Bio-Rad EXQuest Spot Cutter - Manual (Page 312)

Integrated Excision Tool
9-23
If spots in the cutter image have not aligned correctly with corresponding spots in the
analysis image, make sure the scanning device has set the correct file size. For
example, the FX, Densitomer, and the GS series automatically set file sizes, whereas
camera scanners cannot. If your image was generated from a camera acquisition
device, (the Fluor-S series, the Gel doc, ChemiDoc, or VersaDoc), it will not have
specified file dimensions. For such images, you will need to enter the physical size
dimensions correctly at the time of acquisition. It is important to have correct physical
dimensions at the beginning, before you proceed with the spot detection and matchset
creation, otherwise auto-alignment will not work correctly.
Step 4 Alignment Confirmation
After the auto-alignment has been completed, set the confidence threshold to an
acceptable level. We recommend it to be a high value. The spots that meet this level
display in green. The spots below that confidence level display in red.
Fig. 9-12. Alignment Confirmation
Use the zoom box button to magnify the images for greater visibility.
Jump and Confirm
Click the Jump and Confirm button to jump to a view of the next
spot in the cut list, whose alignment is below the specified
confidence threshold. The spot being confirmed will be displayed
in blue and will be at the center of the window. If the spot is aligned correctly in the
two images, click on the Jump and Confirm button again to jump to the next spot
below the confidence threshold. If the spot is not correctly aligned, drag it on the