https://github.com/biocpy/spatialfeatureexperiment

https://github.com/biocpy/spatialfeatureexperiment

Last synced: 11 months ago
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• Host: GitHub
• URL: https://github.com/biocpy/spatialfeatureexperiment
• Owner: BiocPy
• License: mit
• Created: 2025-03-01T01:04:32.000Z (11 months ago)
• Default Branch: master
• Last Pushed: 2025-03-01T01:07:41.000Z (11 months ago)
• Last Synced: 2025-03-01T02:19:53.160Z (11 months ago)
• Language: Python
• Size: 29.3 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.txt
  • Authors: AUTHORS.md

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README

          
[![PyPI-Server](https://img.shields.io/pypi/v/SpatialFeatureExperiment.svg)](https://pypi.org/project/SpatialFeatureExperiment/)

![Unit tests](https://github.com/BiocPy/SpatialFeatureExperiment/actions/workflows/run-tests.yml/badge.svg)

# SpatialFeatureExperiment

A Python package for storing and analyzing spatial-omics experimental data. This package provide the `SpatialFeatureExperiment` class, based on the [R package and class](https://github.com/pachterlab/SpatialFeatureExperiment).

## Install

To get started, install the package from [PyPI](https://pypi.org/project/SpatialFeatureExperiment/)

```bash

pip install spatialfeatureexperiment

```

## Quick Usage

This package uses shapely and geopandas to support the `*_geometries` slots.

```python

from spatialexperiment import SpatialFeatureExperiment

import numpy as np

import geopandas as gpd

from shapely.geometry import Polygon

nrows = 200

ncols = 500

counts = np.random.rand(nrows, ncols)

polys = gpd.GeoSeries(

    [

        Polygon([(1, -1), (1, 0), (0, 0)]),

        Polygon([(3, -1), (4, 0), (3, 1)]),

    ]

)

colgeoms = {"polygons" : gpd.GeoDataFrame({"geometry": polys})}

tspe = SpatialFeatureExperiment(assays={"spots": counts}, col_geometries=colgeoms)

```

## Note

This project has been set up using [BiocSetup](https://github.com/biocpy/biocsetup)

and [PyScaffold](https://pyscaffold.org/).