The Cytokine Array Assay is an automated image analysis tool designed to process cytokine array images and extract quantitative data from them. This tool analyzes raw images of cytokine arrays, detecting spots, measuring their intensities, and generating normalized quantitative output in multiple formats.
Key features:
- Automatic spot detection using image processing techniques
- Accurate spot center positioning with local fitting
- Intensity measurement with multiple available methods (average, weighted average, percentile-based, etc.)
- Automated normalization based on positive and negative controls
- Output generation in multiple formats (CSV, Excel, visualization plots)
This tool is designed for researchers and lab technicians working with cytokine array assays to facilitate rapid, accurate, and reproducible analysis of experimental results.
Install and run the full application, including the Streamlit UI, which will be available in your browser at http://localhost:8501.
Make sure the following tools are installed on your system:
- Conda (v4.x recommended)
- GNU Make
Python is automatically managed via the Conda environment.
Clone the repository, create the Conda environment, and start the Streamlit application:
git clone https://github.com/MSDLLCpapers/InCytokine.git
cd InCytokine
make env
make app
Once the app launches, open your browser and navigate to:
http://localhost:8501
After launching, you should see the InCytokine interface in your browser. If not, check that:
- Port 8501 is free
- Your Conda environment is active
- No errors occurred during
make envormake app
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Conda dependency issues: Update Conda or ensure Python ≥ 3.8 is available.
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UI does not appear: Check Streamlit logs and ensure access to
localhost:8501. -
Apple Silicon (M1/M2): If needed, create the environment in Intel emulation mode:
CONDA_SUBDIR=osx-64 make env
To see available Make commands and their documentation, run:
make
The InCytokine application provides an intuitive workflow for analyzing cytokine array images.
Below is a visual overview of the steps:
1. Upload
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2. Blob Detection
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3. Template Setup
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4. Run Execution
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5. Results
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Open the application at http://localhost:8501.
Create a new project and upload your cytokine array images (TIF format).
The app supports batch processing of multiple images.
Review automated blob detection and adjust parameters:
- Contrast range
- Sigma range
- Threshold
- Radius filter
- Grid tolerance
Choose the best blob map as the template.
The app auto-aligns the grid; you can add missing wells and label controls.
Start the analysis by entering a run name.
The workflow aligns blobs across all images, extracts signal intensities, and normalizes measurements.
Navigate to “Visualise results” to explore interactive plots showing detection overlays and intensity data.
Export results as CSV or Excel for downstream processing.
Terminology for directions in the documentation follows two different conventions depending on context:
- Screen-based directions (up/down, left/right, horizontal/vertical) refer to how the image is visually oriented in the application interface.
- Axis-based directions (x and y) follow Matplotlib’s coordinate system:
- x-axis increases from top to bottom
- y-axis increases from left to right
The variable names in the code follow the Matplotlib convention, while the user interface uses screen-oriented terminology.
Cytokine Array Assay is an open and extensible platform, contributions are welcome.
If you have ideas about what to improve or which tools could be integrated, please submit any feature requests using the Issues tab.