Cell_segmentation_pipeline

Visium HD is a high-resolution spatial transcriptomic platform. It can measure transcriptomic profile of 2µm squares on a hematoxylin and eosin stained slide. This record includes an example for this pipeline. The folder "Cell_segmentation_and_aggregation" contains the data, code and result for cell segmentations and aggregation from 2µm squares to cells. The folder "Aggregation_result_visualization" contains the data, code and result for visualization of cells colored by different cell types. The locations of cells were based on the coordinates of polygons and the cell types were classified based on the aggregated transcriptomic profile.