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# System prepended metadata

title: 2023/10/12 SpatialData community meeting

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# 2023/11/09 SpatialData community meeting 

[Zoom link](https://embl-org.zoom.us/j/97353680729?pwd=di8zbmF1akVxU0ZqTUxMQ0pVSVp5QT09)
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:* Luca Marconato, Benjamin Rombaut

## Agenda and notes

Please add topics of discussion and include a time estimate

- (Luca) 10X people are okay with Xenium Explorer converter, so that's good
    - new release support coordinate systems
    - closed source alternative to Napari
    - good performance and UI
- (Luca) finalized saving/exporting new elements with Michiel
- (Benjamin) GitHub Issue for better support for highly multiplexed images (15min)
    - Bug 1: many channels in ImageElement and no omero metadata gives errors in viewers
        - e.g. vizarr, vitessce, 3D cell viewer
        - see [add_ome_attr function](https://github.com/berombau/spatialdata-io/blob/6a5e5cd780843e457d52dc68ef6ac1ed329788e4/src/spatialdata_io/readers/_utils/_utils.py#L76) in spatialdata-io fork, should probably be in ome-zarr-py or spatialdata
        - Solution: add omero metadata in ImageElement
    - Bug 2: SpatialData reader bug when ImageElement metadata contains omero dict with 'channels' key
        - Solution: find the bug and fix, probably in spatialdata instead of ome-zarr-py
    - Bug 3: vtk.js viewer does not work for ImageElement if the name doesn't end in .zarr
        - Solution: create issue there, not that needed
    - Bug 4: bug in animated-cell viewer when data does not have Z and/or T channel
        - Solution: create issue there, would be nice
    - Bug 5: Vitessce scale bar does not show up
        -  Solution: create valid datasets that should show scale bar (https://github.com/scverse/spatialdata/issues/357)
        -  add omero metadata for physical coordinates

## Actionable items 

- (Benjamin) Add Issues and create links to test datasest

# Shareable invitation to this meeting
## SpatialData Community Meeting: Thursday, Nov 9th. 11AM-12PM CET
You are welcome to join the next SpatialData Community Meeting on Thursday, Nov 9th. 11AM-12PM CET.
- [zoom](https://embl-org.zoom.us/j/97353680729?pwd=di8zbmF1akVxU0ZqTUxMQ0pVSVp5QT09) (passcode: 668182)
- [agenda](https://hackmd.io/HUmv7vsTSPinI3dpAiswlg)

General information:
- [all the future meetings and agendas](https://hackmd.io/enWU826vRai-JYaL7TZaSw?both)
- [zulip chat](https://scverse.zulipchat.com/#narrow/stream/315824-spatial/topic/spatialdata.20meetings)