Metadata-Version: 2.4
Name: CIMA
Version: 1.1.3
Summary: CIMA: Chromatin Imaging Analysis is a Python package designed to facilitate the automated detection, assessment, and analysis of complex chromatin tracing experiments.
Author: Ivan Piacere, Anthony Palmieri
Author-email: Irene Farabella <irene.farabella@iit.it>, Mattia Roccatello <mattia.rocatello@iit.it>, Iago Maceda Porto <iago.maceda@iit.it>
License-Expression: BSD-3-Clause
Project-URL: homepage, https://gitlab.iit.it/ina-public/cima/
Project-URL: documentation, https://cima-rtd.readthedocs.io/en/stable/index.html
Project-URL: issues, https://gitlab.iit.it/ina-public/cima/-/issues
Keywords: bioinformatics,chromatin,chromatin imaging,genomics,microscopy,chromosome structure
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: POSIX :: Linux
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
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Requires-Dist: hdbscan==0.8.42
Requires-Dist: ipykernel==7.2.0
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Requires-Dist: scikit-learn==1.8.0
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Requires-Dist: scipy==1.17.1
Requires-Dist: seaborn==0.13.2
Requires-Dist: tqdm==4.67.3
Provides-Extra: all
Requires-Dist: CIMA[dev,docs,release]; extra == "all"
Provides-Extra: docs
Requires-Dist: sphinx>=8; extra == "docs"
Requires-Dist: myst-nb; extra == "docs"
Requires-Dist: sphinx-copybutton; extra == "docs"
Requires-Dist: sphinx-rtd-theme; extra == "docs"
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Dynamic: license-file

# CIMA

![Model](docs/_static/images/cima-log.png)

**Chromatin IMaging Analysis (CIMA)** is a Python package designed to facilitate the automated detection, assessment, and analysis of complex chromatin tracing experiments

| | |
| :--- | :--- |
| **Latest release** | [![PyPI version](https://img.shields.io/pypi/v/CIMA?label=PyPI)](https://pypi.org/project/CIMA/) [![Bioconda version](https://img.shields.io/conda/v/bioconda/cima?label=Bioconda)](https://anaconda.org/bioconda/cima) |
| **License** | [![License: BSD-3-Clause](https://img.shields.io/badge/license-BSD-yellow)](https://gitlab.iit.it/ina-public/cima/-/blob/main/LICENCE)
| **Python** | ![Python 3.12+](https://img.shields.io/badge/python-3.12%2B-blue.svg)
| **Documentation status** | [![Documentation](https://readthedocs.org/projects/cima-rtd/badge/?version=stable)](https://cima-rtd.readthedocs.io/en/stable/) |
| **Downloads** | [![PyPI downloads](https://static.pepy.tech/personalized-badge/CIMA?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPI%20downloads)](https://pypi.org/project/CIMA/) [![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/cima?label=Bioconda%20downloads)](https://anaconda.org/bioconda/cima)
| **Citation** | [![Citation](https://img.shields.io/badge/Citation-Citation-orange.svg)](#citation) |
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| **Citation** | [![Citation](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtz540-blue)](https://doi.org/10.1371/journal.pgen.1007872) | 
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## Installation

See the
[Installation Guide](https://cima-rtd.readthedocs.io/en/stable/installation.html)
for detailed instructions.


## Tutorials

CIMA includes a collection of tutorial notebooks covering:

- chromatin segment detection
- quality assessment
- 3D reconstruction assessment
- comparison with orthogonal methods
- morphological feature extraction

The tutorials are available in the
[Tutorial documentation](https://cima-rtd.readthedocs.io/en/stable/tutorial/index.html).


## Command-line tools

> **NOTE**
> The command-line interface is currently being rewritten due to the updates for CIMA 1.0.
> It will be available in a future release.


## API Reference

The complete API documentation is available on
[Read the Docs](https://cima-rtd.readthedocs.io/en/stable/genindex.html)


## Citation

If you use CIMA in your research, please cite the software using the
information provided in `CITATION.cff`.

If your work specifically relies on the chromatin tracing methodology, please also cite:

> Nir* G, Farabella* I, Pérez Estrada* C, Ebeling* CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet. 2018 Dec 26;14(12):e1007872. doi: 10.1371/journal.pgen.1007872. PMID: 30586358; PMCID: PMC6324821. [LINK](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007872)

If your work relies on TEMPy-based functionality, please also cite:

> Farabella et al (2015) TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits. J. Appl. Cryst. 48, 1314-1323 [LINK](https://journals.iucr.org/j/issues/2015/04/00/vg5014/index.html)


## Support

If you have questions or encounter issues, you can:

- Open an issue on GitLab
- Contact:
    - irene.farabella@iit.it
    - iago.maceda@iit.it
