From 77790d0a43118c120f77d6d30b7d7359f89c9001 Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Tue, 20 Jun 2023 18:40:55 +0100 Subject: [PATCH] Add spatial obsm to adata on MCMICRO loading --- scimap/preprocessing/_mcmicro_to_scimap.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/scimap/preprocessing/_mcmicro_to_scimap.py b/scimap/preprocessing/_mcmicro_to_scimap.py index 658d0d1a..b7287088 100644 --- a/scimap/preprocessing/_mcmicro_to_scimap.py +++ b/scimap/preprocessing/_mcmicro_to_scimap.py @@ -165,7 +165,8 @@ def load_process_data (image): # Create an anndata object adata = ad.AnnData(entire_data) adata.obs = meta - adata.uns['all_markers'] = markers + adata.uns['all_markers'] = markers + adata.obsm['spatial'] = adata.obs[['X_centroid','Y_centroid']].to_numpy() # Add log data if log is True: @@ -240,4 +241,4 @@ def main(argv=sys.argv): mcmicro_to_scimap(**vars(args)) if __name__ == '__main__': - main() \ No newline at end of file + main()