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simulation_guide.md

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+# Guide: Running the OpenFlexure Microscope Simulation Server
+
+This guide walks you through running the simulation server for the OpenFlexure Microscope, along with useful tips for using the simulation features.
+
+---
+
+## Starting the Simulation Server
+
+1. **Activate your virtual environment** (the same one created during installation, as described in the [README](./README.md)).
+2. **Run the simulation server** using the following command:
+
+   ```bash
+   openflexure-microscope-server --fallback -c ./ofm_config_simulation.json
+   ```
+
+   > Note: If you are using Windows, we advise running this command in PowerShell. If it doesn't work this, might be a permission issue on managed machines, in which case try executing the command in a CMD terminal.
+
+This can fail with an error that the chosen port is already in use. In that case, append `--port 8081`
+
+---
+
+## Video Walkthrough
+
+For a step-by-step demonstration, watch the [full video walkthrough on running the simulation server](https://youtu.be/Z8verCqfj9s).
+
+---
+
+## Simulation Settings and Tips
+
+---
+
+### Autocalibration
+
+* Your simulated microscope should prompt you to complete the auto-calibration wizard upon your first use of the simulated server.
+* If the stage moves in the wrong direction in the **View** or **Navigate** tabs, you can re-run **Auto-calibration** from the UI to correct it.
+* To auto-calibrate your microscope, go to: **Settings → Camera to Stage Mapping → Auto-Calibrate Using Camera**.
+
+---
+
+### Sample Coverage
+
+* The default **sample coverage** of 25% is often too high for simulations. A figure closer to 10% performs better.
+* You can adjust this in the **Background Detect tab** under:
+  **Configure → Sample Coverage**
+
+---
+
+### Background and Samples
+
+* You can **load a sample** to simulate imaging conditions, using the **Load Sample** options in the **Settings tab**.
+* To remove a sample and reset the view, use the **Remove Sample** option in the **Settings tab**.
+* You can load and remove simulated samples under: **Settings → Camera → Load/Remove Sample**
+
+---
+
+### Scans
+
+* If you perform a scan with **0 images** (i.e. cancelling the scan before any images are collected), it will **disappear** from the scan list as soon as a new scan starts.
+* Scans are automatically given **Scan IDs** in numerical order if the user does not provide one.
+
+---
+
+### Screen Size
+
+* During a Smart Scan (performed in the **Slide Scan tab**), some screen sizes can cause unwanted jitter as shown in the animation below.
+* If this happens, change the size of your window until the UI stabilises.
+
+    ![Jitter in the OFM Simulator caused by screen size](/docs/images/ofm_sim_jitter.gif "Jitter in the OFM Simulator caused by screen size")
+
+---
+
+If you need further help, reach out to the community on the [OpenFlexure Forum](https://openflexure.discourse.group/).