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add notebook (#399)
Jan 17, 2025
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README.md
README.md
Nov 27, 2024
cellbrowser_to_vitessce_config_conversion.ipynb
cellbrowser_to_vitessce_config_conversion.ipynb
Jul 19, 2023
config_to_python.ipynb
config_to_python.ipynb
Jan 10, 2023
data_conversion.ipynb
data_conversion.ipynb
Jan 10, 2023
data_export_files.ipynb
data_export_files.ipynb
Jan 16, 2023
data_export_s3.ipynb
data_export_s3.ipynb
Jan 16, 2023
environment.yml
environment.yml
Jul 19, 2023
example_configs.py
example_configs.py
Apr 26, 2022
spatial_data.ipynb
spatial_data.ipynb
Dec 18, 2024
spatial_data_blobs.ipynb
spatial_data_blobs.ipynb
Nov 27, 2024
web_app_brain.ipynb
web_app_brain.ipynb
Jan 10, 2023
widget_brain.ipynb
widget_brain.ipynb
Jan 16, 2023
widget_brain_h5ad.ipynb
widget_brain_h5ad.ipynb
Sep 9, 2024
widget_brain_with_base_dir.ipynb
widget_brain_with_base_dir.ipynb
Jul 5, 2023
widget_from_dict.ipynb
widget_from_dict.ipynb
Jan 16, 2023
widget_genomic_profiles.ipynb
widget_genomic_profiles.ipynb
Feb 22, 2023
widget_imaging.ipynb
widget_imaging.ipynb
Jan 10, 2023
widget_imaging_beta.ipynb
widget_imaging_beta.ipynb
Sep 12, 2023
widget_imaging_segmentation.ipynb
widget_imaging_segmentation.ipynb
Jan 10, 2023
widget_loom.ipynb
widget_loom.ipynb
Jan 16, 2023
widget_modify_config.ipynb
widget_modify_config.ipynb
Jan 17, 2025
widget_on_colab.ipynb
widget_on_colab.ipynb
Jan 10, 2023
widget_pbmc.ipynb
widget_pbmc.ipynb
Sep 11, 2024
widget_pbmc_remote.ipynb
widget_pbmc_remote.ipynb
Jan 10, 2023
widget_plugin_custom.ipynb
widget_plugin_custom.ipynb
Jul 24, 2024
widget_plugin_demo.ipynb
widget_plugin_demo.ipynb
Jul 24, 2024
widget_plugin_spatial-query.ipynb
widget_plugin_spatial-query.ipynb
Aug 2, 2024
widget_segmentations_beta.ipynb
widget_segmentations_beta.ipynb
Oct 2, 2024
widget_shortcut.ipynb
widget_shortcut.ipynb
Jan 10, 2023

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