PyReconstruct user guide
The full, current user guide is at PyReconstruct User Guide on pyreconstruct.org.
These wiki pages collect reference material and lab-specific workflows for PyReconstruct, an extensible successor to RECONSTRUCT™ written in Python. Please have a look at the source code on our lab's GitHub site. Questions can be directed toward PyReconstruct's primary developers, Julian Falco (julian.falco@utexas.edu) and Michael Chirillo (m.chirillo@utexas.edu). You can navigate around this wiki by clicking the links below or in the sidebar to the left.
Citation for PyReconstruct:
Chirillo MA, Falco JN, Musslewhite MD, Lindsey LF, Harris KM. (2025) PyReconstruct: A fully open-source, collaborative successor to Reconstruct. PNAS 122 (31) e2505822122. https://doi.org/10.1073/pnas.2505822122
Research Resource ID for PyReconstruct: RRID:SCR_027562
Install PyReconstruct and get it up and running. | |
Go all out and get the developer version of PyReconstruct. | |
Start a new series and begin tracing. | |
Understand the layout and the various functions of the main window. | |
Find out more about alignments and aligning. | |
Get access to lists and list operations. | |
Learn how to filter using regular expressions. | |
Perform operations with and to your series. | |
Visualize objects in three dimensions. | |
Make a zarr from section images, or crop one around an object, on the lab's GPU server. | |
Curation (on pyreconstruct.org) | Make sure your work is in tip-top shape. |
Metadata (on pyreconstruct.org) | Leave comments in the field, assign curators to objects, and more. |
Miscellaneous (not written yet) | Explore a random collection of possibilities. |