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save_segmentation_labels function in segmentation notebook is confusing #626

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cliu72 opened this issue Jun 28, 2022 · 0 comments · Fixed by #661
Closed

save_segmentation_labels function in segmentation notebook is confusing #626

cliu72 opened this issue Jun 28, 2022 · 0 comments · Fixed by #661
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enhancement New feature or request

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@cliu72
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cliu72 commented Jun 28, 2022

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'].

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