Step #2

The gel image and the lane data are loaded into memory and the lanes are displayed as lines superimposed onto the gel image.

This is the only time in the editing cycle, that you see the actual raw image, as it had been scanned.

If the lanes couldn't be tracked correctly, there are various method provided to edit the lane map and move lanes into the right place.

Drag & Drop

The lane map is divided into zones, and at each intersection of a zone border and a lane, there is a little "active" box. Click on it and drag this box up and down until the line fits the actual lane on the gel.

Marker lanes

The drag boxes for the marker lanes are red and somewhat special. While dragging them it interpolates all sample lanes in between to their regular spaced distances to the neighboring markers.

Make sure all markers are correctly adjusted before editing individual sample lanes, because dragging the sample again will loose the changes made to the samples in between.

Sample lanes

The drag boxes for the marker lanes are yellow and they allow you to adjust a single sample lane.

Note that these modification might get lost, when a neighboring marker lane is adjusted, which reinterploates all the samples back to their regularly spaced positions

Adjusting large parts of the lanemap

To adjust more than one lane-drag&drop box at a time there several functions to edit the marker lanes over bigger areas.

The lane tabs

At the left hand side of the display there are circular check boxes for each marker lane. They are "active" and can be picked up with the mouse and dragged vertically to reposition that entire marker lane. All sample lanes will be interpolates accordingly.

The lane up/down buttons

To use the [lane up] or [lane down] button you have to select first, which parts of lanes or which marker lanes to move up or down. The up/down cursor keys are to the same functions.

click on one or more of the lane tabs (they'll be turn black) and then select [lane up/down] to move a whole lane up/down by a small distance.
drag a box in the image window around the red dragboxes of marker lanes. All red marker lane drag boxes in the rectangular area between holding the left mouse button and releasing it will becomes active to the [lane up/down] function (buttons in control panel or cursor keys). The selected ones will be marked in green and when they are moved the sample lanes will be interpolated again, as usual.

When you're finished click [Next >>] to advance to Step 3

Additional functions

Other functions that may prove useful can be accessed by these keystrokes:

key S to save current lane data. Saving the data from time to time might be useful if the machine or the network is unstable and prone to crash, or the program itself decides to present a bug to you and crashes without warning. You can save your work during an editing session with this function.
key R to force rerunning of the lane tracking. The upcoming dialog boxes allow you to (a) cancel the request to re-track and (b) to submit it as a background process in so called "batch" mode. This might be useful if you've lost the lane data and want to re-track the gel.

Modifying the image

The second line of buttons, provide you with a set of functions to alter the image. The first functions will also alter the the lane data, if it exists, whereas the functions in brackets will change the image severely and you have to re-calculate the lanes explicitly - a button called "recalc lanes" will come up automatically.

Look up the page on Image conversion , to find out how to automate this process, during the loading of the gel image