Morph Labels#
Parameters#
labels layer: The napari labels layer on which to apply operations.
points layer: A napari points layer used to select instances for morphological operations.
Note
If no points are placed, the selected morphological operation will be applied to all labels in the image (or stack if Apply in 3D is selected).
Operation: List of morphological operations to apply.
Dilate: This operation expands or thickens the boundaries of objects in the label map. It can be used to join broken parts or increase the size of objects.
Erode: This operation erodes away the boundaries of objects in the label map. It can be used to remove small noise or thin structures.
Close: This operation combines dilation and erosion to close small gaps and holes in the label map.
Open: This operation combines erosion and dilation to remove small objects and smooth the boundaries of larger objects.
Fill holes: This operation fills small holes or gaps in the selected label.
Radius: The radius of the (disk (2D) or sphere (3D)) structuring element used for erosion, dilation, close, and open operations.
Hole size: The maximum size of holes to fill if the operation is set to “Fill holes”.
Apply in 3D: Whether to apply the morphological operation within the entire 3D labelmap. Generally should be checked when proofreading 3D segmentations and unchecked when proofreading a stack of 2D segmentations (for example, leave it unchecked when proofreading the output of 2D Batch Mode inference).
Output#
Applies the selected morphological operation to the selected label or to the entire label layer.
Examples#
Radius of 3 used
Radius of 3 used
Radius of 5 used
Radius of 5 used
Hole size of 100 used
