README.md

spatialdata-db

Currently focusing on the following datasets for diversity in testing:

• 10ktp: Visium, Mouse, Brain
• 4b368: Visium, Mouse, Lung
• m1v5v: Xenium, Human, Lung
• oeuwa: Xenium, Mouse, Brain
• jqmx8: VisiumHD, Mouse, Intestine

Setup vitessce

Currently, the SpatialDataWrapper is not yet merged and released. Therefore, we have to install it via

pip install anywidget starlette uvicorn
pip install git+https://github.com/vitessce/vitessce-python.git@ig/spatial_data

from Ilan's PR: vitessce/vitessce-python#333

UID logic

• Absolute ID will be a 5 char string of lowercase letters and digits -> 60466176 IDs
• Leaving out the letters [l, b, o, g, q] due to their similarity to [1, 6, 0, 9, 9] -> 28629151 IDs
• Reserve ID spaces for technology providers
  • 10 _ _ _ -> 29791 IDs for 10X Genomics
  • vg _ _ _ -> 29791 IDs for Vizgen
  • ns _ _ _ -> 29791 IDs for Nanostring
  • xx _ _ _ -> 29791 IDs for miscellaneous, such as publication