SCALLOPS: a scalable, integrated computational framework for Optical Pooled Screens

Gould, J.; Hleap, J. S.; Wu, P.; Kudo, T.; Guan, J.; Zhu, A.; Lubeck, E.; Ge, X.-Y. M.; Waterman, A. A.; Biancalani, T.; Rozenblatt-Rosen, O.; Metcalfe, C.; Singh, A.; Richmond, D.; Regev, A.; Li, B.

doi:10.64898/2026.05.22.727250

bioRxiv · 10.64898/2026.05.22.727250

SCALLOPS: a scalable, integrated computational framework for Optical Pooled Screens

Gould, J.·Hleap, J. S.·Wu, P.·Kudo, T.·Guan, J.·Zhu, A.·Lubeck, E.·Ge, X.-Y. M.·Waterman, A. A.·Biancalani, T.·Rozenblatt-Rosen, O.·Metcalfe, C.·Singh, A.·Richmond, D.·Regev, A.·Li, B.

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Abstract

Optical pooled screens (OPS) link pooled genetic perturbations to high-dimensional image-based phenotypes at scale, but their widespread adoption is hindered by computational bottlenecks in processing terabyte-scale, multimodal image data. We present SCALLOPS, a unified, modular, and cloud-native computational framework that overcomes these bottlenecks. SCALLOPS implements a "well-centric" processing strategy that integrates robust stitching with a non-linear two-stage registration strategy, enabling accurate alignment of multi-magnification images, reliable single-cell genotype-phenotype linkage, and efficient morphological feature extraction. Benchmarking with public and newly-generated datasets demonstrated SCALLOPS superior performance over existing solutions. Crucially, SCALLOPS uniquely enables robust processing of 4x magnification in situ sequencing data, accelerating image acquisition by around six-fold. We applied SCALLOPS to an optical pooled screen investigating the estrogen receptor (ER) degrader vepdegestrant in a breast cancer cell line, successfully recovering its known mechanism of action, highlighting the value of OPS in translational research. SCALLOPS provides a scalable end-to-end solution, making large-scale OPS routine.

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Gould, J., Hleap, J. S., Wu, P., Kudo, T., Guan, J., Zhu, A., Lubeck, E., Ge, X.-Y. M., Waterman, A. A., Biancalani, T., Rozenblatt-Rosen, O., Metcalfe, C., Singh, A., Richmond, D., Regev, A., Li, B.. 2026-05-26. SCALLOPS: a scalable, integrated computational framework for Optical Pooled Screens. https://doi.org/10.64898/2026.05.22.727250

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