CIMA

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

Latest release
License
Python
Documentation status
Downloads
Citation

Installation

See the Installation Guide 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.

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

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

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

Support

If you have questions or encounter issues, you can:

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