2024/08/22 SpatialData community meeting

Zoom link
6PM to 7PM Berlin time.

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: Luca, Quentin, Minh Trinh, Hong Jiang, Tamara Ströbel, Giovanni, Isaac

Agenda and notes

Please add topics of discussion and include a time estimate

• (Hong) Introduction (03 min)
  • external user, read the tutorials, I have some pretty naiive questions as an outsider. Maybe you could recommend some courses?

Notes

• (Hong) questions:
  • are points in pixel coordinates or different spaces?
  • can I generated simulated dataset?
  • which scaled should be used for stereoseq?
    • notebook on binned data: TODO ADD
    • fast aggregation of binned data: TODO ADD
    • which coordinate system to use?
• (Tamara) here to learn more, may have question later on
• (Minh) feedback tricky points:
  • difficult to parse the images because large
  • tricky to downscale the OME.TIFF files, then all good
  • shapes and labels were fine
  • tables difficult to work with. When you have them things are good, but loading them into the table was difficult
    • idea: allow to parse a dataframe instead of the AnnData object
    • spatialdata-io
• (Luca) update on the framework
• (Luca, Giovanni, Isaac) discussion on spaitaldata-io

Actionable items

• (Luca, Minh) meeting next week

Shareable invitation to this meeting

You are welcome to join the next SpatialData Community Meeting on Thursday 2024/08/22. 6PM-7PM Berlin time.

• zoom (passcode: 570601)
• agenda

General information:

• all the future meetings and agendas
• zulip chat