Update create-a-document.md

docs/docs/tutorial-basics/create-a-document.md

@@ -2,56 +2,50 @@
 sidebar_position: 2
 ---
 
-# Create a Document
+# Computing the Mean Cell Shape
 
-Documents are **groups of pages** connected through:
+This guide will walk you through each step in the process, ensuring you get the most out of our tool.
 
-- a **sidebar**
-- **previous/next navigation**
-- **versioning**
+### 📜 Step-by-Step Walkthrough
 
-## Create your first Doc
+1. **Initialization and Sidebar Header**:
+   - The sidebar displays the header "STEP 2: Compute Mean Shape".
 
-Create a Markdown file at `docs/hello.md`:
+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.
 
-```md title="docs/hello.md"
-# Hello
+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.
 
-This is my **first Docusaurus document**!
-```
+4. **Analyzing Cell Data**:
+   - The app provides preprocessing steps, including interpolation, duplicate removal, and quotienting, to prepare your data for analysis.
 
-A new document is now available at [http://localhost:3000/docs/hello](http://localhost:3000/docs/hello).
+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.
 
-## Configure the Sidebar
+6. **Data Preprocessing**:
+   - Your data undergoes preprocessing to convert it into a suitable format for analysis.
 
-Docusaurus automatically **creates a sidebar** from the `docs` folder.
+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.
 
-Add metadata to customize the sidebar label and position:
+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.
 
-```md title="docs/hello.md" {1-4}
----
-sidebar_label: 'Hi!'
-sidebar_position: 3
----
+### 🚀 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.
 
-# Hello
-
-This is my **first Docusaurus document**!
-```
-
-It is also possible to create your sidebar explicitly in `sidebars.js`:
-
-```js title="sidebars.js"
-module.exports = {
-  tutorialSidebar: [
-    'intro',
-    // highlight-next-line
-    'hello',
-    {
-      type: 'category',
-      label: 'Tutorial',
-      items: ['tutorial-basics/create-a-document'],
-    },
-  ],
-};
-```
+🔍 **Note**: Proper data preparation and understanding of each step are key to extracting meaningful insights from your cell shape data. Happy Analyzing! 🎉