A Rectangle can be anything from the full picture down to just a few pixels wide and high. The Active Rectangle is the area that can be worked on. It is the area inside the dotted box in Full view, or the entire visible area in Normal and Magnified views. There are three ways to change the size, shape and position of a Rectangle. The simplest is using the letter 'A' or the equivalent View menu item. If you are not in the Full viewing mode, pressing 'A' will switch to this mode. Repeatedly pressing 'A' can cycle through four different sized rectangles each with different properties:
In Full view the Active Rectangle is shown with a dotted border.
The second method of defining a rectangle can only be used in Full or Normal view. Decide where you would like one corner to be, point the mouse at this point, press and hold down the Left Mouse button, and drag to the diagonally opposite corner. In Full view the old dotted rectangle will disappear and a new one will be drawn. In normal view the newly selected Rectangle will immediately be Magnified for close inspection or editing at the pixel level. When finished doing this, press the Right Mouse button to return to Normal view where you can select further Rectangles to work on.
Thirdly you can alter the size of an existing Rectangle with the X, Y and Z keys; see List of Keys.
The Active Rectangle defines the area that will be saved and reloaded by the appropriate File and Undo menu items. This is a convenient way to crop your finished work to the desired size.
All of the functions on the Rectangle menu only work within the Active Rectangle. For example you can Clear, Fix, Unfix, or Overwrite a rectangular region of the Picture.
Fix, Unfix, and Invert Fixed are used to control which pixels can be changed and which cannot. For example, if you wish to highlight a certain feature in a Picture you could create a new Frame, drag a box around the feature, Fix the Active Rectangle thus defined, press 'A' to make the whole Picture Active, then use the Colour and Brightness function Red to give the rest of the Picture a red tint. Note you can only Fix pixels that exist in the Picture. Empty ones cannot be Fixed, so you may sometimes need to fill the Picture with a dummy. Use Paste Active Over for this purpose. Apart from Unfix, the only function that affects the Fixed state of a Pixel is Clear All. Clear Unfixed leaves Fixed Pixels intact.
To manually copy a whole Rectangle to the Picture from the Active Frame, use Paste Active Over or Paste Active Under. The former covers everything in the Picture with information from the Active Frame, apart from Pixels that are Transparent in that Frame. The latter will only fill Pixels that are Empty in the Picture with those from the Active Frame.
In combination with Planes, Rectangles form a powerful tool for tidying Stacked images. Press 'P' and you are in Plane Mode. Now you will be able to see isolated dots where pixels have been selected from the wrong Frames. Draw a box around one or more of these dots and press 'Delete', and the visible contents of the rectangle will be cleared. On pressing P again to leave Plane Mode, there will be holes where the dots were deleted. Just use Fill Gaps to fill them in. Visit all Planes by using the Up and Down Arrows before leaving Plane Mode and Filling Gaps.
Colour and Brightness and Contrast operate on the Active Frame within the confines of the Active Rectangle, and place their output in Out. Note the message boxes that appear. When you try to use these functions on Out or the Picture, you are asked if you wish to create a New Frame, and when you finish by pressing return, you are asked if you wish to overwrite the original in the Active Frame.
Contrast is used to enhance pictures by removing grayness. When you first invoke it, it stretches the colours out to generate a suggested optimum value. If you wish to alter this further use the Left and Right Arrow keys to do so in small steps and 'M' and 'N' for larger steps. Press Return when you are satisfied, or Escape to abandon.
The Colour and Brightness functions work together. The best approach here is to get the colour right first, then adjust the brightness. Don't be tempted to press Return after each adjustment, just press it once at the end so that you don't lose some of the range of colour and end up with a posterized picture. These functions use the same keys as Contrast above. The colour functions are a little unusual. If you try to make a picture redder, then green and blue will be reduced if it would otherwise mean red becoming oversaturated. Thus to see the red channel alone repeatedly press 'M' after starting the Red function. This facility, along with manually moving frames and Adding them, enables 3D pictures to be viewed through coloured glasses to be generated.
The Two Frame Functions will only become active if Active Frame 2 has been defined. Go to the desired Frame and click on Make Active Frame 2, or press '.' and A2 on the title line will reflect your selection.
The Add function uses the equation A1+N*A2 which means that Active Frame 2 is multiplied by a constant and then added to Active Frame 1, if N is -1 a straight subtraction is done. Control the value of N with the Arrow keys and 'M' and 'N' as mentioned above.
Blend will mix Active Frames 1 and 2. The proportions of each frame in the mix are controlled by the same keys as in the above functions.
Correct Brightness takes a reference Frame A2 and decides what must be done to make it a uniform colour, then applies the same correction to Frame A1. If you have a microscope picture without the subject you can correct for unevenness in the lighting or other unwanted artifacts. There are several ways to obtain this picture: directly by taking a picture of nothing; Fix the detail and just use the original Frame; or Create Background on the Frame menu and paint over the detail to make a correction Frame.
The last few menu items mentioned above are called Tools. Their names appear on the Title Line, e.g. T=Red. Pressing Return while the initial Frame and Rectangle are active finishes the Tool. Move to a different Frame or Rectangle and you are given the option to apply the same Tool with its current settings to the new Active selection. Suppose you alter the top frame, then move down to the next frame and press return twice. Repeat this (down and return twice) for the whole Stack, and you will have changed all Frames.