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Single-Cell Image Analysis Package

Project description

Single-Cell Image Analysis Package

Scimap is a scalable toolkit for analyzing single-cell imaging data using anndata data structuring framework. It includes preprocessing, visualization, clustering, spatial analysis and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

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Setup

Requirements

  • Python 3.7+

Installation

Install it directly into an activated virtual environment:

$ pip install scimap

Usage

After installation, the package can imported:

$ python
>>> import scimap
>>> scimap.__version__

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