Meso2EM: a cross-scale CLEM workflow linking mesoscale functional imaging to targeted electron microscopy

Oomoto, I.; Murate, M.; Sohn, J.; Tamura, M.; Hatada, S.; Egawa, N.; Odagawa, M.; Suga, M.; Kawaguchi, Y.; Murayama, M.; Kubota, Y.

doi:10.64898/2026.08.25.746890

bioRxiv · 10.64898/2026.08.25.746890

Meso2EM: a cross-scale CLEM workflow linking mesoscale functional imaging to targeted electron microscopy

Oomoto, I.·Murate, M.·Sohn, J.·Tamura, M.·Hatada, S.·Egawa, N.·Odagawa, M.·Suga, M.·Kawaguchi, Y.·Murayama, M.·Kubota, Y.

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Abstract

Meso2EM is a correlative light and electron microscopy workflow that transfers neurons selected from mesoscale functional images to targeted electron microscopy. We recorded Ca{superscript 2} signals from layer 2/3 neurons across a contiguous 3 x 3 mm cortical field in awake mice and reidentified a selected neuron after fixation and tangential sectioning. Lectin-labeled vascular architecture served as a shared landmark across in vivo two-photon imaging, confocal microscopy, laboratory micro-CT of resin-embedded tissue, and block-surface scanning electron microscopy, guiding focused-ion-beam scanning electron microscopy to the target cell body. The same progressive-targeting principle also supported serial ATUM-SEM reconstruction of an in vivo-tracked dendrite and serial transmission electron microscopy of optically selected dendrites from a patch-clamp-recorded Martinotti cell. Meso2EM therefore provides a practical route for preserving target identity across large changes in scale and specimen state while restricting electron-microscopy acquisition to a selected region.

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Oomoto, I., Murate, M., Sohn, J., Tamura, M., Hatada, S., Egawa, N., Odagawa, M., Suga, M., Kawaguchi, Y., Murayama, M., Kubota, Y.. 2026-09-01. Meso2EM: a cross-scale CLEM workflow linking mesoscale functional imaging to targeted electron microscopy. https://doi.org/10.64898/2026.08.25.746890

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