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SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data\n\u003cbr\u003e\n\n[![build-unix-mac-win](https://github.com/labsyspharm/scimap/actions/workflows/build-unix-mac-win.yml/badge.svg)](https://github.com/labsyspharm/scimap/actions/workflows/build-unix-mac-win.yml)\n[![docs](https://github.com/labsyspharm/scimap/actions/workflows/docs.yml/badge.svg)](https://github.com/labsyspharm/scimap/actions/workflows/docs.yml)\n[![Downloads](https://pepy.tech/badge/scimap)](https://pepy.tech/project/scimap)\n[![PyPI Version](https://img.shields.io/pypi/v/scimap.svg)](https://pypi.org/project/scimap)\n[![PyPI License](https://img.shields.io/pypi/l/scimap.svg)](https://pypi.org/project/scimap)\n[![DOI](https://joss.theoj.org/papers/10.21105/joss.06604/status.svg)](https://doi.org/10.21105/joss.06604)\n\n\u003cbr\u003e\n\n\u003cimg src=\"./docs/assets/scimap_logo.jpg\" style=\"max-width:700px;width:100%\" \u003e\n\n\u003cbr\u003e \n\n*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.\n\n## Citing scimap\nNirmal et al., (2024). SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data. *Journal of Open Source Software*, 9(97), 6604, [https://doi.org/10.21105/joss.06604](https://joss.theoj.org/papers/10.21105/joss.06604#)\n\n## Installation\n\nWe strongly recommend installing `scimap` in a fresh virtual environment.\n\n```\n# If you have conda installed\nconda create --name scimap python=3.10\nconda activate scimap\n```\n\nInstall `scimap` directly into an activated virtual environment:\n  \n**Firstly, we suggest installing `scimap` and `napari` together to enable visualization out of the box. Keep in mind, `napari` needs a GUI toolkit, such as PyQt. If you run into any issues because of your computer's operating system, install `scimap` and `napari` separately by following the guidance in `napari's` documentation.**\n\nHere's how you can install both using pip:\n\n```python\npip install \"scimap[napari]\"\n```\n\n**If you encounter a problem with PyQt6 during the installation, you can install `scimap` alone first. 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Check out our guidelines at [https://scimap.xyz/contribute/](https://scimap.xyz/contribute/) for detailed instructions.\n\n\n## Funding\nThis work was supported by the following NIH grant K99-CA256497\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flabsyspharm%2Fscimap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flabsyspharm%2Fscimap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flabsyspharm%2Fscimap/lists"}