bugfix - was passing channel index for nifti (#9)

was defaulting to the first channel, which coincidentally worked fine for the lifecanvas data
khanlab · Jun 28, 2024 · d9c2a7b · d9c2a7b
1 parent ff40c00
commit d9c2a7b
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/spimquant/workflow/scripts/ome_zarr_to_nii.py b/spimquant/workflow/scripts/ome_zarr_to_nii.py
@@ -42,6 +42,6 @@
 
 
 with ProgressBar():
-    ZarrNii.from_path(in_zarr,level=level).downsample(along_z=zdownsampling).to_nifti(snakemake.output.nii)
+    ZarrNii.from_path(in_zarr,level=level,channels=[channel_index]).downsample(along_z=zdownsampling).to_nifti(snakemake.output.nii)