Mark Keller
Mark Keller
**User story** Background: - https://github.com/ome/ngff/issues/192 - https://github.com/ome/ome-zarr-py/pull/261 - https://github.com/scverse/spatialdata/pull/517 **Preferred solution** **Possible alternatives**
**User story** User has segmentations that are represented using polygon shapes within a SpatialData object. User wants to visualize these segmentations using Vitessce without converting them to a different data...
**User story** User has a SpatialData object that contains multiple regions but they only want to visualize a particular region of interest. **Preferred solution** When loading data from the SpatialData...
**User story** User has transcript coordinates from MERFISH-like experiment that are represented using point elements within a SpatialData object. User wants to visualize these points using Vitessce without converting them...
**User story** A SpatialData object can define coordinate systems and transformations between the coordinate systems for any of its spatial elements. When visualizing the data, the user expects these coordinate...
**User story** Currently, visualization of a SpatialData object in Vitessce requires defining a [JSON configuration](http://vitessce.io/docs/view-config-json/) (either writing the JSON directly or using the [JS API](http://vitessce.io/docs/view-config-js/)). However, this can be time...
Towards #1824 Demo: http://localhost:3000/?dataset=salcher-2022 #### Background #### Change List **TODO: re-implement minimally on fresh branch, with minimal changes needed to support useSql hook (e.g. in plugin views)** TODO: For proof...
**User story** It can currently be tricky to contribute to Vitessce due to the many edge cases in which variables can be `null`, for example if a subset of all...
**User story** Some of the code to stratify data based on observation sets and sample sets is getting complex https://github.com/vitessce/vitessce/blob/3b03b98a76316f47dc587a3642b7d5c41818686f/packages/view-types/statistical-plots/src/expr-hooks.js#L79 Related to #1816 **Preferred solution** - Explore loading Zarr data...
Fixes #1775 #### Background TODO: - [ ] Allow to filter points by sample set membership - use stratification hook - [x] Option to weight points by the selected gene...