Explore and annotate your multi-channel large TIF files with this user-friendly viewer.
Explore and annotate your multi-channel, large TIF files with this user-friendly viewer designed for high-resolution multiplex imaging.
ImmunoViewer is designed to efficiently handle high-resolution multiplex imaging files, such as those generated by Orion Rarecyte or Keyence Immuno Fluorescence scanners. It supports multi-channel images and allows users to add annotations, customize colors, and adjust signal intensities for each channel. Your suggestions for additional features are highly welcomed!
ImmunoViewer requires Python 3.10 or higher. We recommend installing ImmunoViewer within a Python virtual environment to manage dependencies effectively.
python -m venv /path/to/new/virtual/environment
source /path/to/new/virtual/environment/bin/activate
conda create -n ImmunoViewer
conda activate ImmunoViewer
git clone https://github.com/davidvi/ImmunoViewer.git
cd ImmunoViewer
pip install .
pip install ImmunoViewer
Configure your data directory to manage input and output files efficiently:
data_directory/
sample1.ome.tiff
sample2/
dapi.tiff
CD68.tiff
Files are automatically processed and stored in a separate 'processed' directory.
Generate image tiles for easier viewing and processing:
ImmunoViewerWatch [data_directory] [processed_directory]
Launch the viewer server with the following command:
ImmunoViewerServe --port [port (default is 8000)] --host [IP address (default = 0.0.0.0)] [processed_directory]
Access the viewer by navigating to http://[IP address]:[port] in your web browser. Note: If you use the default IP address (0.0.0.0), ensure the port is properly secured if exposed over the network.
See instructions in folder cloud-deploy.
ImmunoViewer uses OpenSeadragon for robust, high-performance image visualization.
FAQs
Explore and annotate your multi-channel large TIF files with this user-friendly viewer.
We found that ImmunoViewer demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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