Installing PyReconstruct

Installing PyReconstruct

There are two ways to install PyReconstruct: a one-click installer (recommended for most users) or a from-source install with pip (for developers and other platforms).

One-click installers (Windows, macOS, and Linux)

Download the latest build from Releases — no Python required.

• Windows — PyReconstruct-<version>-Windows-x86_64-Setup.exe. This is a per-user installer (no administrator rights required). Builds are unsigned for now, so Windows SmartScreen may warn that the publisher is unknown; choose More info ▸ Run anyway. Re-running a newer installer upgrades the existing installation in place.

• macOS (Apple Silicon or Intel) — PyReconstruct-<version>-macOS-arm64.dmg on Apple Silicon, or PyReconstruct-<version>-macOS-x86_64.dmg on an Intel Mac. Open the .dmg and drag PyReconstruct onto the Applications shortcut. Builds are unsigned for now, so the first launch of a browser-downloaded copy is blocked by Gatekeeper. Clear the quarantine flag once in Terminal:

  xattr -dr com.apple.quarantine /Applications/PyReconstruct.app
  

  Alternatively, the first time macOS shows the "could not verify" dialog, open System Settings ▸ Privacy & Security and click Open Anyway.

📸 Screenshot: the macOS .dmg window showing the app and the Applications drop target.

Both macOS builds are native (arm64 and x86_64), and the in-app updater serves each Mac its matching architecture.

• Linux — PyReconstruct-<version>-Linux-installer.tar.gz. Extract it and run bash install.sh — a no-root .sh installer that builds an isolated virtual environment, puts a pyreconstruct launcher on your PATH, and adds an application-menu entry. It needs a system Python 3.11 (python3.11 + venv; on Debian/Ubuntu, sudo apt install python3.11 python3.11-venv) and targets x86_64. To update, re-run install.sh.

From source (Linux, other platforms, and developers)

In a Python 3.11 environment (the project pins >=3.11,<3.12):

pip install git+https://github.com/dustenhubbard/PyReconstruct
PyReconstruct

pip pulls in the runtime dependencies (PySide6, VTK, vedo, NumPy, SciPy, scikit-image, shapely, trimesh, zarr, and others). For a full development setup (conda environment, tests, code layout), see CONTRIBUTING.md.

Launching the app

• From an installer: launch PyReconstruct like any other installed application.
• From a source install: run PyReconstruct on the command line.

The command accepts a few optional flags, e.g. PyReconstruct -f path/to/series.jser to open a series directly on launch. (Run PyReconstruct --help for the full list.)

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