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README.md
README.md
 
 
cellbrowser_to_vitessce_config_conversion.ipynb
cellbrowser_to_vitessce_config_conversion.ipynb
 
 
config_to_python.ipynb
config_to_python.ipynb
 
 
data_conversion.ipynb
data_conversion.ipynb
 
 
data_export_files.ipynb
data_export_files.ipynb
 
 
data_export_s3.ipynb
data_export_s3.ipynb
 
 
environment.yml
environment.yml
 
 
example_configs.py
example_configs.py
 
 
spatial_data.ipynb
spatial_data.ipynb
 
 
spatial_data_blobs.ipynb
spatial_data_blobs.ipynb
 
 
web_app_brain.ipynb
web_app_brain.ipynb
 
 
widget_brain.ipynb
widget_brain.ipynb
 
 
widget_brain_h5ad.ipynb
widget_brain_h5ad.ipynb
 
 
widget_brain_with_base_dir.ipynb
widget_brain_with_base_dir.ipynb
 
 
widget_from_dict.ipynb
widget_from_dict.ipynb
 
 
widget_genomic_profiles.ipynb
widget_genomic_profiles.ipynb
 
 
widget_imaging.ipynb
widget_imaging.ipynb
 
 
widget_imaging_beta.ipynb
widget_imaging_beta.ipynb
 
 
widget_imaging_segmentation.ipynb
widget_imaging_segmentation.ipynb
 
 
widget_loom.ipynb
widget_loom.ipynb
 
 
widget_modify_config.ipynb
widget_modify_config.ipynb
 
 
widget_on_colab.ipynb
widget_on_colab.ipynb
 
 
widget_pbmc.ipynb
widget_pbmc.ipynb
 
 
widget_pbmc_remote.ipynb
widget_pbmc_remote.ipynb
 
 
widget_plugin_custom.ipynb
widget_plugin_custom.ipynb
 
 
widget_plugin_demo.ipynb
widget_plugin_demo.ipynb
 
 
widget_plugin_spatial-query.ipynb
widget_plugin_spatial-query.ipynb
 
 
widget_segmentations_beta.ipynb
widget_segmentations_beta.ipynb
 
 
widget_shortcut.ipynb
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README.md

Example Notebooks

The notebooks contained in this directory demonstrate the Vitessce Python package functionality.

Setup

Some of the example notebooks rely on external single-cell data analysis packages. An environment containing these additional packages can be installed with conda or pip.

cd docs/notebooks
uv sync --extra dev --extra docs --extra all

Run

uv run jupyter lab

Troubleshooting

If you previously had the vitessce Python package v1 installed, you may need to uninstall the previous lab extension due to conflicts between the v1 and v2 widget JS code.

jupyter labextension uninstall vitessce-jupyter