5.2 Template Edit

After an image has been cropped and its lane boundaries determined, your next step is to detect the bands in the marker lanes. You do this by clicking [Std Bands] in the Operations Submenu. Before attempting automatic detection of these standard bands, you are asked if you would like to edit the template of standard bands. In the Basic Tutorial, you declined; and the program performed automatic band detection.

Recall that the template is a listing of fragment sizes and mobilities against which an image is "normalized" so that images using the same template might be compared. But perhaps the image to be analyzed contains artifacts or is partially blurred such that not all bands in the image's marker lanes are clearly distinguishable. For this reason, you may choose to temporarily eliminate a band or several from the template. Before normalizing the image, the number of band bars in each marker lane must correspond to the number of band bars in the template. Thus, if some bands in the image are not clearly visible, the appropriate band bars in the template should be eliminated. Caution: the normalization algorithm needs at least 4 band bars in each marker lane. This tool is used only to delete bands from a previously defined template.

• From the Operations Submenu, click [Std Bands] .

• The Template Edit Dialog appears (Figure 5.3), asking whether to do Template Edit; click [Yes] .

• The Template Edit Popup appears (Figure 5.4, left). Red bars appear to the left, signifying the relative mobilities of the template bands. Fragment sizes, in boxes, appear to the right. Lines are drawn between corresponding bands and sizes.

• No new bands may be added to the template.

• To delete a band from the template, move the pointer to the band or to the corresponding fragment size number and click MB2; the band and its size will disappear. The line between remains, leaving a visual clue of elimination. Figure 5.4, right, shows that two bands have been eliminated.

• Clicking MB1 restores all bands.

• Clicking MB3 stores the edited list of template bands and removes the Template Edit display.

• Automatic detection of the image's marker bands commences immediately. Editing of the marker bands follows.

• If the number of marker bands in each marker lane does not correspond to the number in the (edited) template, the program will not allow the image to be normalized.

Figure 5.3: Template Edit Dialog.

Figure 5.4: Template Edit Popup Before (left) and After (right) Edit.