GEL1DTOOL
Macro: None
Function: Computes and displays profiles from 1D medical gel electrophoretic autoradiograms. The lanes in the autoradiograms have to be vertical. At the begining only 2 menu items can be used. When an action is performed new menu items become available.
Operation: 1 Window with 3 Panels and Menus.
1. The 3 Panels are:
-- Gel Panel (Canvas): displays the 1D autoradiograms;
-- Peaks Panel (Canvas): displays the computed profiles and peaks and some statistic values;
-- Help Panel: shows the parameters to specify and the mouse buttons to use.
2. The different Menu Items are:
-- 2.1 Inital data: allows the user to specify the plane in which the image resides and the number of lanes in it.
-- 2.2 Show gel: displays in the Gel Panel the 1D gel used.
-- 2.3 Preestimated borders: the lane borders are preestimated as stright vertical lines.
-- 2.3.1 Calculate: makes the calulations.
-- 2.3.2 Show: displays in the Gel Panel the computed preestimated borders.
-- 2.3.3 Manual corrections: allows the user to edit manually the borders.
-- 2.3.3.1 Add a band: inserts a lane at the position of the 1D gel where the left mouse button is activated. The right mouse button is used to cancel. 
-- 2.3.3.2 Supress a band: removes the band at the position where the left mouse button is activated. The right mouse button is used to cancel.
-- 2.3.3.3 Displace a border: The user can move a lane border by dragging over it with the left mouse boutton. The right mouse button is used to cancel.
-- 2.4 Precise borders: the lane borders are estimated as 3 degree polynomials.
-- 2.4.1 Calculate: makes the calulations.
-- 2.4.2 Show: displays in the Gel Panel the computed precise borders.
-- 2.4.3 Manual corrections: allows the user to edit manually the borders. The border to edit is selected with the left mouse button. To draw the new position of the border the user have to specify between 4 and 30 points from the 1D gel. Those points are shown by grey crosshairs. Drawing the new border is done using the right mouse button. The middle mouse button is used to undo some point placement.
-- 2.5 Band profiles: computes and shows the profiles of the determinated lanes in the previous action.
-- 2.5.1 Calculate: computes the lane profiles.
-- 2.5.2 Show ideal gel: creates and displays in the Gel Panel an idealized displaying gel using the computed profiles. All the lanes in that gel are stright and have the same size. To have a global view all the profiles are also displayed over the idealized lanes.
-- 2.5.3 Show a single profile: Displays in the Peaks Panel a selected lane profile. The left mouse button is used to select the lane and the right one to cancel the operation.
-- 2.6 Smoothing: Smoothes the peak curves for all the lanes using a sliding average window. The size of the window then has to be specified (in pixels).
-- 2.7 Evaluate peaks: computes, displays or manually edits the peaks in all the lanes.
-- 2.7.1 Automatic search: searches the peaks in all the lanes found.
-- 2.7.2 Add a peak: manually adds a peak by dragging with the left mouse button in the Peaks Panel. The right mouse button is used to cancel the operation.
-- 2.7.3 Supress a peak: manually removes the peak under the cursor. The left button is used to specify the peak and the right one to cancel the operation.
-- 2.7.4 Supress cosecutive peaks: manually removes several peaks by dragging with the left mouse button. The right mouse  button is used to cancel the operation.
-- 2.7.5 Specify matter quantity: allows the user to enter the matter quantity for each lane in the 1D gel. After doing this, one can now see the matter quantity in each peak of each lane.
-- 2.7.6 Search parameters: The search parameters are the minimal threshold and the minimal area (default values 0 for both). All the peaks having a level below the minimal threshold or an area below the minimal area are ignored. Once those two values are given the automatic search has to be performed again to get the new peaks.
-- 2.7.7 Save peaks: save the peaks computed in a text file for later use by other programs.
-- 2.8 Read preprocessed gel: reads the gel with its preestimated and precise borders, profiles and peak values (see 2.8)
-- 2.8 Save preprocessed gel: saves the gel with its preestimated and precise borders, profiles and peak values. The image is saved in two files in a standard way. The preestimated and precise borders, profiles and peak values are saved in a third data file with the same name and with ".gel" extension.
-- 2.9 Quit: leaves the tool after asking a for a confirmation.
