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bioRxiv · 10.64898/2026.08.14.744809

Streamlining large-scale high-resolution electron tomography with VolWeaver

Bregy, I.·Mesman, R.·Tassan-Lugrezin, S.·Kooij, T. W. A.·van Niftrik, L.
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Abstract

Researchers using electron microscopy must often balance a trade-off between obtaining high-resolution structural information and preserving sufficient cellular context. At one end of this spectrum, single particle cryo-electron microscopy and cryo-electron tomography provide near-molecular detail but are typically limited to relatively small fields of view. At the other, volume electron microscopy approaches, such as scanning electron microscopy of resin-embedded specimens, capture large cellular volumes but generally at lower resolution. Consequently, linking nanoscale structural information to larger cellular architecture remains a significant challenge. To address this gap, we optimised a transmission electron tomography workflow for resin-embedded malaria parasites that allows us to visualise targeted regions of interest at nanometre-scale resolution while retaining several micrometres of surrounding cellular context. Here, we present our current best-practice pipeline for sample preparation, tomogram acquisition, and reconstruction. In addition, we introduce VolWeaver, a data-processing framework, that integrates high-resolution tomographic datasets into serial section volume reconstructions, enabling the visualisation and interpretation of ultrastructural features within their broader cellular environment.

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Bregy, I., Mesman, R., Tassan-Lugrezin, S., Kooij, T. W. A., van Niftrik, L.. 2026-08-18. Streamlining large-scale high-resolution electron tomography with VolWeaver. https://doi.org/10.64898/2026.08.14.744809

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