Metadata-Version: 2.1
Name: campa
Version: 1.1.0
Home-page: https://github.com/theislab/campa
Download-URL: https://pypi.org/project/campa/
Author: Hannah Spitzer, Scott Berry
Author-email: hannah.spitzer@helmholtz-muenchen.de, scott.berry@unsw.edu.au
Maintainer: Hannah Spitzer, Scott Berry
Maintainer-email: hannah.spitzer@helmholtz-muenchen.de, scott.berry@unsw.edu.au
License: BSD
Project-URL: Documentation, https://campa.readthedocs.io/en/stable
Project-URL: Source Code, https://github.com/theislab/campa
Keywords: bio-informatics,image analysis,multiplexed imaging,single-cell,spatial data analysis,subcellular landmarks
Platform: Linux
Platform: MacOSX
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Typing :: Typed
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Environment :: Console
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst; charset=UTF-8
License-File: LICENSE
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Requires-Dist: pandas (>=1.2.0)
Requires-Dist: scanpy[leiden] (>=1.8.0)
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CAMPA - Conditional Autoencoder for Multiplexed Pixel Analysis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CAMPA is a framework for quantiative analysis of subcellular multi-channel imaging data.
It consists of a workflow that generates consistent subcellular landmarks (CSLs)
using conditional Variational Autoencoders (cVAE).
The output of the CAMPA workflow is an `anndata`_ object that contains interpretable
per-cell features summarizing the molecular composition
and spatial arrangement of CSLs inside each cell.

.. image:: https://raw.githubusercontent.com/theislab/campa/main/docs/source/_static/img/Figure1ab.jpg
    :alt: CAMPA title figure
    :width: 600px
    :align: center
    :target: https://www.biorxiv.org/content/10.1101/2022.05.07.490900v1

Visit our `documentation`_ for installation and usage examples.


Manuscript
----------
Please see our preprint
*"Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps"*
(`Spitzer, Berry et al. (2022)`_) to learn more.


Installation
------------

CAMPA was developed for Python 3.9 and can be installed by running::

    pip install campa


Contributing
------------
We are happy about any contributions! Before you start, check out our `contributing guide`_.

.. _anndata: https://anndata.readthedocs.io/en/stable/
.. _documentation: https://campa.readthedocs.io/en/stable/
.. _`data and experiment paths`: https://campa.readthedocs.io/en/stable/overview.html#campa-config
.. _`Spitzer, Berry et al. (2022)`: https://www.biorxiv.org/content/10.1101/2022.05.07.490900v1
.. _contributing guide: https://github.com/theislab/campa/blob/main/CONTRIBUTING.rst
