PyReconstruct is an actively maintained, extensible version of Reconstruct written in Python in the lab of Kristen Harris at the University of Texas at Austin. Please check out our paper introducing PyReconstruct and feel free to send us a message if you have any questions:
- Michael Chirillo: michael.chirillo@uri.edu
- Dusten Hubbard: dusten@utexas.edu
An installation guide, quickstart, and manuals can be found at our lab's wiki site hosted at UT Austin and at the PyReconstruct repo wiki. A quick launch guide follows below.
PyReconstruct can be installed into a virtual environment using the command line or it can be installed using a graphical installer similar to a normal desktop app.
In a virtual environment running Python 3.11, install bleeding-edge PyReconstruct:
pip install git+https://github.com/synapseweb/pyreconstruct
or stable PyReconstruct:
pip install pyreconstruct
then launch PyReconstruct from the command line:
PyReconstruct
To install a dev version of PyReconstruct, see here.
Not comfortable using command line? You can install PyReconstruct like a normal desktop app by downloading an installer and following the instructions below.
(Note for Windows and macOS users: PyReconstruct isn't yet "code-signed", which means you must explicitly give your system permission to run the app. The steps below walk you through this process.)
Download the .exe installer for Windows and open it. Your system may warn you this PyReconstruct isn't yet "code-signed". If you trust us, simply click More info then Run anyway.
Download the .dmg installer, open it, and drag PyReconstruct into your Applications folder. Your system may warn you that PyReconstruct isn't yet "code-signed" and a short Read Before First Launch note that walks you through the process.
Download the installer shell script and run it. This will add PyReconstruct to your applications menu.
If you notice a problem, would like to suggest a feature, or have ideas on improving our documentation, please submit an issue. We appreciate the help!
If you use PyReconstruct in published work, please cite our paper:
@article{Chirillo2025,
title = {{PyReconstruct}: {A} fully open-source, collaborative successor to {Reconstruct}},
author = {Chirillo, Michael A. and Falco, Julian N. and Musslewhite, Michael D. and Lindsey, Larry F. and Harris, Kristen M.},
journal = {Proceedings of the National Academy of Sciences},
volume = {122},
number = {31},
pages = {e2505822122},
year = {2025},
month = {July},
doi = {10.1073/pnas.2505822122},
url = {https://www.pnas.org/doi/10.1073/pnas.2505822122}
}
and this repo if you'd like:
@software{Falco2025,
author = {Kristen Harris Lab},
title = {PyReconstruct},
version = {1.20.0},
month = {June},
year = {2026}
url = {https://github.com/synapseweb/pyreconstruct},
}