The Project Defaults Dialog

Every gel which is processed with Image gets a set of parameters which describe certain aspects of the gel. There is quite a large number of those parameters, and therefore it would be useful to provide default parameters for each new gel, so only a small number of parameters needs to be edited.

Every project has its own set of default parameters. Only gels that are produced with the same methods should be grouped in a project. So all the gel characteristics can be set once, and they will then apply more or less for all gels in that project.

This window is a blocking dialog. This means you need to finish with this window by clicking [OK] or [Cancel] before you can do anything else.

  • OK - Save the values that are displayed and activate all changes.
  • Cancel - Loose all modifications and close window.

The parameters

All values in this window describe the gels in the given project and their processing.

The values in the top half of the window can be set here for all new gels, but they can be changed for each gels individually in the gel parameter dialog. The help page on gel parameters explains each individual parameter and its possible settings.

The entry fields in the lower half of the window will apply to all gels in this project without the opportunity to change them on a gel-by-gel basis.
If gels should require different settings, they probably don't belong in the same project together.

image file format:
Every gel file within one project will come from the same kind of data gathering tool, that writes a specific image format. The Amersham scanner writes a "dat" file, whereas PC or MAC based instruments, like the FluorImager are likely to produce a "tif" file. Select the correct image format from the option-menu.
background subtraction:
The next two settings configure the old lanetracker amStep2 which is provided with the Image package prior to release 3.9. The default lanetracker is pathfinder which doesn't use these parameters. They are retained only for backwards compatibility. If you have configured image to use amStep2 then the values are used as follows. In order to track the lanes on the image, the program finds band like features on the gel and fits a grid of lanes through it. For this feature finding the background noise of the image is removed by a process called background subtraction.
For each scan line the mean of pixel values over a sliding window is subtracted from each pixel. This is done n times. You can specify the size of that window in percentage of the gel length (in direction of the lanes). The values "number of iterations" specifies how many times to carry out the operation per scan line. A higher value ( >5 ) will erode the image too much and fine detail is lost, whereas too low a value may not perform enough background subtraction to find any features.
A bigger iteration number might cause very strong blobs to be separated out better for lanetracking, whereas a number smaller than 3 relies on very distinct features on a flat uniform background.
The "sliding window length" value specifies the length of that window. If the background varies a lot across the gel (left to right) a smaller percentage than the default 20 is advised.
export lane strip images:
The third block of parameter settings in this dialog box are for quite a specialized feature. When the gel processing is finished, a range of data files is produced which are then transferred to fpc. Apart from the usual bands files it is also possible to produce an image file for each clone, which is traced along the lanegrid on the gel and then normalised. This forms a thin image strip which can be lined up with others for analysis in other programs.
Currently this function is only performed if the standard file that is used contains size information (the 4th column in the standard file).
The parameters that can be set at the bottom of the dialog determine the size of the image strips that will be produced for each lane. The images are written in the PGM format and the finished image files can be compressed to conserve diskspace. The option-menu called "compression method" allows the user to specify the compression program which will be run on each PGM lanestrip file. Possible options are gzip, compress or none. The programs gzip and compress have to be present in the path environment when amStep5 is run. "none" obviously means no compression will be performed.
"compress" should be available as standard on every UNIX system, the "gzip" program is available free from the GNU project's FTP-sites.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/6ekq5lcv