88 lines
3.9 KiB
Markdown
88 lines
3.9 KiB
Markdown
# Guide: Running the OpenFlexure Microscope Simulation Server
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This guide walks you through running the simulation server for the OpenFlexure Microscope, along with useful tips for using the simulation features.
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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:
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* Camera stage mapping and 'click to move'
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* Scanning and stitching*
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* Autofocus
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* Image capture
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* Stage navigation
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**Please note: the final stitch at the end of a scan currently doesn't work on Windows.*
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---
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## Starting the Simulation Server
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1. **Activate your virtual environment** (the same one created during installation, as described in the [README](./README.md)).
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2. **Run the simulation server** using the following command:
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```bash
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openflexure-microscope-server --fallback -c ./ofm_config_simulation.json
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```
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> 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.
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This can fail with an error that the chosen port is already in use. In that case, append `--port 8081`
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---
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## Video Walkthrough
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For a step-by-step demonstration, watch the [full video walkthrough on running the simulation server](https://youtu.be/Z8verCqfj9s).
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---
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## Running a simulated scan
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To run a simulated scan, you must first complete the calibration wizard.
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1. Go to the **Slide Scan** tab
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2. Click the **Start Smart Scan** Button.
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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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---
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## Simulation Settings and Tips
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---
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### Autocalibration
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* Your simulated microscope should prompt you to complete the auto-calibration wizard upon your first use of the simulated server.
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* You can press the **Escape** key at any point to exit the wizard but this will leave your smulated microscope in an uncalibrated state.
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* If your microscope is not calibrated the wizard will launch each time you load the UI prompting you to complete remaining calibrations.
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* You can always launch the full calibration wizard by going to: **Settings → Launch Calibration Wizard**.
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The calibration steps are:
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1. The Camera Calibration will set the background image needed for background detect.
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* You can rerun this calibration by going to: **Settings → Camera → Full Auto-Calibrate**.
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2. The Camera-Stage Mapping calibration is used to find the relationship between stage and image coordinated.
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* 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.
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* To re-run Camera-Stage Mapping, go to: **Settings → Camera to Stage Mapping → Auto-Calibrate Using Camera**.
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---
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### Background Detect
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* You can **load a sample** to simulate imaging conditions, using the **Load Sample** options in the **Settings tab**.
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* To remove a sample and reset the view, use the **Remove Sample** option in the **Settings tab**.
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* You can load and remove simulated samples under: **Settings → Camera → Load/Remove Sample**.
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* The Full Auto-Calibratie option in camera settings can be used to **Remove the sameple → Run background detection → Re-load the sample**.
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* 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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---
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### Scans
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* 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.
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* Scans are automatically given **Scan IDs** in numerical order if the user does not provide one.
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---
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If you need further help, reach out to the community on the [OpenFlexure Forum](https://openflexure.discourse.group/).
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