diff --git a/src/metrics/quality/config.vsh.yaml b/src/metrics/quality/config.vsh.yaml index 6f91bb4c..f89fd73b 100644 --- a/src/metrics/quality/config.vsh.yaml +++ b/src/metrics/quality/config.vsh.yaml @@ -25,6 +25,15 @@ info: min: 0 max: 1 maximize: true + - name: number_of_cells + label: Number of Cells + summary: "The number of cells in the spatial dataset." + description: | + The number of cells in the spatial dataset. + references: + doi: "10.1101/2023.02.13.528102" + min: 0 + maximize: true resources: - type: python_script diff --git a/src/metrics/quality/script.py b/src/metrics/quality/script.py index 7f103ada..cae3425c 100644 --- a/src/metrics/quality/script.py +++ b/src/metrics/quality/script.py @@ -23,6 +23,7 @@ metrics = { "proportion_of_assigned_reads": proportion_of_assigned_reads(sdata)[0], "proportion_of_annotated_cells": proportion_of_annotated_cells(sdata), + "number_of_cells": sdata['counts'].n_obs, } print("Write output AnnData to file", flush=True)