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Touch up of spatial release article (#1345)
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* Fix set of listed attributes, class names, added links to tiledbsoma docs

* Add links to spatialdata class and docsite

* Update docs/articles/2025/20250117-spatial.md
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ivirshup authored Feb 3, 2025
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24 changes: 12 additions & 12 deletions docs/articles/2025/20250117-spatial.md
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Expand Up @@ -7,7 +7,7 @@ The Census team is pleased to announce the release of Spatial data on Census!

This has been a large joint effort between the Census team and TileDB to create an easy-to-use and backwards-compatible spatial schema that enables easy analysis with non-spatial and spatial data!

This first release is a **beta release** with the ability to export all spatial data (10x Visium and Slideseq) from an `obs/var` query in `SpatialData`. The ability to export `SpatialData` with spatial-based filters, transforms, etc., is not supported and will be implemented in a future release.
This first release is a **beta release** with the ability to export all spatial data (10x Visium Spatial Gene Expression and Slide-seqV2) from an `obs/var` query to {class}`~spatialdata.SpatialData` ([spatialdata.scverse.org](https://spatialdata.scverse.org/en/stable/)). The ability to query census with spatial-based filters, transforms, etc., is not supported and will be implemented in a future release.

---

Expand All @@ -17,37 +17,37 @@ This first release is a **beta release** with the ability to export all spatial

### Building Blocks

#### **SOMAExperiment**
#### **{class}`tiledbsoma.Experiment`**

A collection encapsulating data from one or more single-cell datasets, with reserved attributes:

| Field Name | Field Description |
|-------------------------|-----------------------------------------------------------------------------------|
| `obs` | A DataFrame for observation metadata |
| `ms` | A collection (`SOMAMeasurement`), with cell-by-gene data matrices and a gene metadata DataFrame |
| `ms` | A collection (`Measurement`), with cell-by-gene data matrices and a gene metadata DataFrame |
| **[NEW] `spatial`** | A collection of `Scene` objects (see below) |
| **[NEW] `obs_spatial_presence`** | A DataFrame to map observations to `Scene` objects |

---

#### **[NEW] SOMAScene**
#### **[NEW] {class}`tiledbsoma.Scene`**

A collection of spatial assets. All assets in one `Scene` should correspond to the same physical coordinate system. The collection provides operations for getting, setting, and transforming between coordinate systems, with reserved attributes:

| Field Name | Field Description |
|--------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|
| `obsl` | A collection of spatial arrays and collections. The rows in these arrays correspond to observations and may correspond to `obs` of a `SOMAExperiment`. |
| `varl` | A collection of collections for spatial arrays on the `SOMAMeasurements`. The top-level collection is indexed by measurement name. The rows in the contained arrays correspond to features and may correspond to `var` of the associated `SOMAMeasurement`. |
| `img` | A `SOMAImageCollection` of images (single and multi-resolution). |
| `obsl` | A collection of spatial arrays and collections. The rows in these arrays correspond to observations and may correspond to `obs` of an `Experiment`. |
| `varl` | A collection of collections for spatial arrays on the `Measurement`s. The top-level collection is indexed by measurement name. The rows in the contained arrays correspond to features and may correspond to `var` of the associated `Measurement`. |
| `img` | A `Collection` of `MultiscaleImage`s |

---

#### **[NEW] SOMAImageCollection**
#### **[NEW] {class}`tiledbsoma.MultiscaleImage`**

A group of multi-resolution images that can be accessed by levels. Below are some sample operations on this collection type. Every `SOMAImageNDArray` in the collection must be mappable to the same physical space by translation and scaling only.
A group of multi-resolution images that can be accessed by levels. Below are some sample operations on this collection type. Every {class}`~tiledbsoma.DenseNDArray` in the collection must be mappable to the same physical space by scaling only.

| Operation | Description |
|-------------------|-------------------------------------------------------------------------|
| `levels` | Sequence of level numbers in the slide |
| `dimensions` | A `(width, height)` tuple for level 0 of the slide |
| `level_dimensions`| A sequence of down-sample factors for each level of the slide |
| `.levels()` | Returns a mapping of `{member_name: (uri, shape)}`. |
| {attr}`~tiledbsoma.MultiscaleImage.coordinate_space` | Coordinate space for the base level of this `MultiscaleImage` |
| {obj}`~tiledbsoma.MultiscaleImage.get_transform_to_level` / {obj}`~tiledbsoma.MultiscaleImage.get_transform_from_level` | Get `ScaleTransform` to and from specified level to base level of image |
1 change: 1 addition & 0 deletions docs/conf.py
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Expand Up @@ -46,6 +46,7 @@
'numpy': ('http://docs.scipy.org/doc/numpy', None),
'scipy': ('http://docs.scipy.org/doc/scipy/reference', None),
'anndata': ('https://anndata.readthedocs.io/en/latest/', None),
'spatialdata': ("https://spatialdata.scverse.org/en/stable/", None),
'pandas': ('https://pandas.pydata.org/docs/', None),
'scanpy': ('https://scanpy.readthedocs.io/en/stable/', None),
'torch': ('https://pytorch.org/docs/stable/', None),
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