The import-segmentation pipeline generates additional metrics in the metrics_summary.csv and analysis_summary.html (Cell segmentation tab). They are generated for the scenarios described in the import-segmentation algorithms section.
| Import-segmentation metric | Description |
|---|---|
| Percentage of pixels found to be ambiguous when importing nucleus segmentation polygons | The percentage of pixels found to be ambiguous when converting polygons into a mask. Ambiguities occur when polygons overlap one another. (Only calculated when polygon GeoJSON boundaries imported with --nucleus and --cell) |
| Percentage of pixels found to be ambiguous when importing cell segmentation polygons | The percentage of pixels found to be ambiguous when converting polygons into a mask. Ambiguities occur when polygons overlap one another. (Only calculated when polygon GeoJSON boundaries imported with --nucleus and --cell) |
| The percentage of imported nucleus polygons that were removed | The percentage of nuclei that were removed when importing polygons for nucleus segmentation. Nuclei are removed when they cannot be made consistent with the 2D nucleus mask. This can happen if there are nuclei completely contained within another or when a nucleus has a large portion of its area overlapping another nucleus. (Only calculated when polygon GeoJSON boundaries imported with --nucleus and --cell) |
| The percentage of imported cell polygons that were removed | The percentage of cells that were removed when importing polygons for cell segmentation. Cells are removed when they cannot be made consistent with the 2D cell mask. This can happen if there are cells completely contained within another or when a cell has a large portion of its area overlapping another cell. (Only calculated when polygon GeoJSON boundaries imported with --nucleus and --cell) |
| Percentage of nuclei without a cell | The percentage of nuclei that are not contained within a cell. This can happen when an imported community-developed cell or nucleus segmentation is not in agreement with the 10x-generated or the community-developed cell segmentation. |
| Number of cell non-simple polygons | Number of non-simple polygon cells in GeoJSON (e.g., polygons with holes) that were modified to keep only the first array of vertices during import-segmentation. |
| Number of cell multipolygons | Number of multipolygon cells in GeoJSON (e.g., multiple disconnected polygons) that were removed during import-segmentation. |
| Number of nucleus non-simple polygons | Number of non-simple polygon nuclei in GeoJSON that were modified to keep only the first array of vertices during import-segmentation. |
| Number of nucleus multipolygons | Number of multipolygon nuclei in GeoJSON that were removed during import-segmentation. |
| Fraction of segmented cells imported | Fraction of cells that were imported by import-segmentation. The remaining cells, if any, are generated by expansion of imported nuclei. |
| Number of segmented cells imported | Number of cells that were imported by import-segmentation. |