Interactive Visualization of Spatial-transcriptomics Data

Workshop on SpatialData visualization

Spatial-omics data Registration

Workflow to produce the Xenium-COMET dataset used in the visualization workshop. Adapted from : https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/alignment_using_landmarks.html

Code

• Example Notebook: https://github.com/scOpenLab/sdata_workshop/blob/fb64a57f491f77e4828da2b9be7fe1f58371608e/registration/MB299-REGISTRATION_EXAMPLE.ipynb
• Original repository: https://github.com/scOpenLab/MultimodalRegistration

Data

• Xenium MB299:

  • View at: Xenium-Vitessce-Example
  • Bioimage Archive: https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD1093?query=MB299
  • Raw zipped folder for tutorial: https://radosgw.public.os.wwu.de/omics-data/REGISTRATION/MB299-xenium.zip

• COMET:

  • View at: VOLE-COMET-EXAMPLE
  • BioImage Archive: https://alpha.bioimagearchive.org/bioimage-archive/galleries/spatialomics/image/fa24b912-3242-42f0-aee9-d83e73c3a2a4
  • Raw tiff image for tutorial: https://radosgw.public.os.wwu.de/omics-data/REGISTRATION/20240115_140647_2_IntG77_Spyre_FFPE_Sequential_IF_QB2.tiff

Visualization

Registered data

Zipped output of the registration tutorial above:

• https://radosgw.public.os.wwu.de/omics-data/VISUALIZATION/ZARR2-MB299-ALIGNED.zarr.zip

Viewer links

COMET Vol-E viewer:

• VOLE-COMET-EXAMPLE

Xenium Vitessce viewer:

• Automatic configuration: https://app.vitessce.io/#?source=https://radosgw.public.os.wwu.de/omics-data/VISUALIZATION/ZARR2-MB299-ALIGNED.zarr$spatialdata.zarr
• Custom configuration: Xenium-Vitessce-Example

Code

• Napari + napari-spatialdata script: https://github.com/scOpenLab/sdata_workshop/blob/b09b386fefb4b5a2277c131897b7028c4fb32aa3/visualization/napari_sd_remote.py
• easy-vitessce: https://github.com/scOpenLab/sdata_workshop/blob/b09b386fefb4b5a2277c131897b7028c4fb32aa3/visualization/easy-vitessce-MB299.ipynb
• harpy-vitessce: https://github.com/scOpenLab/sdata_workshop/blob/4e8394969e38da07717901db07776cb8f4677c2d/visualization/harpy-vitessce-MB299.ipynb