A parallelly distributed microscope and software system for scalable high-throughput multispectral 3D imaging

Jiang, H.; Walker, L. A.; Li, Y.; Duan, B.; Niu, X.; Hsieh, J.-C.; Cheng, M.-C.; Su, H.; Sheng, K.; Tang, J. P.; Athukorala, K.; Greene, S.; Pan, R.; Parlapalli, A.; Yin, P.; Cui, M.; Cai, D.

doi:10.1101/2025.05.31.657163

bioRxiv · 10.1101/2025.05.31.657163

A parallelly distributed microscope and software system for scalable high-throughput multispectral 3D imaging

Jiang, H.·Walker, L. A.·Li, Y.·Duan, B.·Niu, X.·Hsieh, J.-C.·Cheng, M.-C.·Su, H.·Sheng, K.·Tang, J. P.·Athukorala, K.·Greene, S.·Pan, R.·Parlapalli, A.·Yin, P.·Cui, M.·Cai, D.

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Abstract

Recent advances in high throughput optical microscopy have achieved whole-organism scale imaging at diffraction-limited resolutions. Current microscopes, however, require making compromises between achieving the optimal resolution, imaging depth, multispectral capability, and data throughput due to limitations in optical design and data stream handling. We have created a parallel-line scanning confocal microscope (plSCM) which provides 1.1 Gigavoxels/second high speed imaging while achieving an optical resolution of [~]180 x 220 x 650 nm with 2 millimeters of imaging depth in 3 simultaneous spectral channels. To handle such a massive imaging data stream, we have engineered a scalable network-distributed image acquisition/processing framework (SNDiF), which allows continuous capture, real-time processing, and cluster storage of petabyte-scale single image datasets in days. Together, our parallelly distributed microscope and software system presents a general solution for large-scale high-throughput and high-resolution multicolor imaging which can operate for days at a time.

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Jiang, H., Walker, L. A., Li, Y., Duan, B., Niu, X., Hsieh, J.-C., Cheng, M.-C., Su, H., Sheng, K., Tang, J. P., Athukorala, K., Greene, S., Pan, R., Parlapalli, A., Yin, P., Cui, M., Cai, D.. 2025-06-03. A parallelly distributed microscope and software system for scalable high-throughput multispectral 3D imaging. https://doi.org/10.1101/2025.05.31.657163

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