Here we describe how to make a custom miniature incubator or chamber for an upright automated/manual biological/industrial microscope. The chamber allows control of temperature in the base, lid and objective lens, cooling and/or heating, humidity and CO2/O2 and most importantly scanning a big area of a sample such as one or two 35mm petri-dishes, well plate, chamber slides and so on, in an automated mode while the chamber is fully closed. Here we discuss some challenges during the development in terms of how to fit this chamber to the microscope and meet all requirements of having a closed chamber for a motorized stage.