An illumination system and method for illumination of a sample in a container is described herein. In some embodiments, the container includes a defined volume for receiving the sample. The illumination system includes, in some embodiments, at least one light source, a mask comprising an opaque portion, preventing light from passing through the mask, and an at least partially transparent portion, allowing light to pass through the mask. The illumination system can be adapted to be positioned such that the light generated by the light source, passing through the mask, illuminates the sample in the container. The light source and the mask are configured such that a shape, a size, and a position of a projection of the light passing through the mask, onto a plane of a bottom surface of the container, match a shape, a size, and a position of the bottom surface.