PyReconstruct¶
PyReconstruct is an open-source desktop application for tracing, annotating, and 3D-reconstructing serial-section and volume electron-microscopy (EM) data. It is the modern, actively maintained successor to Reconstruct.
This site documents an independently developed and maintained distribution of PyReconstruct. It tracks the upstream SynapseWeb/PyReconstruct project and builds on it with 3-4x faster opens on large series, one-click installers, an in-app updater with Stable and Beta channels, and ongoing quality-of-life fixes and features.
Who it's for¶
Neuroscientists and EM researchers who trace neural structures across stacks of
serial sections - segmenting objects, aligning sections, measuring morphology,
and building 3D reconstructions of cells, organelles, and synapses from
volume-EM datasets. It reads and writes the .jser series format and handles
large autosegmented series with hundreds of thousands of traces.
Install¶
Download a one-click build for the current stable release, v1.21.0 - no Python required.
| Platform | Download |
|---|---|
| Windows (x86_64) | PyReconstruct-1.21.0-Windows-x86_64-Setup.exe |
| macOS (Apple Silicon) | PyReconstruct-1.21.0-macOS-arm64.dmg |
| macOS (Intel) | PyReconstruct-1.21.0-macOS-x86_64.dmg |
| Linux (x86_64) | PyReconstruct-1.21.0-Linux-installer.tar.gz |
All builds, checksums, and past versions are on the
Releases page.
Developers can install from source with pip or uv.
Full instructions, including the macOS Gatekeeper step and the in-app updater, are in the User Guide.
Where to go next¶
- User Guide - install, open a series, the tracing tools, data lists, alignment, 3D reconstruction, and backups.
- Performance - benchmarks for the fork's speed work.
- Developing with uv - the uv-based development workflow.
- Contributing
- dev setup, branch/commit conventions, tests, and the PR process.
- Source code and issues on GitHub.
Citation¶
PyReconstruct was developed in the Kristen Harris Lab at The University of Texas at Austin and introduced in PNAS (2025), doi:10.1073/pnas.2505822122. See the README for full provenance, performance notes, and citation details.