STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes

This repository is for a 10X Visium spatial transcriptomics dataset that was originally generated in "Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys" (Gharaie et al. 2023) and then utilized in "STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes" (Clifton et al. 2025). NL3 is a normal mouse left kidney section, also referred to as "control" or "ctrl". IL3 is a mouse left kidney section from a kidney with ischemia-reperfusion injury, also referred to acute kidney injury or "AKI". In Clifton et al. 2025, Visium spots were annotated with region labels (cortex, outer medulla, inner medulla, and other) via semi-supervised transcriptional clustering. The region labels are provided here as one-hot encoding. In order to increase structural alignment between the control and AKI datasets, the region labels were used to create images to be aligned with STalign, a spatial alignment tool. With STalign, an affine alignment was performed to generate new AKI spot positions to be more aligned to the control dataset. The code to perform this alignment is provided in "visium-visium-region-alignment-affine-only.ipynb".