P-TABM-462 - P-TABM-462
G2565AA MicroArray Scanner Protocol.Equipment: Agilent 2565AA MicroArray Scanner System 1.Switch on the computer and log on.2.Switch on the scanner. 3. When the green light of the scanner burns uninterruptedly, open the program 'Agilent Scan Control’ on the desktop. 4.Go to Settings - Modify Default Settings and check the ‘Split and rotate’ option at the bottom left. For all NON-Agilent chips it is necessary to split and rotate your TIFF images. For Agilent chips, do NOT split and rotate your TIFF images. 5. Fill in your initials in the ‘operator’ field 6. Select how many slots you will use. 7. Go to ‘Edit Slot Values’: When necessary change Scan Region, Red and Green PMT, Scan Resolution, Dye Channel and Output Path. The default settings are: Scan Region: 61x21.6 mm, Red and Green PMT: 90%, Scan Resolution: 10 µm, Dye Channel: Red&Green. 8.Press ‘Set Values’ each time you change or fill in a setting. 9. Fill in your barcodes and check that you put the chip in the correct slot in the scanner, then press ‘Set Values’. The scanner can read some types of barcodes. Therefore select all your slots and press ‘Read barcode from Carousel’. Wait until all the numbers of the barcodes are posted and check if it is correct. 10. When the lasers have warmed up the message ‘Scanner ready’ will be shown. Press ‘Scan slot x-y’. 11. Do NOT touch the scanner while running 12. When the scanner is ready look at the scan report to check if no slides were skipped. Skipped slides need to be scanned again. Take a look at all your images (in Feature Extraction or Array Vision) to check that all the images were scanned correctly (this is without stripes or auto-focus errors). 13. Bad images need to be rescanned: mark in your report or in Yamad which slides had multiple scannings (this effects the intensities).14. Do NOT turn off the lasers before you checked that all your slides are scanned correctly and that nobody else from the lab needs the scanner. 15. Turn off lasers. 16. Take your slides out of the scanner and put them in the correct slide map (maps of hybridised slides are stored in the clean room) 17. Turn off the scanner. 18. REMOVE your images out of the ouput folder and save them in the correct folder on the network.