squidpy.im.segment

squidpy.im.segment(img, layer=None, library_id=None, method='watershed', channel=0, chunks=None, lazy=False, layer_added=None, copy=False, **kwargs)[source]

Segment an image.

Parameters:

  • img (ImageContainer) – High-resolution image.

  • layer (str | None) – Image layer in img that should be processed. If None and only 1 layer is present, it will be selected.

  • library_id (str | Sequence[str] | None) – Name of the Z-dimension(s) that this function should be applied to. For not specified Z-dimensions, the identity function is applied. If None, all Z-dimensions are segmented separately.

  • method (str | SegmentationModel | Callable[..., ndarray[tuple[Any, ...], dtype[Any]]]) –

    Segmentation method to use. Valid options are:

    Alternatively, any callable() can be passed as long as it has the following signature: numpy.ndarray (height, width, channels) -> numpy.ndarray (height, width[, channels]).

  • channel (int | None) – Channel index to use for segmentation. If None, use all channels.

  • chunks (str | int | tuple[int, int] | None) – Number of chunks for Dask. For automatic chunking, use chunks = 'auto'.

  • lazy (bool) – Whether to lazily compute the result or not. Only used when chunks != None.

  • layer_added (str | None) – Layer of new image layer to add into img object. If None, use 'segmented_{model}'.

  • thresh – Threshold for creation of masked image. The areas to segment should be contained in this mask. If None, it is determined by Otsu’s method. Only used if method = 'watershed'.

  • geq – Treat thresh as upper or lower bound for defining areas to segment. If geq = True, mask is defined as mask = arr >= thresh, meaning high values in arr denote areas to segment. Only used if method = 'watershed'.

  • copy (bool) – If True, return the result, otherwise save it to the image container.

  • kwargs (Any) – Keyword arguments for the underlying model.

Return type:

ImageContainer | None

Returns:

If copy = True, returns a new container with the segmented image in '{layer_added}'.

Otherwise, modifies the img with the following key: