Metadata-Version: 2.5
Name: spatialscape
Version: 0.6.0
Summary: Build static spatialscape viewer bundles from AnnData / SpatialData
Project-URL: Homepage, https://mictott.github.io/spatialscape/docs/
Project-URL: Documentation, https://mictott.github.io/spatialscape/docs/
Project-URL: Repository, https://github.com/mictott/spatialscape
Project-URL: Issues, https://github.com/mictott/spatialscape/issues
Project-URL: Changelog, https://github.com/mictott/spatialscape/blob/main/CHANGELOG.md
Author-email: Michael Totty <mictott@gmail.com>
License-Expression: MIT
License-File: LICENSE
Keywords: deck.gl,single-cell,spatial-transcriptomics,visium,visualization,xenium,zarr
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.11
Requires-Dist: anndata>=0.12
Requires-Dist: imageio>=2.34
Requires-Dist: numcodecs>=0.15
Requires-Dist: numpy>=1.26
Requires-Dist: pandas>=2.0
Requires-Dist: pillow>=10
Requires-Dist: pyarrow>=15
Requires-Dist: pydantic>=2.6
Requires-Dist: pyyaml>=6
Requires-Dist: scikit-image>=0.22
Requires-Dist: scipy>=1.11
Requires-Dist: tifffile>=2024.1
Requires-Dist: typer>=0.12
Requires-Dist: zarr>=3.0
Provides-Extra: dev
Requires-Dist: build>=1.2; extra == 'dev'
Requires-Dist: h5py>=3.10; extra == 'dev'
Requires-Dist: pytest>=8; extra == 'dev'
Requires-Dist: ruff>=0.5; extra == 'dev'
Provides-Extra: images
Requires-Dist: imagecodecs>=2024.1.1; extra == 'images'
Provides-Extra: tracks
Requires-Dist: pybigwig>=0.3.18; extra == 'tracks'
Description-Content-Type: text/markdown

# spatialscape (Python)

The command-line tool behind **spatialscape**, a static, reactive browser for spatial transcriptomics and
snRNA-seq. It turns a saved R object (`SpatialExperiment` / `SingleCellExperiment` as `.rds` or `.rda`, parsed in
Python) or AnnData / SpatialData files into viewer bundles (sharded Zarr v3 expression, observation arrays in
microns, OME-Zarr images, domain outlines, cell polygons), and ships the viewer itself so you can open them locally
or publish them as a website.

```bash
pip install spatialscape
spatialscape init analysis/spe_dlpfc.rds --id dlpfc    # writes dlpfc.yaml, a menu of what the data contains
# edit dlpfc.yaml: keep the annotations you want, name them, pick colors and the opening gene
spatialscape build dlpfc.yaml                          # -> bundles/dlpfc; rerun after any edit
spatialscape serve bundles --open                      # viewer + data at http://127.0.0.1:8787/
spatialscape site build bundles -o site                # folder to upload to any static host
```

`sscape` is a short alias for the same command. Documentation: https://mictott.github.io/spatialscape/docs/
Source and issues: https://github.com/MicTott/spatialscape
