From cfc1bbbe4c30032e1adabb17b71de6c9544c9204 Mon Sep 17 00:00:00 2001 From: Julian Stirling Date: Sun, 26 Oct 2025 14:12:10 +0000 Subject: [PATCH] Update simulation guide now sim camera calibrates, and sample is more dense. --- simulation_guide.md | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/simulation_guide.md b/simulation_guide.md index 22ac0004..49572925 100644 --- a/simulation_guide.md +++ b/simulation_guide.md @@ -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. --- @@ -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**. + --- -### 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 +### 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%. ---