Interface .
Publisher Copyright:
© 2020 Elsevier Inc.
PY - 2021/1/7
Y1 - 2021/1/7
N2 - Comprehensively resolving neuronal identities in whole-brain images is a major challenge. We achieve this in C. elegans by engineering 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 resolves all 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. We showcase three applications 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 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 for these stimuli.
AB - Comprehensively resolving neuronal identities in whole-brain images is a major challenge. We achieve this in C. elegans by engineering 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 resolves all 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. We showcase three applications 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 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 for these stimuli.
KW - C. elegan
KW - atlas
KW - expression pattern
KW - nervous system
KW - whole nervous sytem imaging
UR - http://www.scopus.com/inward/record.url?scp=85098950835&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85098950835&partnerID=8YFLogxK
U2 - 10.1016/j.cell.2020.12.012
DO - 10.1016/j.cell.2020.12.012
M3 - Article
C2 - 33378642
AN - SCOPUS:85098950835
SN - 0092-8674
VL - 184
SP - 272-288.e11
JO - Cell
JF - Cell
IS - 1
ER -