phenotypic.enhance.SobelFilter

class phenotypic.enhance.SobelFilter

Bases: ImageEnhancer

Sobel edge filter to highlight colony boundaries.

Computes the gradient magnitude using the Sobel operator to emphasize edges (rapid intensity changes). On agar plate images, this highlights colony perimeters and helps downstream steps that rely on edge strength (e.g., contour finding, watershed seeds, or boundary-based scoring).

Use cases (agar plates): - Emphasize colony outlines before contour detection or watershed. - Separate touching colonies when combined with a distance or marker-based

segmentation strategy.

Guidance: - Consider light smoothing with GaussianBlur beforehand to suppress noise;

Sobel is sensitive to high-frequency artifacts (dust, texture).

Caveats: - Output is an edge map, not a background-corrected image. Use in tandem

with background removal or thresholding for full segmentation.

• Strong illumination gradients can still produce spurious edges; correct background first if needed.

Methods

__init__
apply	Applies the operation to an image, either in-place or on a copy.
dispose_widgets	Drop references to the UI widgets.
sync_widgets_from_state	Push internal state into widgets.
widget	Return (and optionally display) the root widget.

__del__()

Automatically stop tracemalloc when the object is deleted.

__getstate__()

Prepare the object for pickling by disposing of any widgets.

This ensures that UI components (which may contain unpickleable objects like input functions or thread locks) are cleaned up before serialization.

Note

This method modifies the object state by calling dispose_widgets(). Any active widgets will be detached from the object.

apply(image, inplace=False)

Applies the operation to an image, either in-place or on a copy.

Parameters:

• image (Image) – The arr image to apply the operation on.

• inplace (bool) – If True, modifies the image in place; otherwise, operates on a copy of the image.

Returns:

The modified image after applying the operation.

Return type:

Image

dispose_widgets() → None

Drop references to the UI widgets.

Return type:

None

sync_widgets_from_state() → None

Push internal state into widgets.

Return type:

None

widget(image: Image | None = None, show: bool = False) → Widget

Return (and optionally display) the root widget.

Parameters:

• image (Image | None) – Optional image to visualize. If provided, visualization controls will be added to the widget.

• show (bool) – Whether to display the widget immediately. Defaults to False.

Returns:

The root widget.

Return type:

ipywidgets.Widget

Raises:

ImportError – If ipywidgets or IPython are not installed.