The cell segmentation （HD and stereoseq）results from spatialdata are currently difficult to integrate with downstream analysis software.
The main issue is with the saved format, especially the image/labels format, which doesn't connect well with many commonly used downstream tools (like Seurat, scanpy, and other spatial analysis packages).
Could the team consider:
Adding export functions to convert segmentation results to more widely-compatible formats
Providing clearer documentation on how to bridge spatialdata outputs with popular downstream tools
This would greatly improve the usability of spatialdata in standard spatial transcriptomics analysis workflows.
The cell segmentation （HD and stereoseq）results from spatialdata are currently difficult to integrate with downstream analysis software.
The main issue is with the saved format, especially the image/labels format, which doesn't connect well with many commonly used downstream tools (like Seurat, scanpy, and other spatial analysis packages).
Could the team consider:
Adding export functions to convert segmentation results to more widely-compatible formats
Providing clearer documentation on how to bridge spatialdata outputs with popular downstream tools
This would greatly improve the usability of spatialdata in standard spatial transcriptomics analysis workflows.