OpenIMC is a comprehensive, open-source PyQt5-based platform for analyzing Imaging Mass Cytometry (IMC) data. It provides an intuitive graphical interface for visualizing, processing, and analyzing multi-channel imaging data from mass cytometry experiments with advanced machine learning capabilities.
See the paper here: https://link.springer.com/article/10.1186/s12859-026-06547-4
Cite as: Tessone, D., Kamal, M., Hennes, V. et al. OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry. BMC Bioinformatics (2026). https://doi.org/10.1186/s12859-026-06547-4
For complete documentation, installation instructions, and usage guides, please visit:
https://dean-tessone.github.io/OpenIMC/overview.html
The preferred installation pattern uses uv:
# Clone the repository
git clone https://github.com/dean-tessone/OpenIMC.git
cd OpenIMC
# Create and activate a uv-managed virtual environment
uv venv --python 3.11
source .venv/bin/activate # On Windows: .venv\Scripts\activate
# Install dependencies
uv pip install -r requirements.txt
# Install the package
uv pip install -e .If you prefer Conda, that workflow is still supported in the Installation documentation.
For detailed installation instructions, including alternative methods and troubleshooting, see the Installation documentation.
A video tutorial is available here: Video Tutorial.
After installation, you can run:
# Start the GUI application
openimc-gui
# Or run the CLI
openimc --helpOpenIMC – Interactive analysis toolkit for IMC data
Copyright (C) 2025 University of Southern California
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program (see LICENSE). If not, see https://www.gnu.org/licenses/.