Learning by doing - an example session with the interactive projects editor

Start the projects editor by issuing the command 'aim-gui' in your shell. Below you see a screenshot of the projects editor window that opens.

Now click the New Project button to make a new project. 'Unnamed Project' will appear in the list on the left. Click onto the list item to select the new project for editing. You may then give your project a proper name by changing the text in the entry field 'Project Name'.

Projects in AIM speaking are sets of slides with common parameters, ideally slides from the same print run. You can put slides from different biological experiments into the same project (although that may not make sense), but you must not put slides with different grid row and colum numbers into the same project, for example. Now click 'Project Parameters' to see the dialog where the common parameters of the project's slides can be entered:

You should select a working directory for your projects first. For testing, you may use just '/tmp'. The working directory will hold some intermediate files as well as the resulting GPR tables of the image analysis.

Since you will probably want to start with only a few slides, you should switch the grid layout buttons to 'Do Without'. Layout estimation makes only sense with larger image series (at least about ten, perhaps) and is not necessary if your images are nice. [1] If your grids do not interleave, i.e. the gaps between them extend across the array image in a straight line, you may switch on 'Aligned globally' for a slightly faster and more reliable image segmentation [2].

Enter the correct number of spot columns and rows per grid in the fields below, then. In case you know that the bottom or another edge row of your grids tends to be dark (e.g. because you put negative control spots there), klick the appropriate button.

Now is a good time to save the data you entered so far. Select 'Save as' from the File menu in the top left corner of the window and enter a filename for your projects metainformation. You may then choose the 'Preferences' item from the 'Settings' menu and enter the same filename there to have your project data loaded immediately when you start 'aim_gui' the next time (Klick 'Apply' to close the window, it writes a dotfile '.aimprojectsgui' into your home directory).

Next, switch to the slides dialog. You may add each of your slides manually here, very similar to the first projects dialog, or you may import slides using an ASCII list in the three-columned format that was described before. Klick the 'Import' button to select a filename.

The next screenshot shows the program after a list with two slides was imported and the triangular expand widget [3] left from the project name was clicked and a slide selected:

Everything you need for an automatic analysis is in place now. Save the project data again after importing the slides and proceed to the 'Compute' dialog. Klick the 'Run' button in the 'Automatic Analysis' frame to start the analysis. This will start an analysis on the currently selected project (Shown in the status line at the windows bottom). Wait then until the analysis is finished. (For the ZmDB images that I tried it took about 2-3 minutes for each image on a 1GHz Athlon PC. Your computer should have at least 256Mb of RAM to avoid excessive swapping which will slow everything down.). Enjoy your coffee.

When the analysis is finished, a dialog comes up. Close it by clicking 'OK' and proceed to the 'Results' dialog. If you are impatient and click on the 'Break' button, the computation will stop with an error. [4]

There you can check whether the automatic gridding went well by selecting slides from the list on the left and then clicking 'View Gridding'. If you do not like the result, click 'Edit Gridding. This will start another tool with wich you can move the grids to the desired places. The grid editing tool is described in the Section called Using the manual gridding editor of this manual.

The other buttons let you see the choice of signal and background pixels which the Mann-Whitney segmentation made ('View Spot Segmentation'), a logfile of the image processing kernel ('View Summary'), the output table ('View Quantitation Table', have a Netscape running to have this work) or produce a quick scatterplot of the spot intensities using GnuPlot ('Draw Scatter Plot')

In case you had to use the manual gridding editor, you have to recompute the output tables before using them. You do so by clicking the second 'Run' button in the 'Compute' dialog (in the 'Recompute' frame). You may edit all slides and recompute them all at once in batch.

The GPR output tables are in the work directory now (.out files). Database export is not yet possible. If you do not want all columns to appear in the GPR files, unselect those you do not want in the 'Output Options' dialog.