Installation & Setup

This guide will walk you through installing OpenHCS on your computer and launching the application for the first time.

System Requirements

Operating Systems: - Linux - Windows 10/11 (via WSL2 - Windows Subsystem for Linux) - macOS

Minimum Requirements: - Python 3.11 or newer

Install OpenHCS with required GUI dependencies:

pip install openhcs[gui]

This will install openhcs along with the GUI dependencies for full functionality.

If you want a minimal installation, you can choose to do a CPU-only install: (for CI/testing environments)

# Install with minimal dependencies
 pip install openhcs --no-deps
 pip install numpy scipy scikit-image pandas

 # Enable CPU-only mode
 export OPENHCS_CPU_ONLY=1

The installation may take several minutes as it downloads and installs all dependencies.

Launching OpenHCS

Once installed, you can launch the OpenHCS graphical interface with a command:

openhcs
#or
python -m openhcs.pyqt_gui

First Launch

When you first launch OpenHCS, you’ll see:

  1. Main Window: The central control panel

  2. Plate Manager: For organizing your microscopy experiments

  3. Pipeline Editor: For creating and editing image processing pipelines

You’re now ready to start using OpenHCS! Proceed to the next section to learn about the basic interface.

Updating OpenHCS

To update to the latest version of OpenHCS:

pip install --upgrade openhcs[all]

It’s recommended to check for updates periodically to get the latest features and bug fixes.