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Add number of cells metric #112

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Merged
LouisK92 merged 1 commit into from
Dec 10, 2025
Merged

Add number of cells metric #112

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9 changes: 9 additions & 0 deletions src/metrics/quality/config.vsh.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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1 change: 1 addition & 0 deletions src/metrics/quality/script.py
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Expand Up @@ -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)
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