Aging MERFISH Brains

The files included fall into one of two categories:
1. Baysor input and output files: The input for Baysor is the decoded transcripts output from the MERlin pipeline on the Vizgen MERSCOPE. The outputs after running Baysor are a .parquet file of the cell boundaries and a .loom file containing the cellxgene matrix with associated metadata.
2. The final QC'd .h5ad file (synonymous with the ABC_cleaned.h5ad file in the accompanying code) which includes cells that had greater than 20 transcripts and removed any Cerebellar neurons which were outside of the cerebellum.
The final object used for analysis in the Simultaneous analysis of single-cell gene expression and morphology provides new insight into how microglia change with age preprint: https://www.biorxiv.org/content/10.1101/2025.02.28.640888v1

The object contains only microglia, the segmented total, soma, and process counts, all metadata used in the manuscript, the original baysor counts from the MERFISH run.

The final .h5ad objects were updated to reflect changes seen from using up to date Allen Brain Atlas annotations in our code.