/promt

Probabilistic Alignment of MERFISH Tissue Slices

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

PROMT

Data Availability

https://cellxgene.cziscience.com/collections/31937775-0602-4e52-a799-b6acdd2bac2e

PROMT Reproducibility

The PROMT pipeline tutorial is available at PROMT_tutorial.ipynb in this repository.

Make sure to split the Anndata object into different slices

import scanpy as sc
adata_full = sc.read_h5ad('path/to/adata.h5ad')
adata_donor_MsBrainAgingSpatialDonor_1 = adata_full[adata_full.obs.donor_id == 'MsBrainAgingSpatialDonor_1']