SCIMAP 0.3.1

Single-Cell Image Analysis Package

Single-Cell Image Analysis Package

Scimap is a scalable toolkit for analyzing single-cell multiplex imaging data. The package uses the anndata framework making it easy to integrate with other popular single-cell analysis toolkits such as scanpy. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

Installation

Install it directly into an activated virtual environment:

$ pip install scimap

After installation, the package can imported:

$ python
>>> import scimap as sm

To get started, read the documentation.