squidpy

Squidpy - Spatial Single Cell Analysis in Python

These details have not been verified by PyPI

Project links

Development Status
- 5 - Production/Stable
Environment
- Console
Framework
- Jupyter
Intended Audience
- Science/Research
License
- OSI Approved :: BSD License
Natural Language
- English
Operating System
- MacOS :: MacOS X
- POSIX :: Linux
Programming Language
Topic
- Scientific/Engineering :: Bio-Informatics
- Scientific/Engineering :: Visualization
Typing
- Typed

Project description

Squidpy - Spatial Single Cell Analysis in Python

Squidpy is a tool for the analysis and visualization of spatial molecular data. It builds on top of scanpy and anndata, from which it inherits modularity and scalability. It provides analysis tools that leverages the spatial coordinates of the data, as well as tissue images if available.

Visit our documentation for installation, tutorials, examples and more.

Manuscript

Please see our preprint on bioRxiv to learn more.

Squidpy’s key applications

Build and analyze the neighborhood graph from spatial coordinates.
Compute spatial statistics for cell-types and genes.
Efficiently store, analyze and visualize large tissue images, leveraging skimage.
Explore anndata and the large tissue image in napari.

Installation

Install Squidpy via PyPI by running:

pip install squidpy
# or with napari included
pip install 'squidpy[interactive]'

Contributing to Squidpy

We are happy about any contributions! Before you start, check out our contributing guide.

Project details

These details have not been verified by PyPI

Project links

Development Status
- 5 - Production/Stable
Environment
- Console
Framework
- Jupyter
Intended Audience
- Science/Research
License
- OSI Approved :: BSD License
Natural Language
- English
Operating System
- MacOS :: MacOS X
- POSIX :: Linux
Programming Language
Topic
- Scientific/Engineering :: Bio-Informatics
- Scientific/Engineering :: Visualization
Typing
- Typed

Release history Release notifications | RSS feed

1.6.2

Nov 12, 2024

1.6.1

Sep 2, 2024

1.6.0

Jul 23, 2024

1.5.0

May 27, 2024

1.4.1

Feb 6, 2024

1.4.0

Feb 6, 2024

1.3.1

Oct 9, 2023

1.3.0

Jun 16, 2023

1.2.3

Oct 18, 2022

1.2.2

May 17, 2022

1.2.1

May 14, 2022

1.2.0

Apr 19, 2022

1.1.2

Sep 10, 2021

1.1.1

Aug 16, 2021

This version

1.1.0

Jul 2, 2021

1.0.1

Jun 13, 2021

1.0.0

Feb 20, 2021

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