Tools for accurate post hoc determination of marker location within whole-brain microscopy images

Tyson, A. L.; Velez-Fort, M.; Rousseau, C. V.; Cossell, L.; Tsitoura, C.; Obenhaus, H. A.; Claudi, F.; Lenzi, S. C.; Branco, T.; Margrie, T. W.

doi:10.1101/2021.05.21.445133

bioRxiv · 10.1101/2021.05.21.445133

Tools for accurate post hoc determination of marker location within whole-brain microscopy images

Tyson, A. L.·Velez-Fort, M.·Rousseau, C. V.·Cossell, L.·Tsitoura, C.·Obenhaus, H. A.·Claudi, F.·Lenzi, S. C.·Branco, T.·Margrie, T. W.

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Abstract

To interpret in vivo experiments designed to understand brain function, high-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and recorded cells in three dimensional brain space that is a critical step for data interrogation. Here we have developed Python-based tools (brainreg and brainreg-segment) to accurately map, in a common coordinate space, the position of dye-labelled probe tracks and two-photon imaged cell populations expressing fluorescent protein. The precise location of probes and cells were validated using physiological recordings and human raters that indicate accuracy levels to less than 70{micro}m. These flexible, open-source methodologies are expected to further evolve with need and to deliver the anatomical precision that is necessary for understanding the functional architecture of the brain.

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Tyson, A. L., Velez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Obenhaus, H. A., Claudi, F., Lenzi, S. C., Branco, T., Margrie, T. W.. 2021-05-23. Tools for accurate post hoc determination of marker location within whole-brain microscopy images. https://doi.org/10.1101/2021.05.21.445133

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