Single-Cell Image Analysis Package

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  • License: MIT License (MIT)
  • Author: Ajit Johnson Nirmal
  • Tags image analysis , multiplex imaging , single cell analysis
  • Requires: Python >=3.7, <4.0
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Project description

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.

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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.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for ajitjohnson from gravatar.com ajitjohnson

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: MIT License (MIT)
  • Author: Ajit Johnson Nirmal
  • Tags image analysis , multiplex imaging , single cell analysis
  • Requires: Python >=3.7, <4.0
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