spateo.segmentation.external.cellpose
=====================================

.. py:module:: spateo.segmentation.external.cellpose

.. autoapi-nested-parse::

   Use Cellpose for cell identification and labeling.
   https://github.com/MouseLand/cellpose

   [Stringer20]_



Attributes
----------

.. autoapisummary::

   spateo.segmentation.external.cellpose.Cellpose


Functions
---------

.. autoapisummary::

   spateo.segmentation.external.cellpose._cellpose
   spateo.segmentation.external.cellpose.cellpose


Module Contents
---------------

.. py:data:: Cellpose
   :value: None


.. py:function:: _cellpose(img: numpy.ndarray, model: Union[typing_extensions.Literal[cyto, nuclei], cellpose.models.CellposeModel] = 'nuclei', **kwargs) -> numpy.ndarray

   Run Cellpose on the provided image.

   :param img: Image as a Numpy array.
   :param model: Cellpose model to use. Can be one of the two pretrained models:
                 * cyto: Labeled cytoplasm
                 * nuclei: Labeled nuclei
                 Or any generic CellposeModel model.
   :param \*\*kwargs: Additional keyword arguments to :func:`Cellpose.eval`
                      function.

   :returns: Numpy array containing cell labels.


.. py:function:: cellpose(adata: anndata.AnnData, model: Union[typing_extensions.Literal[cyto, nuclei], cellpose.models.CellposeModel] = 'nuclei', diameter: Optional[int] = None, normalize: bool = True, equalize: float = 2.0, layer: str = SKM.STAIN_LAYER_KEY, out_layer: Optional[str] = None, **kwargs)

   Run Cellpose to label cells from a staining image.

   :param adata: Input Anndata
   :param model: Cellpose model to use. Can be one of the two pretrained models:
                 * cyto: Labeled cytoplasm
                 * nuclei: Labeled nuclei
                 Or any generic CellposeModel model.
   :param diameter: Expected diameter of each segmentation (cells for `model="cyto"`,
                    nuclei for `model="nuclei"`). Can be `None` to run automatic detection.
   :param normalize: Whether or not to percentile-normalize the image. This is an
                     argument to :func:`Cellpose.eval`.
   :param equalize: Controls the `clip_limit` argument to the :func:`clahe` function.
                    Set this value to a non-positive value to turn off equalization.
   :param layer: Layer that contains staining image. Defaults to `stain`.
   :param out_layer: Layer to put resulting labels. Defaults to `{layer}_labels`.
   :param \*\*kwargs: Additional keyword arguments to :func:`Cellpose.eval`
                      function.

   :returns: Numpy array containing cell labels.