G Scope Manual - dlx-designlab/Attune GitHub Wiki

Manual

Each G-scope should have a small booklet included in the box, describing the functionality of each button on the G-Scope. Get familiar with the manual as some buttons have multiple functionalities which might come in handy when working with the scope.

Genie Tech Software Downloads Page

⚙️ Updating Firmware

⚠️ This can only be done on Windows OS ⚠️
IMPORTANT: Make sure the firmware version is matching with the G-Scope version, see the last page in the firmware update manual below.

  1. Download the Firmware Uploader and Drivers
  2. Download the latest firmware
  3. Follow this manual to install the driver and update the firmware

📏 Scale Calibration

⚠️ This can only be done on Windows OS ⚠️
Some G-Scopes scale calibration might be 1-10% off.
Firmware 1.5.5 and above allows re-calibrating the g-scope for focus values range 80-140.
You will need to use a microscope calibration slide such as this one.

Check Calibration

  1. Make sure the G-Scope is sitting firmly in its stand and you are comfortable with making fine adjustments on the Z-Axis
  2. Make sure the G-scope is set to x250 magnification and the "Capillary Cap" is attached
  3. Put the calibration slide under the scope and lower the scope so it's touching the slide.
    It's recommended to put a white piece of paper below the slide for better image quality and contrast.
  4. Connect the G-Scope to the PC
  5. Download and run the Official G-SCOPE® Windows App from Genie Tech's Software Downloads Page
  6. Open the "Auto Measurement" Window via this button:
    Auto Measure Button
  7. Adjust the calibration slide - make sure the measurement ruler is not tilted, is in the frame centre and in sharp focus: Auto Measure Window
  8. Download and run the latest AMCAP_eva app.
  9. In the AMCAP app menu goto: EX-Unit > Control-Panel
  10. Arrange the "Control Panel" and the "Auto Measurement" windows to be side by side
  11. In AF/Lens Control Tab: adjust the focus value to be between 140-130
  12. Adjust the scope height (z-axis) so the image in the "Auto Measurement" window is in focus again
  13. If needed, repeat step 7 above
  14. In the "Auto Measurement" window, use the "line-tool" to make a measurement between two notches on the ruler which are 1mm apart: Auto Measurement Tool
  15. If the measurement is correct = 1mm (±10μm) check the calibration for other focus values between 80 and 140 (steps 11-14)
  16. If the measurement is off by more than a few microns (±10μm) the scope needs calibration. In this case, follow the steps below.

Calibration

  1. Goto "Control Panel" > "Measurement Calibration" tab > "Capillary Calibration" section: Measurement Calibration Window
  2. Click "Read" to get the values from the scope
  3. The calibration is done via the 7 focus value boxes:
    • The left box is the "Focus Value" and the right box is the "Scale Code"
    • The "Focus Values" should be within the calibration range of 140-80 and go from high to low
    • A valid step between two values is an integer between 5 and 20
    • A sample set of "Focus Values" is:
      135, 125, 115, 105, 95, 85, 80
      Or, if you want more accurate calibration for lower focus values:
      120, 105, 100, 95, 90, 85, 80
  4. Starting from the highest "focus value" box - set it to match the current scope "focus value" (e.g. 135, Check the "AF/ Lens Control" Tab) and click "Apply"
  5. Check the measurement in the "Auto Measurement" window. If needed reposition/resize the red line to match the 1mm notches of the ruler
  6. Adjust the value in the "Scale Code" box until the measurement is correct = 1mm (±10μm):
    • If the measurement value is too low (<1mm) decrease the "Scale Code" value
    • If the measurement value is too high (>1mm) increase the "Scale Code" value
    • Press "Apply" and check the measurement
    • Keep adjusting until the measurement is matching the real size of the ruler - 1mm (±10μm ±0.01mm)
  7. Move on to the next "Focus Value" box and change the "focus value" to the next value in your range (e.g. 125)
  8. Goto "AF / Lens Control" tab and change the focus to the same value
  9. Adjust the scope height (z-axis) so the scope's image feed is in sharp focus
  10. Go back to the "Measurement Calibration" tab
  11. Repeat steps 5-10 for all 7 boxes
  12. Here is an example of calibrated scope values:
  13. Hold "Ctrl" and press the "Apply" button (which will now say "Save") to "Save" your calibration
  14. Double-check your calibration by taking measurements for different focus values within your determined range.
    Try values which are different from the ones in the "focus value" boxes.
  15. Adjust the "Scale Code" values if needed
  16. Ctrl + "Save" the calibration.

IMPORTANT: Measurements outside of minimum and maximum focus will be replaced by PD values of minimum and maximum focus values.

📐 Pixel Dimensions (PD) Settings

Intro

  • The Attune Capture App saves the image scale information in the captured images' metadata.
  • For the scale information to be correct, you must set the Intercept and Slope values of the PD_Calc property inside the capture app scope_settings.json file after calibrating the G-Scope scale (as described above) since each G-Scope has different values.
  • To calculate the Intercept and Slope values use this script and this spreadsheet to save and verify your calculations.

Using the Script

⚠️ It's recommended to run the script on macOS or Linux or adjust the code for Windows OS Path syntax ⚠️

The script requires:

  • A well-calibrated G-Scope
  • About 50-70 images for the entire calibrated focus range (e.g140~70)
  • The images don't have to be in perfect focus
  • The images should be placed in a folder named gscope## next to the script
  • See an example set of images here. The focus value is the 3rd digit from the end of the file name

Use the "Official G-SCOPE®" app and the AMCAP_EVA - Control Panel to capture a series of images for all the focus values within the calibrated range:

  1. Check the min and max values in "AMCAP > EX_Unit > Control Panel > Measurement Calibration" tab
  2. Adjust the focus value to the highest value in the calibration range (e.g 135) in "AMCAP > EX_Unit > Control Panel > AF/ Lens Control" tab
  3. Capture an image via the "Official G-SCOPE®" app
  4. Reudce the focus value by one step in the "AF/ Lens Control" tab and capture another image
  5. Repeat step 4 to capture images for all the focus values in the calibrated range
  6. Copy the files into a folder named gscope## next to the calibration script
  7. Run the script: sudo python3 focus-to-pd-convert.py --scope gscope##
    Note: you might need to install some dependencies: PIL, numpy, matplotlib
  8. The "Slope" and "Intercept" values will be printed
  9. A chart validating the calculations will be displayed. The fitted line should correspond to the observations.
  10. IMPORTANT: Check the data does not include outlier values as those will affect the calculation: Outliers Example 01 Outliers Example 02
  11. A gscope##.csv file containing all the Focus and PD values from the captured images will be generated next to the script
  12. You can copy the values from the CSV, and the calculated "slope" and "intercept" into this spreadsheet to double-check the calculation
  13. After validating, copy the Intercept and Slope values and update the PD_Calc property inside the capture app scope_settings.json