Install

Download the app for your computer, or run Honeychrome as a Python package if you want to use plugins.

Most people should download the app for their platform. It needs no Python, R or other software, and the macOS and Windows builds are signed. Run Honeychrome with Python instead if you want to use plugins, or if there is no app for your system.

	Get it	Plugins
macOS (Apple Silicon)	honeychrome-v1.0.0-macos.dmg	No
Windows (x64)	Microsoft Store	No
Linux (Ubuntu 24.04 or later, x64)	honeychrome-v1.0.0-linux-x64.tar.gz	No
Any system with Python 3.12 or later	pip install honeychrome	Yes

Install the app

macOS

1. Download Honeychrome for macOS (Apple Silicon).
2. Open the disk image and drag honeychrome.app to your Applications folder.
3. Double-click the app in Applications to run it.

Windows

1. Open Honeychrome in the Microsoft Store.
2. Click Get or Install. The Store keeps Honeychrome up to date.
3. Start Honeychrome from the Start menu.

Linux

1. Download Honeychrome for Linux (x64, built for Ubuntu 24.04 or later with Wayland).
2. Extract the honeychrome folder and put it somewhere suitable for a single user or for the whole system.
3. In a terminal, change to the honeychrome folder and run ./install_linux.sh.

For other Linux distributions, run Honeychrome with Python as below.

The Windows app is checked and hosted by the MS Store. The macOS app is signed and notarised by Apple.

Run Honeychrome with Python

This works on any platform with Python 3.12 or later, and is the way to use plugins. You can install the package from PyPI or run the source code; both run plugins.

Install the package from PyPI

1. Create a virtual environment:

   python3 -m venv .venv
   

2. Activate it:
   • Linux or macOS: source .venv/bin/activate
   • Windows: .venv\Scripts\activate
3. Install Honeychrome:

   pip install honeychrome
   

   Use pip to install anything else your plugins need as well.

4. Run Honeychrome:

   honeychrome
   

Run from the source code

1. Clone the repository:

   git clone https://github.com/Cytkit/honeychrome.git
   cd honeychrome
   

2. Create and activate a virtual environment (Python 3.12 or later):

   python3 -m venv .venv
   source .venv/bin/activate
   

   On Windows, activate with .venv\Scripts\activate.

3. Upgrade pip and install the dependencies:

   pip install --upgrade pip
   python install_annoy.py
   pip install -r requirements.txt
   python install_opentsne.py
   

   install_opentsne.py builds openTSNE with OpenMP on macOS (it needs brew install libomp); on other systems it does nothing.

4. Install Honeychrome in editable mode, so that all its modules are found:

   pip install -e .
   

5. Run it:

   python3 -m honeychrome.main
   

Next steps

• Spectral unmixing: your first experiment, from FCS files to unmixed data.
• Watch the 30-minute introduction on YouTube (recorded with version 0.8).

Edit this page on GitHub