jYCaMP: an optimized calcium indicator for two-photon imaging at fiber laser wavelengths


Femtosecond lasers at fixed wavelengths above 1,000 nm are powerful, stable and inexpensive, making them promising sources for two-photon microscopy. Biosensors optimized for these wavelengths are needed for both next-generation microscopes and affordable turn-key systems. Here we report jYCaMP1, a yellow variant of the calcium indicator jGCaMP7 that outperforms its parent in mice and flies at excitation wavelengths above 1,000 nm and enables improved two-color calcium imaging with red fluorescent protein-based indicators.

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Fig. 1: jYCaMP1 is a redshifted variant of jGCaMP7 capable of detecting single action potentials.
Fig. 2: jYCaMP1 enables brighter two-color calcium imaging together with red GECIs, improving correlation analysis of overlapping compartments.

Data availability

Example raw datasets and summary statistics are available through Figshare; https://doi.org/10.25378/janelia.12098361. All other data associated with this study are available from the corresponding author.

Code availability

Custom code is available from the corresponding author, and at https://github.com/KasparP/twoColorUnmixing and github.com/KasparP/SLAP.


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We thank H. Davies, C. Morkunas and M. Jeffries for logistical support and S. Di Lisio, K. Ritola, D. Walpita, J. Hasseman and the GENIE Project Team for experimental support. We thank S. Vishwanathan for the gift of Emx1-Cre mice. This work was funded by the Howard Hughes Medical Institute. M.A.M. was supported by the Janelia Graduate Research Fellowship Program. E.J.M., C.-Y.L. and A.A. were supported by the Janelia Undergraduate Scholars Program. Work by J.L.C. and A.M.A. was supported by the National Science Foundation Neuronex Neurotechnology Hub (NEMONIC no. 1707287) and National Institutes of Health BRAIN Initiative Award (no. UF1NS107705).

Author information




K.P. conceived and K.P., E.R.S., J.S.M. and M.A.M. refined the idea. J.S.M. and M.A.M. produced Venus-GCaMPs. E.J.M. performed spectral screening with the help of K.P. C.-Y.L. M.A.M. and A.A. characterized proteins in vitro and M.A.M. and D.S.K. in cultured neurons. A.A. performed individual mutation depletion. Y.L. performed mouse virus injections. K.P., J.J.K. and M.A.M. performed mouse in vivo imaging. A.M.W. and M.A.M. generated fly lines and D.B. designed, performed and analyzed fly experiments. A.M.A. and J.L.C. designed and performed multi-area imaging experiments. R.P. and J.J.M. performed multiphoton spectroscopy and analyzed data. M.A.M., K.P., A.A., J.J.K., D.S.K. and E.R.S. analyzed data. M.A.M., K.P. and E.R.S. prepared the manuscript with input from all authors. K.P., E.R.S. and L.L.L. supervised the work.

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Correspondence to Kaspar Podgorski.

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Peer review information Rita Strack was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Supplementary Figs. 1–9 and Table 1.

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Mohr, M.A., Bushey, D., Aggarwal, A. et al. jYCaMP: an optimized calcium indicator for two-photon imaging at fiber laser wavelengths. Nat Methods 17, 694–697 (2020). https://doi.org/10.1038/s41592-020-0835-7

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