CombineZ supports several popular file formats, but not 16 bit images. Start the program, go to the File menu, click on New, and a standard File Selector will appear. Navigate to the place where your stack is stored, incidentally it is good practice to keep all of the Frames that make one stack in a folder of it's own. You don't need to load Frames one at a time, just highlight them all. If your operating systems allows you can enable thumbnail view, and resize the dialog.
Notice the Main Window disappears and a Progress... dialog appears whenever CombineZ5 is busy, you can make this vanish by pressing the Minimize button. The Main Window will reappear when loading of frames is complete. You can get the Progress box back at any time by pressing F2 to see a history of all of the actions you have performed.
I'll use my Onion stack as an example here if you want to 'play along'.
On loading your Frames the top one in the stack will be displayed, they are sorted into alpha numeric order. If your naming convention places the stack upside down the menu item Stack->Reverse Order will put things right. Some methods of processing the stack require it to be in order others don't. To view the Frames you just loaded use the Up and Down arrow keys. In this example notice how the in focus area moves roughly from the upper left to the lower right.
At the top of the Main Window is the Title Line, it tries to keep you informed as to the current state of play in a somewhat cryptic fashion. T= indicates the current tool in this case there is none active. M= lets you know what action pressing the left mouse button will do, in this case you can select rectangles by pressing it down and dragging out a box. V indicates what is being displayed on the screen, VFull means the current view is of the Full picture this may entail stretching or shrinking. after VFull= is the name of what you are looking at. A1= and A2= let you know what the Active Frames are, notice A1= change as you press the Up or Down arrow keys, as also does VFull=.
At the top of the Macro menu are two items which I call the Standard Macros 'Do Stack' and 'Do Average and Filter' these can be used unmodified to process a wide range of Stacks. If you wish to restore these to their original settings use Macro->Restore Standard Macros, this will also restore the rest of the Macros (who's lineup may change between versions of CZ).
Click on Do Stack.
And the Main Window will disappear again, to be replaced by the Progress box. Notice how a list is produced of the actions taken to process your stack. When the job is done the Main Window reappears. On the Title Line you will see VFull=out, out is a special purpose 'Accumulator' for the result of various operations. The letter 'O' or the equivalent item on the View menu toggles back and forth between a view of out and the Active frame (A1=...).
You can save whatever is visible on the screen by using File->Save Frame/Picture As. CombineZ adds an extra border around Frames when loaded and hence there is a border around the finished picture. To save a cropped version of the result go to one corner of the desired area with the mouse pointer, hold down the left mouse button and drag out a box to enclose this area. Now use File->Save Rectangle As.
There are two more key strokes that I would like to introduce on this page 'Tab' and 'D' both have equivalents on the View menu.
Out is really an interpolated sharpened and contrast enhanced version of the true output from the Stacking process, the true result is stored in another special location I call the 'picture'. You can toggle between a view of the Picture and the Active Frame by pressing Tab. The Picture is a very useful device it receives a direct copy of the Pixels that are in focus on each frame. So if CZ makes a mistake you can put it right just by assigning the correct Pixels at the appropriate place.
And immediately the Picture is replaced by a 'Depthmap', D is another toggle key it toggles between the Picture and Depthmap. This emphasizes the fact that the highest point in the stack is at the upper left corner. Each Frame in the Stack is colour coded, so you can see where the Pixels that make up the Picture come from. Notice that there are no sharp steps between contributions from different Frames, the program has smoothed them out, and to get a better looking result a process called 'Interpolation' is used to generate a picture in Out without sharp transitions.
The Depthmap is not just a pretty thing, it can be used to highlight mistakes which can be edited out to get a cleaner result.
Up and Down Arrows - Move up and down the stack, and set the Active Frame A1.
O - Toggles between a view of Out and the Active Frame
Tab - Toggles between a view of the Picture and the Active Frame.
D - Toggles between Picture and Depthmap.
Also note that pressing O and Tab alternately switches from Out to the Picture and back so you can compare them.
Finally pressing 'Escape' may restore the appearance of the screen if you get hopelessly lost.