Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data

Heidari, E.; Moorman, A.; Unyi, D.; Pasnuri, N.; Rukhovich, G.; Calafato, D.; Mathioudaki, A.; Chan, J.; Nawy, T.; Gerstung, M.; Pe'er, D.; Stegle, O.

doi:10.1101/2025.03.14.643160

bioRxiv · 10.1101/2025.03.14.643160

Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data

Heidari, E.·Moorman, A.·Unyi, D.·Pasnuri, N.·Rukhovich, G.·Calafato, D.·Mathioudaki, A.·Chan, J.·Nawy, T.·Gerstung, M.·Pe'er, D.·Stegle, O.

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Abstract

The accurate assignment of transcripts to their cells of origin remains the Achilles heel of imaging-based spatial transcriptomics, despite being critical for nearly all downstream analyses. Current cell segmentation methods are prone to over- and under-segmentation, misassign transcripts to cells, require manual intervention, and suffer from low sensitivity and scalability. We introduce segger, a versatile graph neural network based on a heterogeneous graph representation of individual transcripts and cells, that frames cell segmentation as a transcript-to-cell link prediction task and can leverage single-cell RNA-seq information to improve transcript assignments. On multiple Xenium dataset benchmarks, segger exhibits superior sensitivity and specificity, while requiring orders of magnitude less compute time than existing methods. The user-friendly open-source software implementation has extensive documentation (https://elihei2.github.io/segger_dev/), requires little manual intervention, integrates seamlessly into existing workflows, and enables atlas-scale applications.

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Heidari, E., Moorman, A., Unyi, D., Pasnuri, N., Rukhovich, G., Calafato, D., Mathioudaki, A., Chan, J., Nawy, T., Gerstung, M., Pe'er, D., Stegle, O.. 2025-03-16. Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data. https://doi.org/10.1101/2025.03.14.643160

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