napari_prism.pl.segment_tma

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napari_prism.pl.segment_tma#

napari_prism.pl.segment_tma(sdata, segmentation_name, image_name=None, channel_label=None, channel_cmap='gray', fill_alpha=0.0, outline_alpha=1.0, contour_px=3, figsize=None, dpi=None, coordinate_system='global', show=True, **kwargs)#

Displays a labels element from the SpatialData object, such as the cell segmentation results.

Parameters:

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

  • segmentation_name (str) – The name of the segmentation 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.

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

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

  • contour_px (int (default: 3)) – Pixel width of contours.

  • 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.

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

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

Returns:

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

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