OPEN SOURCE · ELECTRON MICROSCOPY
PyReconstruct¶
An open-source desktop application for tracing, annotating, and 3D reconstruction of serial-section and volume electron microscopy (EM) data.
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¶
Stable release v1.22.3. Choose the build 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.
Installation help · All releases & checksums · Stable & Beta channels
Documentation¶
The user guide, performance notes, and developer setup.
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).