Skip to content

Latest commit

 

History

History
315 lines (185 loc) · 7.77 KB

notebooks.md

File metadata and controls

315 lines (185 loc) · 7.77 KB

Tutorials

Notebooks tailored to showcase specific functionalities of the SpatialData ecosystem. See the bottom of this page for links to analysis tutorials for external methods that use SpatialData as a data model.

Basic

.. grid:: 2 3 3 3

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/intro.png
                :target: notebooks/examples/intro.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/intro.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/transformations.jpg
                :target: notebooks/examples/transformations.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/transformations.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/spatial_query.jpg
                :target: notebooks/examples/spatial_query.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/spatial_query.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/napari_rois.jpg
                :target: notebooks/examples/napari_rois.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/napari_rois.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/alignment_using_landmarks.png
                :target: notebooks/examples/alignment_using_landmarks.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/alignment_using_landmarks.ipynb

Intermediate

.. grid:: 2 3 3 3

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/models1.png
                :target: notebooks/examples/models1.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/models1.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/models2.png
                :target: notebooks/examples/models2.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/models2.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/table.png
                :target: notebooks/examples/tables.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/tables.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/intro.png
                :target: notebooks/examples/sdata_from_scratch.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/sdata_from_scratch.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/aggregation.jpg
                :target: notebooks/examples/aggregation.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/aggregation.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/interchangeability_labels_polygons.png
                :target: notebooks/examples/labels_shapes_interchangeability.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/labels_shapes_interchangeability.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/squidpy_integration.jpg
                :target: notebooks/examples/squidpy_integration.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/squidpy_integration.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/densenet.png
                :target: notebooks/examples/densenet.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/densenet.ipynb

Technology-specific

Many different technologies can be visualised out-of-the-box. See below for a couple of examples. See the example datasets for additional technologies represented in SpatialData.

.. grid:: 2 3 3 3

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/visium.png
                :target: notebooks/examples/technology_visium.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/technology_visium.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/mibitof.png
                :target: notebooks/examples/technology_mibitof.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/technology_mibitof.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/merfish.png
                :target: notebooks/examples/technology_merfish.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/technology_merfish.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/cosmx.png
                :target: notebooks/examples/technology_cosmx.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/technology_cosmx.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/visium_hd.jpg
                :target: notebooks/examples/technology_visium_hd.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/technology_visium_hd.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/xenium.png
                :target: notebooks/examples/technology_xenium.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/technology_xenium.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/spacem_helanih3t3.png
                :target: notebooks/examples/technology_spacem.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/technology_spacem.ipynb

Advanced

Advanced tutorials that showcase more complex functionalities of the SpatialData ecosystem.

.. grid:: 2 3 3 3

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/speed.png
                :target: notebooks/examples/speed_up_illustration.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/speed_up_illustration.ipynb

    .. grid-item::

        .. container:: custom-card

            .. image:: _static/img/transformations.jpg
                :target: notebooks/examples/transformations_advanced.html

            .. toctree::
                :maxdepth: 1

                notebooks/examples/transformations_advanced.ipynb

External tutorials

Links to the tutorials for (some) external analysis methods that use SpatialData as a data model.

Methods:

Workshop tutorials: