This data contains Xenium spatial transcriptomics data generated from soybean nodules and used for segmentation optimization and downstream analysis in plant tissues. The dataset includes the core Xenium output files required for spatial transcriptomics analysis. The morphology image (morphology.ome.tif) provides the high-resolution tissue image used for visualization and segmentation. Transcript coordinates are provided in both zarr (transcripts.zarr.zip) and tabular parquet format (alltranscripts.parquet) for downstream analysis. The cells.zarr.zip file contains the default Xenium cell segmentation results, and the experiment.xenium file stores the Xenium Explorer project metadata. Together, these files provide the spatial transcript coordinates, morphology images, and default cell segmentation outputs necessary for evaluating segmentation workflows and molecule-to-cell assignment in soybean nodule tissues.