Operating instructions for the Axon GenePix scanner
Preparation for scanning:
- After power-on, give the scanner 15 minutes to warm up before acquiring any images
- Load the slides upside down in the scanner
- Start GenePixPro by clicking on the 'GenePixPro' icon
Preview scanning and defining the scan area:
- Press 'Preview Scan' to start a preview scan
- You can then press the 'Scan Area' button:
- Move the mouse cursor to the top left of the features on the image
- Hold down the mouse cursor and drag a rectangle around the region containing the features
- Confirm that all features have been included within the scan area
Optimising the scanner settings:
Maximizing the dynamic range:
- Open the 'Hardware Settings' dialog box
- Start a 'Preview Scan' and change the 'PMT Gain' for each wavelength whilst scanning
- You should aim to use the highest scan setting that does not lead to a signficant level of saturation
- Ensure that the image resolution has been set to 5 µm per pixel
Balancing the PMTs:
- Start a 'Preview Scan' and 'Zoom' in on the features
- Switch to the 'Histogram' tab and set the 'Min Intensity' and 'Max Intensity' fields to 500 and 65530
- While scanning, adjust the PMT Gain in each channel until the ratio 'Count Ratio' is about 1.0
- Save the 'Hardware Settings' by clicking the 'File' button and selecting 'Save Settings As'
- Type in an appropriate file name and then press 'Save'
Performing a Data Scan and Saving an Image:
- Press 'Data Scan' to start a full scan
- To save the image, click on 'File' and select 'Save Images'
- Navigate to the correct file location and select 'Single Image TIFF Files'
- Type in an appropriate file name and then press 'Save'
Calibrate System (doesn't needed to be performed very often!):
- Click 'Hardware Diagnostic' and select 'Calibrate System'
- Check both the laser check boxes to calibrate both wavelengths
- Click 'Start' and the wizard will then guide you through the procedure
R. Auburn (07-06-2004).
