phenotypic.refine.LowCircularityRemover#

class phenotypic.refine.LowCircularityRemover(cutoff: float = 0.785)[source]

Bases: ObjectRefiner

Remove objects whose Polsby-Popper circularity falls below a cutoff.

Computes circularity as 4 * pi * area / perimeter^2 for each labeled object and discards those below the threshold. Keeps well-formed, roughly circular colonies while filtering out elongated artifacts, merged blobs, and segmentation debris.

Parameters:

cutoff (float) – Minimum Polsby-Popper circularity in [0, 1] required to retain an object. Typical range: 0.5–0.9. Higher values keep only near-circular shapes; lower values tolerate irregular morphologies. Default: 0.785.

Returns:

Input image with objmap and objmask updated to exclude objects below the circularity cutoff.

Return type:

Image

Raises:

ValueError – If cutoff is outside [0, 1].

Best For:

  • Post-threshold cleanup to exclude elongated scratches or merged colonies before phenotyping.

  • Enforcing morphology consistency in high-throughput grid assays.

  • Plates with round yeast or bacterial colonies where irregular detections indicate artifacts.

Consider Also:

See also

How To: Refine Noisy Detection Boundaries for shape-based cleanup workflows. Refinement Strategies for a comparison of morphological refinement methods.

Methods

__init__

Initialize the remover.

apply

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

widget

Return (and optionally display) the root widget.
__init__(cutoff: float = 0.785)[source]

Initialize the remover.

Parameters:

cutoff (float) – Minimum allowed circularity in [0, 1]. Increasing the cutoff favors compact, round objects (often cleaner masks), whereas lowering it retains irregular colonies but may keep more debris or merged objects.

Raises:

ValueError – If cutoff is outside [0, 1].

__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.

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