Drop atlas label 0 (background) from qc_roi_summary before plotting

Background regions (index == 0) are outside the brain and should be
excluded from the per-ROI summary bar charts.

Agent-Logs-Url: https://github.com/khanlab/SPIMquant/sessions/e1add057-49be-45a2-8dbf-1e8d402fd215

Co-authored-by: akhanf <11492701+akhanf@users.noreply.github.com>

Author: Copilot

spimquant/workflow/scripts/qc_roi_summary.py

@@ -50,6 +50,10 @@ def main():
     stats_df = pd.read_csv(snakemake.input.segstats, sep="\t")
     label_df = pd.read_csv(snakemake.input.label_tsv, sep="\t")
 
+    # Drop background (atlas label 0) — those voxels are outside the brain
+    if "index" in stats_df.columns:
+        stats_df = stats_df[stats_df["index"] != 0].copy()
+
     # Merge region names (label_df has 'index' and 'name' columns)
     if "name" not in stats_df.columns and "index" in stats_df.columns:
         stats_df = stats_df.merge(label_df[["index", "name"]], on="index", how="left")