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Computing the Mean Cell Shape

This guide will walk you through each step in the process, ensuring you get the most out of our tool.

📜 Step-by-Step Walkthrough​

  1. Initialization and Sidebar Header:

    • The sidebar displays the header "STEP 2: Compute Mean Shape".

  2. Data Selection:

    • The app first checks if you have uploaded or selected a dataset.
      • If not, a warning prompts you to upload or select data using the "Load Data" option.
      • If data is already uploaded, the filename is displayed for confirmation.

  3. Step Zero - Data Uploading:

    • If you haven't uploaded your data, navigate to the "Load Data" page and follow the instructions to ensure proper formatting.

  4. Analyzing Cell Data:

    • The app provides preprocessing steps, including interpolation, duplicate removal, and quotienting, to prepare your data for analysis.

  5. Sampling Points Selection:

    • Use the slider to select the number of sampling points, which are crucial for the shape analysis. The default is set to 150.

  6. Data Preprocessing:

    • Your data undergoes preprocessing to convert it into a suitable format for analysis.

  7. Exploring the Geodesic Trajectory (Optional):

    • If you wish to explore the geodesic trajectory between two cell shapes, activate the "Explore Geodesic Trajectory" toggle in the sidebar.
    • Choose the desired treatment and cell line for your analysis.
    • Use the provided sliders to select cell indices.
    • The geodesic trajectory between the two chosen cell shapes is then visualized in a series of plots.

  8. Compute Mean Shape:

    • Activate the "Compute Mean Shape" toggle in the sidebar to begin this analysis.
    • The computed mean shape will be displayed, which is essentially an average representation of all the cell shapes in your dataset.
    • Three plots provide visual insights:
      • A plot showcasing the mean estimate.
      • A combined plot illustrating individual cell shapes alongside the mean estimate.
      • A global mean shape superimposed on the entire dataset of cells.

🚀 Usage Tips:​

  • Always Check Data: Ensure you've uploaded the correct dataset before proceeding with the analysis.
  • Sampling Points: Adjusting the number of sampling points can provide different levels of granularity in the analysis. However, higher values may increase computation time.
  • Geodesic Trajectory: This visualization helps understand the transition between two cell shapes, useful for comparing different treatments or cell lines.

🔍 Note: Proper data preparation and understanding of each step are key to extracting meaningful insights from your cell shape data. Happy Analyzing! 🎉