phenotypic.refine.CenterDeviationReducer#

class phenotypic.refine.CenterDeviationReducer[source]#

Bases: ObjectRefiner

Keep the object closest to center and remove off-center detections.

Intuition:

For isolated-colony images (e.g., single-spot captures or per-grid-cell crops), the true colony is typically near the center. Spurious blobs from glare, dust, or agar texture may appear off-center. This operation keeps only the object whose centroid is closest to the image center, removing all others.

Why this is useful for agar plates:

When imaging a grid of pinned colonies, per-cell crops may contain extra detections (ringing, condensation, halo). Selecting the most centered object stabilizes downstream phenotyping by focusing on the intended colony in each crop.

Use cases:

  • Single-colony crops from a grid plate where occasional debris is picked up near edges.

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

Caveats:

  • If the true colony is notably off-center (misalignment, drift), this method can remove it and keep a distractor.

  • Not suitable for multi-colony fields; it will drop all but one object.

(No public attributes)

Examples

>>> from phenotypic.refine import CenterDeviationReducer
>>> op = CenterDeviationReducer()
>>> image = op.apply(image, inplace=True)

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.