Metadata-Version: 2.1
Name: scimap
Version: 0.16.12
Summary: Single-Cell Image Analysis Package
Home-page: https://pypi.org/project/scimap
License: MIT
Keywords: image analysis,multiplex imaging,single cell analysis
Author: Ajit Johnson Nirmal
Author-email: ajitjohnson.n@gmail.com
Requires-Python: >=3.7,<4.0
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Dist: PhenoGraph (>=1.5.7,<2.0.0)
Requires-Dist: TiffFile (>=2020.11.18,<2021.0.0)
Requires-Dist: anndata (>=0.7.4,<0.8.0)
Requires-Dist: dask[array] (>=2.30.0,<3.0.0)
Requires-Dist: gensim (>=3.8.3,<4.0.0)
Requires-Dist: llvmlite (<=0.34.0)
Requires-Dist: matplotlib (>=3.2.1,<4.0.0)
Requires-Dist: mkdocs (>=1.1.2,<2.0.0)
Requires-Dist: mkdocs-material (>=7.1.1,<8.0.0)
Requires-Dist: napari (>=0.4.2,<0.5.0)
Requires-Dist: numba (<=0.51.2)
Requires-Dist: numpy (>=1.18.5,<2.0.0)
Requires-Dist: pandas (>=1.0.4,<2.0.0)
Requires-Dist: plotly (>=4.12.0,<5.0.0)
Requires-Dist: pytest (>=5.4.3,<6.0.0)
Requires-Dist: pytest-xvfb (>=2.0.0,<3.0.0)
Requires-Dist: scanpy (>=1.6.0,<2.0.0)
Requires-Dist: scipy (>=1.4.1,<2.0.0)
Requires-Dist: seaborn (>=0.11.0,<0.12.0)
Requires-Dist: shapely (>=1.7.1,<2.0.0)
Requires-Dist: sklearn (>=0.0,<0.1)
Requires-Dist: tifffile (>=2020.6.3,<2021.0.0)
Requires-Dist: zarr (>=2.5.0,<3.0.0)
Project-URL: Documentation, https://scimap.readthedocs.io
Project-URL: Repository, https://github.com/ajitjohnson/scimap
Description-Content-Type: text/markdown

# Single-Cell Image Analysis Package
<br>

[![build: Unix-Mac-Win](https://github.com/ajitjohnson/scimap/actions/workflows/build-unix-mac-win.yml/badge.svg)](https://github.com/ajitjohnson/scimap/actions/workflows/build-unix-mac-win.yml)
[![Docs](https://github.com/ajitjohnson/scimap/actions/workflows/docs.yml/badge.svg)](https://github.com/ajitjohnson/scimap/actions/workflows/docs.yml)
[![Downloads](https://pepy.tech/badge/scimap)](https://pepy.tech/project/scimap)
[![PyPI Version](https://img.shields.io/pypi/v/scimap.svg)](https://pypi.org/project/scimap)
[![PyPI License](https://img.shields.io/pypi/l/scimap.svg)](https://pypi.org/project/scimap)
[![Gitter chat](https://badges.gitter.im/scimap_io/community.png)](https://gitter.im/scimap_io/community)

<br>

<img src="./docs/assets/scimap_logo.png" style="max-width:700px;width:100%" >

<br> 

Scimap is a scalable toolkit for analyzing spatial molecular data. The underlying framework is generalizable to spatial datasets mapped to XY coordinates. The package uses the [anndata](https://anndata.readthedocs.io/en/stable/anndata.AnnData.html) framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. The Python-based implementation efficiently deals with large datasets of millions of 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:

```python
$ pip install scimap
```

After installation, the package can be imported as:

```python
$ python
>>> import scimap as sm
```

## Get Started


#### Detailed documentation of `scimap` functions and tutorials are available [here](http://scimap.xyz/).

*SCIMAP* development is led by [Ajit Johnson Nirmal](https://ajitjohnson.com/) at the Laboratory of Systems Pharmacology, Harvard Medical School.

## Funding
This work is supported by the following NIH grant K99-CA256497


