.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/data/plot_3d.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_data_plot_3d.py>`
        to download the full example code or to run this example in your browser via Binder

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

.. _sphx_glr_auto_examples_data_plot_3d.py:


==========================================
Datasets with 3 or more spatial dimensions
==========================================

Most scikit-image functions are compatible with 3D datasets, i.e., images with
3 spatial dimensions (to be distinguished from 2D multichannel images, which
are also arrays with
three axes). :func:`skimage.data.cells3d` returns a 3D fluorescence microscopy
image of cells. The returned dataset is a 3D multichannel image with dimensions
provided in ``(z, c, y, x)`` order. Channel 0 contains cell membranes, while channel
1 contains nuclei.

The example below shows how to explore this dataset. This 3D image can be used
to test the various functions of scikit-image.

.. GENERATED FROM PYTHON SOURCE LINES 17-40



.. raw:: html
    :file: images/sphx_glr_plot_3d_001.html





.. code-block:: default

    from skimage import data
    import plotly
    import plotly.express as px
    import numpy as np

    img = data.cells3d()[20:]

    # omit some slices that are partially empty
    img = img[5:26]

    upper_limit = 1.5 * np.percentile(img, q=99)
    img = np.clip(img, 0, upper_limit)

    fig = px.imshow(
        img,
        facet_col=1,
        animation_frame=0,
        binary_string=True,
        binary_format="jpg",
    )
    fig.layout.annotations[0]["text"] = "Cell membranes"
    fig.layout.annotations[1]["text"] = "Nuclei"
    plotly.io.show(fig)


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

   **Total running time of the script:** (0 minutes 3.619 seconds)


.. _sphx_glr_download_auto_examples_data_plot_3d.py:

.. only:: html

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


    .. container:: binder-badge

      .. image:: images/binder_badge_logo.svg
        :target: https://mybinder.org/v2/gh/scikit-image/scikit-image/v0.22.x?filepath=notebooks/auto_examples/data/plot_3d.ipynb
        :alt: Launch binder
        :width: 150 px



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

      :download:`Download Python source code: plot_3d.py <plot_3d.py>`

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

      :download:`Download Jupyter notebook: plot_3d.ipynb <plot_3d.ipynb>`


.. only:: html

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

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