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Jupyter Notebook Python
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10X Visium Dataset

The 10X Visium data was obtained from from 10x Genomics. The data was not included in this repo because of GitHub size limitations but can be easily obtained from 10x Genomics Datasets.

Reference Dataset

Similarly to the Seurat spatial vignette we used a single cell RNA-seq dataset (~14,000 Mouse cortical cells produced by the Allen Institute) as a reference dataset for labeling the Visium data.


This project was influenced by the Seurat spatial vignette from the Satija lab and we are very grateful for thier public examples.

MyBinder link


Nicolas Fernandez

Assaf Magen

Adeeb Rahman

Manuel Garcia-Quismondo

Tutorial Video


Contact and Feedback

Please contact us through the Gitter Discussion Board or issue tracker with questions comments or concerns.

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