pyhim 0.9.1

Pipeline and functions to analyse multiplexed DNA-FISH data

pyHiM

pyHiM implements the analysis of multiplexed DNA-FISH data, as described in our Hi-M paper.

Documentation

Find the full documentation in ReadtheDocs and tutorials illustrating the main steps of pyHiM analysis pipeline.

To install, please follow the instructions here.

After you installed pyHiM, you may want to consult a guide on how to use it.

If you are a developer, follow instructions here.

Publications

For more information on Hi-M, please see the following resources:

• Hi-M protocol
• Hi-M method
• A recent Hi-M application using pyHiM

Dependencies

pyHiM was entirely written in python and makes extensive use of the following packages:

• Astropy
• scikit-image
• starDist

pyHiM also uses functions from Big-FISH to perform Gaussian 3D fits.

Support

If you have any question relative to the repository, please open an issue. You can also contact Marcelo Nollmann.

License

pyHiM is licensed under GPLv3 (see LICENSE.txt). Packages used by pyHiM are licensed under the revised 3-clause BSD style license.

Check COPYRIGHT.txt for a list of authors and the git history for their individual contributions.

pyHiM is a software package developed by the Nollmann Lab at the Center of Structural Biology, a department of the CNRS and the INSERM.