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Furthermore, only the costs you actually paid can be used, you can’t take anything for the value of your own labor.  

Improvements made to the whole house are allocated to the office on a square foot basis, listed as assets, and depreciated.  The portion allocated to the rest of the house is added to the cost basis and may reduce your capital gains when you sell.  Improvements specifically to the office can be  depreciated 100%, while improvements that are unrelated to the office (like remodeling the master bath) are not used at all as business expense.