Step 1 - Edit/Preview gel image

This display appears if the raw image could be successfully converted to the internal image format used by Image. The actual gel image appears for the first time in the main display. The rest of the screen contains the usual user interface controls.

In most cases you do not need to do anything, other press the forward button to proceed to Step 2.

Menubar

  • File
    • Print - brings up print dialog to print the gel image.
    • Quit - saves all current changes and quits the program.
  • Edit (modify the gel image)
    • Cut top
    • Cut bottom
    • Flip X
    • Flip Y
    • Invert
    • Re-load image
  • 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.
    • Help on conversion - describes the image conversion.

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").
grey ramp tool
modify contrast using the greyramp tool.
Batch
This button will be sensitive if the gel hasn't been lane-tracked yet, or if the lanes had been lost (e.g. editing the image renders the lanes out-of-date and removes them). This button is a toggle button and if checked the program to calculate the lanetracking 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 the gel parameter dialog, which will pop up to show all parameters, which can be inspected or changed. In this state the [OK] button will return back into Step 1, whereas [Cancel] will go back to the start (i.e. the gel chooser).
  • step forward to Step 2.

    If the lane grid doesn't exist yet or had been erased, the external lanetracker will be run to generate the lanes. 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 lanes had been previously calculated, this arrow will switch straight to Step 2, where the lane tracking can be edited.

Edit the gel image

All of these operation may change the converted gel image (the raw image is left untouched). This will affect the image which is displayed on the screen and possibly the other images which had been converted into higher colour resolutions for the analysis programs (such images cannot not displayed).

By changing the analysis gel image, all subsequent gel data is rendered out-of-date, and you will therefor loose all lanes, bands, traces etc. It is therefore only advisable to edit the gel image at the start of the gel processing when none of such data exists.

Cut top / bottom

If the image had been rotated properly (see "rotation" parameter) the lanes on the gel should run horizontally. Sometimes however there is a large gap at the top or bottom in which there is no actual data. This background area may confuse the lanetracker and sometimes it is advisable to crop this off.

When you select this menu item your left mouse button becomes sensitive in the gel image display. Hold the button down and then drag it across the gel to position the line at which to crop the image. This operation can be performed at any magnification factor.

Depending on whether you had selected to cut at the "top" or "bottom", the image will be cropped horizontally and saved to disk immediately.

Flip image X / Y

No further mouse interaction is needed; the image will be mirrored (flipped) horizontally or vertically respectivly. If a scanner was used the gel film may have been inserted upside down, this edit-function will compensate that mistake.

Invert image

(Only provided for completeness) The external analysis programs may make assumptions about the pixel values in the gel image. They may assume that background areas have low pixel values, and band blobs have higher pixel values. Adjust the greyramp tool to 0 at the bottom and 255 at the top to see the image pixel values as they analysis programs see it. This function will invert the actual pixel values (the greyramp tool only adjusts the displayed contrast) in case your scanner had produced an inverse image.

Re-load image

This function will reload the hidump file from disk and redisplay it. It may only be useful if you have re-run the image conversion by hand (e.g. by typing the command-line in a shell window). The new image file is loaded and it is assumed that the gel image is different, therefore all subsequent analysis data is lost - You have been warned!

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/toaw5bl8