notebooks.md

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

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                notebooks/examples/intro.ipynb

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                notebooks/examples/transformations.ipynb

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                notebooks/examples/spatial_query.ipynb

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                notebooks/examples/napari_rois.ipynb

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                notebooks/examples/alignment_using_landmarks.ipynb

Intermediate

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                notebooks/examples/sdata_from_scratch.ipynb

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                notebooks/examples/labels_shapes_interchangeability.ipynb

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            .. image:: _static/img/squidpy_integration.jpg
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                notebooks/examples/squidpy_integration.ipynb

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            .. image:: _static/img/densenet.png
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                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.

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                notebooks/examples/technology_visium.ipynb

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            .. image:: _static/img/merfish.png
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                notebooks/examples/technology_merfish.ipynb

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            .. image:: _static/img/visium_hd.jpg
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                notebooks/examples/technology_visium_hd.ipynb

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                notebooks/examples/technology_visium_hd_mouse_4.0.1.ipynb

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                notebooks/examples/technology_spacem.ipynb

Advanced

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

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            .. image:: _static/img/speed.png
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                notebooks/examples/speed_up_illustration.ipynb

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                notebooks/examples/transformations_advanced.ipynb

External tutorials

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

Methods:

• Squidpy: Spatial Single Cell Analysis in Python
• SPArrOW: A library for Spatial Transcriptomics Data Analysis
• SOPA: Spatial-omics pipeline and analysis
• Bento: a toolkit for subcellular analysis of spatial transcriptomics data

Workshop tutorials:

• A hands-on introduction into the analysis of targeted spatial transcriptomics data using the SPArrOW pipeline developed by the Yvan Saeys group (VIB)