Vizgen MERSCOPE Vizualizer Clustering Template

This notebook demonstrates how to use Scanpy to perform data pre-processing, dimensionality reduction, and single-cell Leiden clustering.

This notebook is designed to take the Anndata output from the MERSCOPE Vizualizer and return a new Anndata object with UMAP dimensionality reduction and Leiden clustering cell metadata.

Before running this notebook upload your data (using the Files tab on the left and upload button) to this Colab notebook (a specific filename is not required, but the file must end with .hdf5).