.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_multiplexed.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_plot_multiplexed.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_plot_multiplexed.py:


Multiplexed Imaging: CODEX
==========================

.. GENERATED FROM PYTHON SOURCE LINES 5-22



.. image-sg:: /auto_examples/images/sphx_glr_plot_multiplexed_001.png
   :alt: plot multiplexed
   :srcset: /auto_examples/images/sphx_glr_plot_multiplexed_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    [       0 18481553 27300386]






|

.. code-block:: Python

    import imageio.v3 as iio
    import napari

    from cellSAM import cellsam_pipeline
    img = iio.imread("../sample_imgs/tissuenet.png")

    # Image is 3-channel RGB where Channel 1 (G) represents a nuclear stain
    # and Channel 2 (B) a membrane stain. Channel 0 (R) is blank.
    print(img.sum(axis=(0, 1)))

    mask = cellsam_pipeline(img, use_wsi=False)

    nim = napari.view_image(img, name="CODEX image");
    nim.add_labels(mask, name="Cellsam segmentation");

    if __name__ == "__main__":
        napari.run()


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (1 minutes 11.274 seconds)


.. _sphx_glr_download_auto_examples_plot_multiplexed.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_multiplexed.ipynb <plot_multiplexed.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_multiplexed.py <plot_multiplexed.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_multiplexed.zip <plot_multiplexed.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_