Step 2 - Edit lanetracking

This step displays the gel image (in the same way as Step 1) and also shows the superimposed lane grid, which can be edited with the mouse and keyboard.

The lane grid will require some human editing in most cases, so it is important to carefully inspect the tracking and correct it if necessary.

Menubar

  • File
    • Save lanes - saves all changes to disk and resets the "Undo" function.
    • Print - brings up print dialog to print the gel image and the superimposed lane grid.
    • Quit - saves all current changes and quits the program.
  • Edit (modify the lane grid)
    • Undo - if possible it reverts to the previous set of lanes. Inactive after lanes have been saved.
    • Delete lane - deletes the top most of currently selected marker lanes. Deletes only one at a time. The new lane grid is immediately saved to disk.
    • Insert lane above - insert a new lane above the currently selected marker lane. It will be placed halfway between the selected lane and the next lane above it, or if the selected lane it the topmost marker lane it will be placed a fixed distance above the selected lane. The new lane grid is immediately saved to disk.
    • Insert lane below - ditto, but new lane is inserted below the selected markerlane in the same fashion.
    • Re-load lanes - discards all changes made since the last save and displays the old set of lanes
    • Re-track - calls the external lanetracker again, to calculate a new lane grid. The current lanes will be lost.
  • View (change magnification of gel image)
    • 100 % - display the gel image to fit the window.
    • 200 % - display the gel image at 2x magnification.
    • 300 % - ...
    • 400 % - ...
    • Set zoom - Lets you enter the magnification factor for the x and y dimension.
  • Help (context sensitive help)
    • current - brings up this help page.

Toolbar

Zoom :
Image of toolbar zoom buttons
change magnification of the gel image to zoom in or out. "+" and "-" zoom both dimensions, the other buttons zoom only horizontally ("x") or vertically ("y").
Lanes :
Image of toolbar lanes buttons
If any circular check-box is selected, those lanes will be shifted up or down. Greater magnification will mean finer positioning.
If any drag-boxes are selected, all of those will be shifted up or down.
The cursor keys "up" and "down" perform the same actions.
grey ramp tool
modify contrast using the greyramp tool.
Batch
This button will be sensitive if the gel hasn't been band-called yet, or if the band data had been lost (e.g. editing the lanes renders the bands out-of-date and removes them). This button is a toggle button and if checked the program to calculate the bandcalling will be executed in the background. Therefore other gels can be edited while this one is still being processed.
The arrow buttons
Image of toolbar arrows
  • go back to the start.
  • step back to Step 1.
  • step forward to Step 3.

    If the band data doesn't exist yet or had been erased, the external band-calling program will be run to calculate the band data. Depending on the state of the [Batch] button, the program will wait for the external program to finish or start it in the background and return to the start.

    If the bands had been previously calculated, this arrow will switch straight to Step 3, where the bands can be edited.

Keyboards shortcuts

Most menu items will have accelerator keys associated with them, which are shown next to the menu item, when you browse through the menu bar.

As well as those accelerators, there are a few more key-strokes which perform useful functions.

Note : The mouse pointer has to be inside the gel image display area to guarantee that these key-strokes will work.

up / down cursor keys
If any check-box or drag-box of a marker lane selected, these keys do the same as the [lane up] / [lane down] button in this case.
If no lanes are selected the gel image is scrolled up and down (if the vertical zoom is greater than 100%).
left / right cursor keys
Has no effect on selected boxes.
The gel image is scrolled left or right (if horizontal zoom is greater than 100%).
D
performs the same action as the "Delete lane" menu item.
A
performs the same action as the "Insert lane Above" menu item.
I
performs the same action as the "Insert lane below" menu item.
S
performs the same action as the "Save lanes" menu item.
R
performs the same action as the "Re-track" menu item.

The lane display

The lanes are presented as a grid of horizontal lines, which are divided into zones. You can also think of the lane-grid as lines connecting the teeth of a set of combs. The number of combs is defined by the "zonenumber" parameter, which can be set in the gel parameter dialog.

There are two types of lanes on the gel :

  • sample lanes (yellow)
  • marker lanes (red) with circular check-boxes on the left edge.

The distinction between sample and marker lanes is made based upon the "markerrepeat" parameter. A marker repeat value of 5 means that every five lanes there is a marker lane, i.e. there are 4 sample lanes between two markers.

Note : You cannot process a whole gel with irregular marker repeats with this software. The lane grid has to be made smaller to fit over a region where the marker repeat is regular. The rest of the gel has to processed as another gel (using the same gel-image).

In the special case where every lane is a marker lane (only useful for multi-dye ABI gels), no sample lanes will be displayed.

Note : You are allowed to have no marker lanes at all (if "markerrepeat" is 0), but you won't be able to process the gel properly, because the marker-locking (and subsequent normalisation) can only be performed if marker lanes are present.

At each intersection of a lane with a comb there is a rectangular drag-box. These drag-boxes can be used to move the intersection point to adjust the lane.

Every marker lane has a circular check-box at the left edge of the gel. These boxes can be checked and unchecked to select/deselect whole lanes or a range of lanes.

Edit functions

The drag-boxes and the check-boxes are all "active" - they can be dragged to shift them on the gel. All of these boxes can only be shifted up or down, never left or right. It is the task of the lanetracker to assign horizontal positions to the intersection points.

To drag a box, click on it with the left mouse button, the hold the button down while moving the mouse up and down. The box will be "dropped" at the correct position when you release the mouse button.

Note : Whenever you adjust a marker lane, all surrounding sample lanes are automatically evenly spaced between them. Therefore make sure that all markers are correctly in place before adjusting the samples lanes individually.

Editing selected marker lanes :

Only marker lanes or segments of them can be selected operations other than shifting their drag-boxes. All these operations (like the [lane up] button or the "Delete lane" menu function) operate on a selected marker lane or a selected segment of a marker lane.

You select a whole lane by clicking on its check-box. The check box will turn black and mark the lane as selected. More than one marker lane can be selected this way. The check-box can be switched off by clicking on it a second time (it is a "toggle" box).

Segments of marker lanes can be selected, by placing the mouse in any gel area between the drag-boxes and dragging a bounding-box around the marker-lane drag-boxes which are to be modified. The drag-boxes that fall within the area of the bounding box will change colour to signal that they have been selected.

The operations "Delete lane", "Insert lane above/below" (from the "Edit" menu) will apply to the top most marker lane that is selected in this fashion. The operations [lane up] and [lane down] will apply to all lanes or segments that are selected.

Interactively shifting lanes by dragging :

The quick and easy way to move the lane-lines onto the lanes on the actual gel image has already been mentioned : by dragging. When a drag a square box, all lanes that are affected by the move will turn grey and interactively follow the mouse movement. This is particularly obvious when the gel has sample lanes - drag a marker lane drag-box up and down and you will see how the neighboring sample lanes adjust themselves.

Adjusting a large area of the lane-grid :

Sometime the lanetracker got the grid totally wrong and no lane matches anything on the gel. You can use the feature that evenly spaces sample lanes between markers to adjust a large number of lanes in one go.

Go back 2 steps until you reach the gel parameter dialog. Verify the parameter called "lane number". If you are sure that you are seeing exactly that many lanes in Step 2, subtract 1 and enter that number in the entry field for "marker repeat". Go back to Step 2. You will see that all lanes apart from the outer ones are marker lanes. Then adjust the outer lanes to exactly fit the lanes on the gel. All lanes in between will be evenly spaced as they are sample lanes for the moment. Then change the "marker repeat" parameter back to what it was before and adjust all the in between lanes until they fit the image. This may save you some time.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/hqty3uqb