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Update simulation guide now sim camera calibrates, and sample is more dense.

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Julian Stirling 2025-10-26 14:12:10 +00:00
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simulation_guide.md
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@ -37,15 +37,11 @@ For a step-by-step demonstration, watch the [full video walkthrough on running t
## Running a simulated scan
To run a simulated scan, you first need to set a background image:
To run a simulated scan, you must first complete the calibration wizard.
1. Click on the settings tab on the left
2. Navigate to the **Camera** settings under **Microscope Settings**
3. Click `Remove Sample`. This removes the simulated sample from the camera stream
4. Click on the **Background Detect** tab on the left and click `Set Background`
5. Repeat the steps 1 and 2 to return to the camera settings and click `Add Sample`
You are now ready to start a simulated scan in the Slide Scan tab.
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.
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@ -56,24 +52,28 @@ You are now ready to start a simulated scan in the Slide Scan tab.
### 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**.
* You can press the **Escape** key at any point to exit the wizard but this will leave your smulated 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 coordinated.
* 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**.
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### 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**
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### Background and Samples
### 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**
* You can load and remove simulated samples under: **Settings → Camera → Load/Remove Sample**.
* The Full Auto-Calibratie option in camera settings can be used to **Remove the sameple → 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%.
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