Hi,
Unlike Excel, Numbers can't "see" the color or other formatting of cells to count them (unless you use a script, which can see the color).
But Numbers can count if it knows what caused the color or other formatting. For example, if you have Numbers turn a cell's background color green whenever you have the value TRUE in it (by for example checking a checkbox) you can easily do something like this.
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The formula in A11, filled right, is:
=COUNTIF(A,TRUE)
Change that to =COUNTIF(A;TRUE) if your region uses , as a decimal separator.
In my example Row 11 is defined as a Footer Row so that it can hold the formulas referring to the entire column above. You can designate how many Footer Rows you want through the Table menu.
I got the cells to turn green by selecting them, choosing Checkbox in Cell > Data Format in the panel at the right, and then applying this Conditional Highlighting like this:
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You may not want to use Checkboxes the way I did. If so, you can analyze what are the conditions where you want a cell to be green, and then adapt the COUNTIF (or COUNTIFS) accordingly.
SG