Serial-section · Volume EM
PyReconstruct¶
Annotation and 3D reconstruction for volume electron microscopy.
Windows, macOS & Linux Free and open source
Who it's for¶
Neuroscientists and EM researchers who trace neural structures across stacks of serial sections, measure morphology, and build 3D reconstructions of cells, organelles, and synapses.
01
Trace & annotate¶
Outline structures across serial sections. Refine segmentation, organize objects, and keep your annotations together.
02
Align & reconstruct¶
Align your image stack and build 3D views to understand how structures connect across sections.
03
Measure & explore¶
Inspect object measurements and work with large autosegmented series in the .jser series format.
Install¶
Download the current stable release, v1.25.0, for your computer.
Windows¶
64-bit · Windows 10 or later
Includes Python. Builds are unsigned; see the first-launch instructions if Windows shows a SmartScreen warning.
Linux¶
64-bit · glibc 2.28 or later
Includes Python. Or install with curl -fsSL https://pyreconstruct.org/install.sh | bash.
Installation help · All releases & checksums · Stable & Beta channels
Documentation¶
The user guide, performance notes, developer setup, and the Harris lab wiki.
About this distribution¶
PyReconstruct is the modern successor to Reconstruct. This site documents an independently maintained distribution that tracks SynapseWeb/PyReconstruct, with performance improvements, installers, and ongoing interface updates.
Citation¶
The upstream PyReconstruct project was developed in the Kristen Harris Lab at The University of Texas at Austin and introduced in PNAS (2025).