---
# System prepended metadata

title: 2024/06/06 SpatialData community meeting

---

# 2023/06/06 SpatialData community meeting 

[Zoom link](https://embl-org.zoom.us/j/91313414488?pwd=Dlu6B9Ecg4fGmUfqaSUGvbIzp2Q5ZG.1)
6PM to 7PM 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, Giovanni, Benjamin, Kasia Kedziora, Wouter-Michiel Vierdag, Isaac

## Agenda and notes

Please add topics of discussion and include a time estimate

- (Benjamin) VIB Hackathon Ghent (5min)
    - Go over interesting SpatialData work items
    - See if there are anymore preparations needed
- (Kasia) Annotation of scatterplots (15 min?)
    - Center for Bioimaging Pittsburgh
        - http://www.cbi.pitt.edu/
    - See [earlier discussion on Zulip](https://scverse.zulipchat.com/#narrow/stream/315824-spatial/topic/napari-spatialdata.20for.20annotating.20objects.20with.20Shapes/near/440135687)
    - Demo of pyqtgraph scatter widget
        - dropdown to select axes in SpatialData/AnnData is good
        - pyqt plotting much faster than matplotlib
        - has menu's when right clicking
        - has annotation mode
        - lasso selection remains editable
    - Users want to see result of dimensionality reduction and explore spatially
        - demo of Luca of old abandoned LayerView widget 
        - https://github.com/BiAPoL/napari-clusters-plotter
    - Is it interesting to store annotation polygon on dim red as Shapes Element?
    - What would be the best strategy to increase the flexibility of annotations on scatterplots?
    - Feasibility of multiple scatterplot widgets
- (Isaac) cellxgene data structure
    - no seperation of elements?
    - schema has changed a lot and isn't final
        - support for labels
        - support for spatial transcriptomics (mostly Visium)
    - key deliverable for cellxgene is to export to public data formats like e.g. SpatialData. Best to let them do it, as it's changing a lot and a moving target


## Actionable items 

- A meeting was schedule with Kasia, Luca and Wouter-Michiel, 17th June 17h CET

# Shareable invitation to this meeting
You are welcome to join the next SpatialData Community Meeting on 2024/06/06. 11AM-12PM CET.
- [zoom](https://embl-org.zoom.us/j/97353680729?pwd=di8zbmF1akVxU0ZqTUxMQ0pVSVp5QT09) (passcode: 668182)
- [agenda](https://hackmd.io/0dbCBxOHRlCoWvMfyGiyWA?both)

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)
