An illumination system (100, 200, 300, 400, 500, 600) for illumination of a sample, the illumination system (100, 200, 300, 500, 600) comprising: a container (10, 20, 50a, 50b, 50c, 50d), such as a well of a microplate or a petri dish, the container (10, 20, 50a, 50b, 50c, 50d) comprising a bottom surface (12, 22, 52a) and side walls (14, 24) which together define a volume for receiving the sample; at least one light source (110, 210, 310, 410, 510, 610) being configured to generate light; a mask (120, 220, 320, 420, 520, 620) arranged such that light from the light source (110, 210, 310, 410, 510, 610) impinges onto the mask (120, 220, 320, 420, 520, 620), wherein the mask (120, 220, 320, 420, 520, 620) comprises an opaque portion (122, 222, 322, 422), preventing light from passing through the mask (120, 220, 320, 420, 520, 620), and an at least partially transparent portion (124, 224, 324, 424, 624), allowing at least part of the light from the light source (110, 210, 310, 410, 510, 610) to pass through the mask (120, 220, 320, 420, 520, 620); wherein the illumination system (100, 200, 300, 400, 500, 600) is adapted to be positioned at a first end of the container (10, 20, 50a, 50b, 50c, 50d) such that the light generated by the light source (110, 210, 310, 410, 510, 610), passing through the mask (120, 220, 320, 420, 520, 620), illuminates the sample in the container (10, 20, 50a, 50b, 50c, 50d); and wherein the at least one light source (110, 210, 310, 410, 510, 610) and the mask (120, 220, 320, 420, 520, 620) are configured for light generated by the at least one light source (110, 210, 310, 410, 510, 610) being passed through the mask (120, 220, 320, 420, 520, 620) such that a shape, a size, and a position of a projection of the light passing through the mask (120, 220, 320, 420, 520, 620), onto a plane of the bottom surface (12, 22) arranged at a second end of the container (10, 20, 50a, 50b, 50c, 50d), opposite to the first end, match a shape, a size, and a position of the bottom surface (12, 22) of the container (10, 20, 50a, 50b, 50c, 50d), such that the side walls (14, 24) of the container (10, 20, 50a, 50b, 50c, 50d) are not illuminated, and such that substantially the full bottom surface (12, 22, 52a) of the container (10, 20, 50a, 50b, 50c, 50d) is illuminated. a container (10, 20, 50a, 50b, 50c, 50d), such as a well of a microplate or a petri dish, the container (10, 20, 50a, 50b, 50c, 50d) comprising a bottom surface (12, 22, 52a) and side walls (14, 24) which together define a volume for receiving the sample; at least one light source (110, 210, 310, 410, 510, 610) being configured to generate light; a mask (120, 220, 320, 420, 520, 620) arranged such that light from the light source (110, 210, 310, 410, 510, 610) impinges onto the mask (120, 220, 320, 420, 520, 620), wherein the mask (120, 220, 320, 420, 520, 620) comprises an opaque portion (122, 222, 322, 422), preventing light from passing through the mask (120, 220, 320, 420, 520, 620), and an at least partially transparent portion (124, 224, 324, 424, 624), allowing at least part of the light from the light source (110, 210, 310, 410, 510, 610) to pass through the mask (120, 220, 320, 420, 520, 620); wherein the illumination system (100, 200, 300, 400, 500, 600) is adapted to be positioned at a first end of the container (10, 20, 50a, 50b, 50c, 50d) such that the light generated by the light source (110, 210, 310, 410, 510, 610), passing through the mask (120, 220, 320, 420, 520, 620), illuminates the sample in the container (10, 20, 50a, 50b, 50c, 50d); and wherein the at least one light source (110, 210, 310, 410, 510, 610) and the mask (120, 220, 320, 420, 520, 620) are configured for light generated by the at least one light source (110, 210, 310, 410, 510, 610) being passed through the mask (120, 220, 320, 420, 520, 620) such that a shape, a size, and a position of a projection of the light passing through the mask (120, 220, 320, 420, 520, 620), onto a plane of the bottom surface (12, 22) arranged at a second end of the container (10, 20, 50a, 50b, 50c, 50d), opposite to the first end, match a shape, a size, and a position of the bottom surface (12, 22) of the container (10, 20, 50a, 50b, 50c, 50d), such that the side walls (14, 24) of the container (10, 20, 50a, 50b, 50c, 50d) are not illuminated, and such that substantially the full bottom surface (12, 22, 52a) of the container (10, 20, 50a, 50b, 50c, 50d) is illuminated.