To use the over the top coloring feature you need some knowledge about boolean logic. The file starts with some optional lines that cover aliases. If you want to use an attribute name many times in the same file, you can type alias alias_name = attribute_name. This means that the attribute with the name attribute_name can now be used in the boolean expression as alias_name. Attribute names should be the full name of the attribute including the attribute's category (excactly as it is typed in the meta.cell file). You do not have to define any aliases if you do not want to. The last line in the file should always be a boolean expression consisting of attribute names (from the meta.cell file) and aliases (defined earlier in the same file). The operators you may use are listed below. You may also use parentheses in your expression. The precedence of the operators are, from highest precedence to lowest; parentheses, NOT, XOR, AND, OR.

An example file might look like this:

alias b = cell_type.b_cell
alias t = cell_type.t_cell
(b | t) & ! (Stage_1.normal_hsc | Stage_1.pre_blast_crisis)

This example file would color only the cells that; belong to either cell_type.b_cell or cell_type.t_cell and do not belong to either Stage_1.normal_hsc or Stage_1.pre_blast_crisis.