---
tags: ome, scverse, anndata
---

## Outputs

### Code

### Decisions

* We want to have multiple region types
* We want to have have tables which refer to multiple regions/ images
* We want to have multiple types of tables
* We've updated specs
* Full anndata for tables
* Updated points
* We want a spatial data package (scverse)
* Depends on ome-ngff and provides python API

## Questions for OME-NGFF community (probably make issues)

#### Named coordinate spaces

Ability to say what coordinate space a particular object exists in. Coordinate transforms the define how to move from one space to another.

#### coordinateTransform types: Pixel vs scalar

Pixel transforms are going to be done with different functions and require transformations.

#### Tables that refer to multiple images/ regions

When dealing with a collection of slides, it's common to concatenate the tables (see [single-cell-data/mams#5](https://github.com/single-cell-data/mams/issues/5)). We would like to move the table out of the image to allow this. Below we propose some metadata that would allow this.

#### Flatten Structure?

Images
Regions
    ShapeRegion
    LabelRegion
    PolygonRegion
Tables
Points (?)

#### New types

* Regions
* LabelRegion
* ShapeRegion
* CircleRegion
* SquareRegion
* `*Region`
* PolygonRegion
* Tables
* RegionTable (refers Region)
* ImageTable (refers to images)
* Point Table (contains points)

`RegionTable`

* Metadata:
* `@type:ngff:region_table`
* `region: str | list[str]`: Region or list of regions this table refers to
* `region_key: Optional[str]`: Key in obs which says which Region container this obs exists in ("library_id"). Must be present if region is a list.
* `instance_key: Optional[str]`: Key in obs that says which instance the obs represents. If not present, `.obs_names` is used.

`PointTable`

* This needs much more specification
* We want a points table to be able to refer to points in multiple coordinate spaces. Use cases include:
* Spatial coordination of genes across multiple slides (or any other multi-slide)
* Metadata
* `@type:ngff:point_table`
* Values:
* Each obs is a point
* Each var is a variable
* Obsm
* Coordinates (must have * `coordinate_space` metadata)
* *Is this optional for concatenated points*
* `uns/metadata/obsm/{key}` for hacky metadata

`LabelRegion`

* Metadata
* `@type:nfgg:label_region`
* `coordinate_space`
* Segmentation mask
* Canonical way of associating image and segmentation mask is through coordinate space

`Polygon`

#### Links

* How to refer to regions
* Paths (relative/ absolute/ where is root?)

#### style guide for naming?

camel case?

## Follow up

### Metadata in anndata

* OME-ngff will handle metadata types
* To use metadata from OME-NGFF with an AnnData go through Spatial data package.

### Meeting

Virtual 2 weeks, in person 1 month?

### Events

* 30 may Luca Janelia seminar series from Luca

### Napari package

* Giovanni takes lead

### SpatialData

* scverse needs to meet about timelines
* Spatial Muon paper timeline
* Spatial muon release? scverse follow up

### Grants to watch out for

#### Helmholtz metadata initiative

* [Link](https://www.helmholtz.de/en/research/current-calls-for-applications/article/funding-opportunities-for-innovative-metadata-projects-1/)
* "An application must be submitted by partners from at least two different Helmholtz Centres (or two AST programmes respectively);"
* All together, a total of approx. € 400,000 is possible for a maximum of 2 years.
* Information sessions 5 May and 16 May

* Idea: SpatialData, metadata handling for anndata
* Metadata transformation

* Will check in with josh on ome at helmholtz

#### CZI Single Cell Data Insights

* [Link](https://chanzuckerberg.com/rfa/single-cell-data-insights/)
* "Opens mid June 2022, closes late July"
* "The maximum budgets for proposed projects are $400,000 total costs for Expanded Projects and $200,000 total costs for Focused Projects. All projects awards will be for an 18-month duration."

* Broad support
* Work on spec
* Implementations in python, java, javascript?
* Contract?

#### Napari plugins

* [Link](https://chanzuckerberg.com/rfa/napari-plugin-grants/)
* Due 1st June 2022
* CZI invites applications for grants of $20,000 in total costs that would enable developers to convert one or more existing image analysis tools for cellular biology to one or more napari plugins.

* Giovanni will talk to Robert