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"--data_ext", default=".mrc", help="The extension of the tomogram data. By default .mrc."
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)
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parser.add_argument(
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"--boundary_threshold", type=float, default=0.4, help="Threshold that determines when the prediction of the network is foreground for the segmentation. Need higher threshold than default for TEM."
"""Segment synaptic compartments in an input volume.
@@ -168,6 +169,7 @@ def segment_compartments(
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return_predictions: Whether to return the predictions (foreground, boundaries) alongside the segmentation.
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scale: The scale factor to use for rescaling the input volume before prediction.
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n_slices_exclude:
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boundary_threshold: Threshold that determines when the prediction of the network is foreground for the segmentation. Need higher threshold than default for TEM.
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Returns:
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The segmentation mask as a numpy array, or a tuple containing the segmentation mask
@@ -193,9 +195,9 @@ def segment_compartments(
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# We may want to expose some of the parameters here.
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