Scalable image-based visualization and alignment of spatial transcriptomics datasets

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bioRxiv. 2024 Jul;. doi: 10.1101/2021.12.07.471629

Scalable image-based visualization and alignment of spatial transcriptomics datasets Scientific Computing Software

Preibisch S, Innerberger M, León-Periñán D, Karaiskos N, Rajewsky N

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Abstract

We present STIM, an imaging-based computational framework focused on visualizing and aligning high-throughput spatial sequencing datasets. STIM is built on the powerful, scalable ImgLib2 and BigDataViewer (BDV) image data frameworks and thus enables novel development or transfer of existing computer vision techniques to the sequencing domain characterized by datasets with irregular measurement-spacing and arbitrary spatial resolution, such as spatial transcriptomics data generated by multiplexed targeted hybridization or spatial sequencing technologies. We illustrate STIM’s capabilities by representing, interactively visualizing, 3D rendering, automatically registering and segmenting publicly available spatial sequencing data from 13 serial sections of mouse brain tissue, and from 19 sections of a human metastatic lymph node.Competing Interest StatementThis work is part of a larger patent application in which the authors are among the inventors. The patent application was submitted through the Technology Transfer Office of the Max-Delbrueck Center (MDC), with the MDC being the patent applicant.

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preprint: http://doi.org/10.1101/2021.12.07.471629

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Scalable image-based visualization and alignment of spatial transcriptomics datasets

Abstract

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