A sample processing assembly for treatment of a sample on a substrate, the assembly including: a mounting surface for the substrate; and a cover member, the cover member being movable between an open position and a substantially closed position, wherein, when the substrate is placed in the assembly and the cover member is in the substantially closed position, a reaction chamber is formed for processing the sample between the cover member and the substrate, and wherein the mounting surface provides for an air gap between the substrate and the mounting surface. An instrument for treatment of a sample on a substrate including at least one sample processing assembly as provided herein. A method of placing a substrate in a sample processing assembly is also provided.