napari_prism.pl.dearray_tma

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napari_prism.pl.dearray_tma#

napari_prism.pl.dearray_tma(sdata, shapes_name, image_name=None, channel_label=None, channel_cmap='gray', figsize=None, dpi=None, coordinate_system='global', fill_alpha=0.0, outline_alpha=1.0, outline_width=2.0, outline_color='blue', tma_annotation_color='white', tma_annotation_fontsize=20, show=True, **kwargs)#

Displays a shapes element from the SpatialData object, such as the generated TMA envelopes and cores.

Parameters:

  • sdata (SpatialData) – The SpatialData object containing the image.

  • shapes_name (str) – The name of the shapes to display.

  • image_name (Optional[str] (default: None)) – The name of the image to display.

  • channel_label (Optional[str] (default: None)) – The label of the channel to display.

  • channel_cmap (str | None (default: 'gray')) – The colormap to use for the channel.

  • figsize (Optional[tuple[int, int]] (default: None)) – The size of the figure.

  • dpi (Optional[int] (default: None)) – The DPI of the figure.

  • coordinate_system (str (default: 'global')) – The coordinate system to use for rendering.

  • fill_alpha (float (default: 0.0)) – Alpha value for filling shapes.

  • outline_alpha (float (default: 1.0)) – Alpha value for shape outlines.

  • outline_width (float (default: 2.0)) – Width of shape outlines.

  • outline_color (str (default: 'blue')) – Color of shape outlines.

  • tma_annotation_color (str (default: 'white')) – Color of TMA annotations.

  • tma_annotation_fontsize (float (default: 20)) – Font size of TMA annotations.

  • show (bool (default: True)) – Whether to show the plot or return it.

  • **kwargs – Passed to spatialdata.pl.render_shapes.

Return type:

None | SpatialData

Returns:

None if show is True, otherwise returns the rendered SpatialData object.

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