phenotypic.refine.CenterDeviationReducer

class phenotypic.refine.CenterDeviationReducer(*args, **kwargs)

Bases: ObjectRefiner

Retain only the object whose centroid is closest to the image center.

Computes the Euclidean distance from each object’s centroid to the image center and keeps the single nearest object, removing all others. Useful for per-cell crops where the intended colony sits near the center and peripheral detections are artifacts.

Returns:

Input image with objmap reduced to the single most centered object.

Return type:

Image

Best For:

• Single-colony crops from grid plates where debris appears near edges.

• Automated pipelines that assume one colony per field-of-view.

• Post-crop cleanup in conjunction with grid-based workflows.

Consider Also:

• GridSectionLargest when the largest object per grid cell is more reliable than the most centered.

• SmallObjectRemover when peripheral artifacts are simply smaller than the true colony.

• ReduceMultipleGridObjects for grid-aware multi-detection reduction using positional regression.

See also

How To: Refine Noisy Detection Boundaries for boundary cleanup workflows. Refinement Strategies for an overview of refinement approaches.

Methods

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

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.