.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_electron_microscopy.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_electron_microscopy.py>`
        to download the full example code.

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

.. _sphx_glr_auto_examples_plot_electron_microscopy.py:


Electron Microscopy
===================

Applying the cellsam_pipeline to segment electron microscopy
images of bacteria.

This dataset comprises an electron microscope image of a bacterial
biofilm.
This FOV is downsampled from data provided by the
`Newman Lab at Caltech`_; image credit Mark Ladinsky @ the Caltech
CryoEM facility.

.. _Newman Lab at Caltech: https://dknweb.caltech.edu/

.. GENERATED FROM PYTHON SOURCE LINES 16-45



.. image-sg:: /auto_examples/images/sphx_glr_plot_electron_microscopy_001.png
   :alt: plot electron microscopy
   :srcset: /auto_examples/images/sphx_glr_plot_electron_microscopy_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    (512, 512)
    /home/administrator/envs/cs-13-dev/lib/python3.13/site-packages/cellSAM/sam_inference.py:351: UserWarning: Low IOU threshold, ignoring mask.
      warnings.warn("Low IOU threshold, ignoring mask.")
    /home/administrator/repos/cellSAM/examples/plot_electron_microscopy.py:40: FutureWarning: `napari.view_image` is deprecated and will be removed in napari 0.7.0.
    Use `viewer = napari.Viewer(); viewer.add_image(...)` instead.
      nim = napari.view_image(img, name="EMimage");






|

.. code-block:: Python

    import zarr
    import skimage
    import napari
    from cellSAM import cellsam_pipeline
    # NOTE: data is stored with zarr_format 3
    assert int(zarr.__version__[0]) > 2

    # Access EM image
    store = zarr.storage.FsspecStore.from_url(
        "s3://cellsam-gallery-sample-data/sample-data.zarr",
        storage_options={"anon": True},
        read_only=True,
    )
    z = zarr.open_group(store=store, mode="r")
    # Load EM image into local memory
    # Limit to lower-right quadrant to reduce CI computation load
    tilesize = 512
    img = z["biofilm_electron_microscopy"][tilesize:, tilesize:]
    print(img.shape)

    # Segment
    mask = cellsam_pipeline(img, use_wsi=False)

    # Visualize
    nim = napari.view_image(img, name="EMimage");
    nim.add_labels(mask, name="Cellsam segmentation");

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


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

   **Total running time of the script:** (0 minutes 7.595 seconds)


.. _sphx_glr_download_auto_examples_plot_electron_microscopy.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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