Move more development information to the dev docs to minimise repitition and getting out of sync

apidocs/dev/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.
+
+The simulation server GUI is a copy of the GUI you would find on the hardware with a simulated sample you can explore. Most functionality included in the hardware operates on the simulation server. This includes:
+
+* Camera stage mapping and 'click to move'
+* Scanning and stitching*
+* Autofocus
+* Image capture
+* Stage navigation
+
+**Please note: the final stitch at the end of a scan currently doesn't work on Windows.*
+
+---
+
+## Starting the Simulation Server
+
+1. **Activate your virtual environment** (the same one created during installation, as described in the [Python documentation](python)).
+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).
+
+---
+
+## Running a simulated scan
+
+To run a simulated scan, you must first complete the calibration wizard.
+
+1. Go to the  **Slide Scan** tab
+2. Click the **Start Smart Scan** Button.
+3. This will scan until the whole sample has been imaged. You can cancel the scan at any time, with the **Cancel** button.
+
+---
+
+## Simulation Settings and Tips
+
+---
+
+### Auto-calibration
+
+* Your simulated microscope should prompt you to complete the auto-calibration wizard upon your first use of the simulated server.
+* You can press the **Escape** key at any point to exit the wizard, but this will leave your simulated microscope in an uncalibrated state.
+* If your microscope is not calibrated, the wizard will launch each time you load the UI, prompting you to complete remaining calibrations.
+* You can always launch the full calibration wizard by going to: **Settings → Launch Calibration Wizard**.
+
+The calibration steps are:
+
+1. The Camera Calibration will set the background image needed for background detect.
+  * You can rerun this calibration by going to: **Settings → Camera → Full Auto-Calibrate**.
+2. The Camera-Stage Mapping calibration is used to find the relationship between stage and image coordinates.
+  * If the stage moves in the wrong direction when double clicking on the camera feed in the **View** or **Navigate** tabs, you may need to re-run Camera-Stage Mapping.
+  * To re-run Camera-Stage Mapping, go to: **Settings → Camera to Stage Mapping → Auto-Calibrate Using Camera**.
+
+
+---
+
+### Background Detect
+
+* 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**.
+* The Full Auto-Calibrate option in camera settings can be used to **Remove the sample → Run background detection → Re-load the sample**.
+* You can adjust the sample coverage needed for the image not to be detected as background in the **Background Detect tab** under: **Configure → Sample Coverage**. The default value is 25%.
+
+---
+
+### 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.
+
+---
+
+If you need further help, reach out to the community on the [OpenFlexure Forum](https://openflexure.discourse.group/).
+