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Is your feature request related to a problem? Please describe.
In segmentation_utils, the save_segmentation_labels function is partly redundant. It is saving {fov}_segmentation_labels.tiff, which seems to be what is already saved as {fov}_feature_0.tif. In the segmentation notebook, the default for channels is None for this function, so a channel overlay with segmentation borders is not being saved by default. It is not obvious that channels should be set to ['nuclear_channel', 'membrane_channel'] to save these overlays.
Describe the solution you'd like
In the save_segmentation_labels function in segmentation_utils, remove redundant file saving. In the notebook, change the default channels to ['nuclear_channel', 'membrane_channel'].
The text was updated successfully, but these errors were encountered:
Is your feature request related to a problem? Please describe.
In segmentation_utils, the
save_segmentation_labels
function is partly redundant. It is saving {fov}_segmentation_labels.tiff, which seems to be what is already saved as {fov}_feature_0.tif. In the segmentation notebook, the default forchannels
is None for this function, so a channel overlay with segmentation borders is not being saved by default. It is not obvious that channels should be set to['nuclear_channel', 'membrane_channel']
to save these overlays.Describe the solution you'd like
In the
save_segmentation_labels
function in segmentation_utils, remove redundant file saving. In the notebook, change the default channels to['nuclear_channel', 'membrane_channel']
.The text was updated successfully, but these errors were encountered: