SCIMAP 0.7.4

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

We strongly recommend installing scimap in a fresh virtual environment.

# If you have conda installed
conda create --name scimap python=3.7
conda activate scimap

Install scimap directly into an activated virtual environment:

$ pip install scimap
$ pip install napari[all] # For visualizing images

After installation, the package can imported as:

$ python
>>> import scimap as sm

Get Started

Detailed documentation of scimap functions and tutorials are available here.