# pyHiM
*pyHiM* implements the analysis of multiplexed DNA-FISH data, as described in our [Hi-M paper](https://www.nature.com/articles/s41596-019-0269-9).
## Documentation
Find the full documentation in [ReadtheDocs](https://pyhim.readthedocs.io/en/latest/).
To install, please follow the instructions [here](https://pyhim.readthedocs.io/en/latest/getting_started/quick_install.html).
After you installed *pyHiM*, you may want to consult a [guide](https://pyhim.readthedocs.io/en/latest/user_guide/pyhim_presentation.html) on how to use it.
If you are a developer, follow instructions [here](https://pyhim.readthedocs.io/en/latest/contributor/dev_env.html).
## Publications
For more information on Hi-M, please see the following resources:
- [Hi-M protocol](https://github.com/NollmannLab/HiM_protocol)
- [Hi-M method](https://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30011-5)
- [A recent Hi-M application using *pyHiM*](https://www.nature.com/articles/s41588-021-00816-z)
## Dependencies
*pyHiM* was entirely written in python and makes extensive use of the following packages:
- [Astropy](https://www.astropy.org/)
- [scikit-image](https://scikit-image.org/)
- [starDist](https://github.com/stardist/stardist)
*pyHiM* also uses functions from [Big-FISH](https://github.com/fish-quant/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](http://www.nollmannlab.org) at the [Center of Structural Biology](http://www.cbs.cnrs.fr), a department of the [CNRS](http://www.cnrs.fr) and the [INSERM](http://www.inserm.fr).
