phenotypic.refine.GridOversizedObjectRemover#

class phenotypic.refine.GridOversizedObjectRemover[source]#

Bases: GridObjectRefiner

Remove objects that are larger than their grid cell allows.

Intuition:

In pinned colony grids, each cell should contain at most one colony of limited extent. Objects spanning nearly an entire cell width/height are often merged colonies, agar edges, or segmentation spillover. Removing these oversized objects improves the reliability of per-cell analysis.

Why this is useful for agar plates:

Grid-based assays assume spatial confinement. Oversized detections disrupt row/column statistics and bias growth comparisons. Filtering them stabilizes downstream measurements.

Use cases:

  • Dropping merged blobs that span adjacent positions.

  • Removing strong edge artifacts near the plate rim that intrude into the grid.

Caveats:

  • If genuine colonies expand to fill the cell (late time points), this remover may exclude real growth.

  • Highly irregular grids or mis-registered edges can cause over- removal; ensure grid metadata is accurate.

(No public attributes)

Examples

Remove objects larger than their grid cell allows
>>> from phenotypic.refine import GridOversizedObjectRemover
>>> op = GridOversizedObjectRemover()
>>> 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.