An interactive data visualization dashboard for Computer-Assisted Sperm Analysis (CASA), designed for analyzing sperm flagellar dynamics and motility parameters.
- Heatmap Analysis: Z-score visualization of flagellar dynamics (VCL, ALH, BCF) grouped by genotype
- Scatter Plot: VCL vs BCF correlation analysis with density contours
- Distribution Plots: Violin plots for key motility metrics comparison
- Real-time Filtering: Dynamic data filtering with customizable thresholds
- Statistical Comparison: Automatic calculation of mean, standard deviation, and p-values (Welch's t-test)
- Multi-group Support: Compare WT (Wild Type) vs KO (Knockout) groups
- Quality Control: Built-in data filtering for validity, minimum velocity, and track length
- VCL (Curvilinear Velocity) - 曲線速度
- VSL (Straight-Line Velocity) - 直線速度
- VAP (Average Path Velocity) - 平均経路速度
- ALH (Amplitude of Lateral Head Displacement) - 側向頭部振幅
- BCF (Beat Cross Frequency) - 頭部交差頻度
- LIN (Linearity = VSL/VCL) - 直線性
- STR (Straightness = VSL/VAP) - 直進性
- Visit the live dashboard
- Click "Load Demo Dataset" to explore with sample data
- Interact with filters and visualization controls in the sidebar
- Prepare CSV files from your CASA system (Shift-JIS or UTF-8 encoding)
- Upload WT (Wild Type) files using the "WT Files" button
- Upload KO (Knockout) files using the "KO Files" button
- The dashboard will automatically process and visualize your data
Your CSV files should contain the following columns (Japanese or English headers):
- Validity (有効性)
- VCL (曲線速度[μm/秒])
- VSL (直線速度[μm/秒])
- VAP (平均速度[μm/秒])
- ALH (頭部振幅[μm])
- BCF (頭部振動数[Hz])
- LIN
- STR
- Points (座標数)
- Threshold Coloring Mode: Separate cells into high/low BCF frequency groups
- BCF Threshold Slider: Adjust the frequency cutoff (0-40 Hz)
- Density Overlay: Toggle 2D histogram contours for distribution visualization
- Min VCL: Filter by minimum curvilinear velocity (0-200 μm/s)
- Min BCF: Filter by minimum beat frequency (0-30 Hz)
- Min VSL: Filter by minimum straight-line velocity (0-80 μm/s)
- Min ALH: Filter by minimum head displacement (0-10 μm)
- Heatmap Sort: Sort cells by BCF, VCL, or ALH
- Group Visibility: Toggle WT/KO groups on/off
- Density Contours: Show/hide distribution density
Click the "Export CSV" button to download your filtered dataset with all calculated metrics for further analysis.
This tool is designed for researchers studying:
- Male fertility and reproductive biology
- Sperm motility patterns and flagellar dynamics
- Genotype-phenotype associations in sperm function
- Pharmacological or genetic interventions affecting sperm motility
- React 18: UI framework
- Plotly.js: Interactive scientific visualizations
- Tailwind CSS: Styling and responsive design
- PapaParse: CSV parsing
- jStat: Statistical calculations
-
Quality Control: The dashboard automatically filters out:
- Invalid tracks (Validity ≠ 1)
- Low velocity cells (VCL ≤ 10 μm/s, VSL ≤ 5 μm/s)
- Short tracks (Points < 50)
-
Statistical Significance: P-values are calculated using Welch's t-test:
****p < 0.0001***p < 0.001**p < 0.01*p < 0.05ns= not significant
-
Heatmap Interpretation:
- Blue = Below mean (negative z-score)
- White = Near mean (z-score ≈ 0)
- Red = Above mean (positive z-score)
This project is open source and available for academic and research purposes.
Contributions, issues, and feature requests are welcome! Feel free to check the issues page.
If you use this dashboard in your research, please cite:
CASA Sperm Motility Dashboard
GitHub: https://github.com/KKAIlab/casa-dashboard
URL: https://kkailab.github.io/casa-dashboard/
For questions or collaboration inquiries, please open an issue on GitHub.
Built with ❤️ for the reproductive biology research community