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Spatial Transcriptomics and Imaging

Spatial single-cell analysis in Python

Palla et al. (Nature Methods, 2022)

Squidpy is a tool for the analysis and visualization of spatial molecular data. It builds on top of Scanpy and anndata, from which it inherits modularity and scalability. It provides analysis tools that leverage the spatial coordinates of the data, as well as tissue images if available.

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Self-supervised retinal thickness prediction using deep learning

Holmberg et al. (Nature Machine Intelligence, 2020)

DeepRT is a self-supervised training scheme for obtaining high-quality, pre-trained networks from unlabelled, cross-modal medical imaging data, which will drive the development of accurate and efficient models.

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