The gel image and the lane data are loaded into memory and
the lanes are displayed as lines superimposed onto the gel
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.
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.
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.
When you're finished click [Next >>] to advance to
- 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.
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