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2023/10/12 SpatialData community meeting

Zoom link
11AM to 12PM CET

If you are an external guest and you plan to attend, please write your name among the attendees and add time for a short introduction or topic to the agenda.

Should you wish to attend from a different time zone, please inform us here of your time-zone and topic so we can plan a more convenient slot.

Attendees: Benjamin Rombaut, Luca Marconato, Tim Treis

Agenda and notes

Please add topics of discussion and include a time estimate

  • (Name) Topic (00min)
    • (Notes)
  • (Luca) Updates on paper, development and hackathons (10min)
    • New coninuous integration system with Airflow
      • Airflow setup to autorun scripts and tests in spatialdata-sandbox and spatialdata-notebooks
      • runs everyday at noon, new data every week
      • conversion of data to zarr at midnight
      • more powerful than GitHub Actions
    • Working on more SpatialData GitHub Issues
    • Refactor of io
    • What's next:
      • more bugfixing, stability and documentation and notebooks in the next month
      • after that: refactor of transformations and multiple tables
      • only after transformation refactor think about ITK transformations
      • work on non-linear transformations
      • towards seperate low level transformation library that SpatialData and others can use (ome-zarr…). Also helps in maintenance and stability
  • (Benjamin) Vitessce configs for SpatialData datasets now there is more support?
  • SpatialData to Xenium explorer converter
    • Good lazy vector data representation (e.g. large Stereo-seq dataset)
    • But is on desktop and requires conversion, not remote like Vitessce
  • Conversion of older SpatialData datasets to newer format
    • Needs manual conversion, needs tutorial if a user wants to update an older dataset
  • List people in different time zones (5min)
    • East coast
      • Mark Keller (Vitessce team)
      • Matt McCormick
    • South Korea
      • Jeongbin Park

Actionable items

  • (Luca) Contact IT for s3.embl.de CORS header fix
  • (Luca) Conversion document for older to newer format
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