Processed MERFISH spatial transcriptomics dataset of mouse spinal cord (SOD1-G93A and control)

Description:This repository provides an AnnData .h5ad object with processed MERFISH data and metadata from our study: all_anndata_final_rotated_w_anno.h5ad Data structure: The normalized expression matrix is stored in .X. The raw counts matrix is stored in the counts layer. Key metadata are stored as observation annotations (.obs) and include: slide - MERSCOPE run identifier slide_section - individual tissue section identifier region - broad spinal cord region (e.g., Lumbar, Cervical) stage - disease stage (Control, Early, Mid, End) cell_class - high-level cell type category (e.g., Astrocytes, Microglia/Macrophages, Cholinergic Neurons) cholinergic_type - subclassification of cholinergic neurons (e.g., Alpha MNs, Gamma MNs, Gamma* MNs) predicted.id - predicted alpha motor neuron subtype from label transfer (e.g., Slow-Firing, Intermediate, Fast-Firing, Early DAMN, Late DAMN) DAMN_status - Disease-Associated Motor Neuron classification (DAMN vs. Non-DAMN) reactive_microglia - boolean flag indicating reactive microglia/macrophages reactive_or_wm_astrocytes - boolean flag indicating reactive/white-matter astrocytes