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# System prepended metadata

title: 2023/10/12 SpatialData community meeting

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# 2023/10/26 SpatialData community meeting 

[Zoom link](https://embl-org.zoom.us/j/91981143644?pwd=M2NuRjlueVhqbmd4VDZFMktyWjAwdz09)
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:* Name, Brian Long (Allen Institute for Brain Science), Luca Marconato, Quentin Blampey, Benjamin Rombaut, Wouter, Nick Fernandez, Giovanni

## Agenda and notes

Please add topics of discussion and include a time estimate

- (Brian Long) Learning about expectations for `spatialdata-io` stability (5-10min)
    - External (commercial) vendor support/investment for up-to-date readers?
    - focus on Xenium and MERSCOPE (Michael). Loading data via spatialdata-io, but some problems with data loading.
- (Quentin Blampey) experience with Xenium and MERSCOPE. MERSCOPE laoder works on their part.
- (Nick Fernandez) Computational Biologist, formerly at Vizgen. Interested in open source.
- (Luca) Focus on stability and bug fixing first, then new features. de.NBI CI/CD system for testing.
    - limitation is not testing all version changes when companies release updates, would be lot of work. Solution would be for companies to make the PR to add this support.
    - mentions https://github.com/quentinblampey/spatialdata_xenium_explorer
    - old HDF5 MERSCOPE format currently note supported.
    - (Nick) converter is available to update old format to newer Parquet format. (https://vizgen.github.io/vizgen-postprocessing/)
- (Giovanni) need for more small open datasets from the companies to check for issues.
- (Luca) transformation, table, geometries not in NGFF spec. Internally for spatialdata not a problem. Spatialdata implementers (vitessce, spatialdata in R) can use the test spatialdata datasets.
- (Luca) no spec for multiscale geometries. Solution: subsampling (napari-spatialdata) or datashader (spatialdata-plot).
- (Luca) for larger datasets need for spatial indexing of GeoPandas (future meeting with GeoPandas developers)
    - (Nick) There’s a format used in geospatial work called Mapbox tiles that does multi-level representations of points and polygons, but it only works in geospatial coordinates (https://observablehq.com/@cornhundred/deck-gl-mvt-layer?collection=@cornhundred/deck-gl)
- (Nick) 3D segmentation. Multipolygon at a single z instead of only polygon (support for multiple cells at a location in a tissue).
    - (Luca) a lot of support for Multipolygon already. But not for 3D, just 3D labels. 
- (Nick) using one .parquet file instead of multiple ones and using row groups is more performant for filtering operations. Custom sorting can be used to improve performance


## Resources
- link to spatial muon: 
    - very early version with (untested) implementation of trimesh for 3D regions support: https://github.com/ilia-kats/spatialmuon/blob/8d6e9f12cf2ab2ed5a1b231cc7818714cd28020a/spatialmuon/datatypes/array.py
    - latest implementation, the framework is more tested and stable, but the 3D support has been removed; it appears commented in some parts of the code like here: https://github.com/ilia-kats/spatialmuon/blob/202202_graphs/spatialmuon/datatypes/regions.py

## Actionable items 
- (Luca) DONE make 10x aware of https://github.com/quentinblampey/spatialdata_xenium_explorer
- (Luca) DONE ask 10x and Vigzen for informing on datasets changes, or for providing small datasets
- (Luca) DONE share the Mapbox tiles example to the NGFF community, Vitessce dev and geopandas developers
- (Luca) DONE discuss regarding spatial indices for speeding up computation with the geopandas devs. Answer: using the Hilbert curve ordering and saving this data will speed up things.
- (Luca) DONE prepare roadmap document and share it
- (Luca) DONE share spatial muon code to Nick


# Shareable invitation to this meeting
## SpatialData Community Meeting: Thursday, Oct 26th. 6PM-7PM CET
You are welcome to join the next SpatialData Community Meeting on Thursday, Oct 26th. 6PM-7PM CET.
- [zoom](https://embl-org.zoom.us/j/91981143644?pwd=M2NuRjlueVhqbmd4VDZFMktyWjAwdz09) (passcode: 570601)
- [agenda](https://hackmd.io/C__F_rwXRz-WgCF1YFuiQg)

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)