pyMINFLUX

Reader, analyzer, and viewer of MINFLUX raw data.

Installation

Apps

Compiled executables (apps) for Linux, macOS and Windows can be downloaded from the release page.

Please note: since pyMINFLUX.exe on Windows and pyMINFLUX.app on macOS come from an unidentified developer and are not (yet) digitally signed, both operating systems may prevent them from running. In this case, please have a look at our troubleshooting guide. Please mind that this only applies to the compiled executables.

On macOS, it is recommended to download the zipped app via curl or wget to prevent Gatekeeper from quarantining the application (see also troubleshooting guide).

$ curl -LJO https://github.com/bsse-scf/pyMINFLUX/releases/download/0.5.0/pyMINFLUX_0.5.0_macos_m1.zip

Alternatively, if wget is installed:

$ wget --content-disposition https://github.com/bsse-scf/pyMINFLUX/releases/download/0.5.0/pyMINFLUX_0.5.0_macos_m1.zip

The equivalent call for Powershell on Windows is:

$ Invoke-WebRequest -Uri "https://github.com/bsse-scf/pyMINFLUX/releases/download/0.5.0/pyMINFLUX_0.5.0_win.zip" -OutFile C:\pyMINFLUX_0.5.0_win.zip 

Adapt the path for the -OutFile argument as needed.

pip

The latest version of pyMINFLUX can also be installed from pypi.org. pyMINFLUX is compatible with and tested on Python 3.10 and 3.11. It is recommended to install pyMINFLUX in a conda environment as follows:

$ conda create -n pyminflux-env python=3.11  # or 3.10
$ conda activate pyminflux-env
$ pip install --upgrade pyminflux

pyMINFLUX can then easily be run from the command line:

$ pyminflux

uv

pyMINFLUX can also be installed with uv. If not yet installed, installing uv requires one line in the terminal depending on your OS, see uv installation guide. After installing uv, pyMINFLUX can be run as follows (installation and execution are combined in one step):

For the latest stable release on PyPI:

$ uvx --refresh pyminflux

For a development version on GitHub (supported for pyminflux versions > 0.6.0):

$ uvx --refresh --from 'git+https://github.com/bsse-scf/pyMINFLUX@bead_alignment' pyminflux

For developers and tinkerers

pyMINFLUX is compatible with and tested on Python 3.10, 3.11, and 3.12. For development, it is recommended to install pyMINFLUX in editable mode in a conda environment as follows:

$ conda create -n pyminflux-env python=3.11  # or 3.10, 3.12
$ conda activate pyminflux-env
$ git clone https://github.com/bsse-scf/pyMINFLUX /path/to/pyminflux
$ cd /path/to/pyminflux
$ python -m pip install -e .
$ pip install -r dev-requirements.txt

If you want to participate to the development of pyMINFLUX, please have a look at how you can contribute and at our code of conduct.

Running pyMINFLUX from console

$ cd /path/to/pyminflux
$ python pyminflux/main.py  # As a Python script, or
$ pyminflux                 # as a standalone tool

Using the pyMINFLUX API from Python scripts or Jupyter Notebooks

The graphical user interface is not the only way to use pyMINFLUX. Indeed, the pyMINFLUX core library can be integrated in Python scripts or Jupyter Notebooks. The documentation for the pyMIMFLUX core API can be found on https://pyminflux.ethz.ch/api/pyminflux/; an example Jupyter Notebook is bundled with the code.

User manual

The user manual is hosted in the project wiki.

Official website

The official pyMINFLUX website is on https://pyminflux.ethz.ch.

pyMINFLUX mailing list

Join the pyMINFLUX mailing list for release announcements and further discussions.

Contributing to pyMINFLUX

We value the contribution of our community members, and to make sure that everyone can profit from this collaboration, we ask you to have a look at our CONTRIBUTING and CODE OF CONDUCT documents.

Citing pyMINFLUX

If you use pyMINFLUX in your research, please cite this repository as follows:

Aaron Ponti, Javier Casares Arias, & Thomas Horn. (2023). pyMINFLUX. Zenodo.