An imaging system, the system comprising: an imaging device comprising a sample holder (205, 400, 401, 402) configured to facilitate automated deposition and removal of a sample, wherein the sample holder (205, 400, 401, 402) comprises an internal sample plate receiving area; at least two walls, each wall defining a cutout portion in a central region of each of the at least two walls, and a beveled edge defining part of the internal sample plate receiving area, the beveled edge adjoining and forming an angle with an internal bottom lip portion on either side of the cutout portion, the angle of the beveled edge relative to the plane of the bottom lip portion of the plate holder being less than 90 degrees; a transport device configured to place a sample in the sample holder (205, 400, 401, 402); a processor in communication with the imaging device and the transport device; and memory operably coupled to the processor, wherein the memory includes instructions stored thereon for acquiring an image of the sample, wherein the instructions, when executed by the processor, cause the processor to: move the sample via the transport device to the sample holder (205, 400, 401, 402) of the imaging device; identify a fiduciary mark on the sample using the imaging device; move the sample holder (205, 400, 401, 402) so that the fiduciary mark is in substantially the same position as in a reference image; and acquire an image of the sample using the imaging device. an imaging device comprising a sample holder (205, 400, 401, 402) configured to facilitate automated deposition and removal of a sample, wherein the sample holder (205, 400, 401, 402) comprises an internal sample plate receiving area; at least two walls, each wall defining a cutout portion in a central region of each of the at least two walls, and a beveled edge defining part of the internal sample plate receiving area, the beveled edge adjoining and forming an angle with an internal bottom lip portion on either side of the cutout portion, the angle of the beveled edge relative to the plane of the bottom lip portion of the plate holder being less than 90 degrees; a transport device configured to place a sample in the sample holder (205, 400, 401, 402); an internal sample plate receiving area; at least two walls, each wall defining a cutout portion in a central region of each of the at least two walls, and a beveled edge defining part of the internal sample plate receiving area, the beveled edge adjoining and forming an angle with an internal bottom lip portion on either side of the cutout portion, the angle of the beveled edge relative to the plane of the bottom lip portion of the plate holder being less than 90 degrees; a transport device configured to place a sample in the sample holder (205, 400, 401, 402); a processor in communication with the imaging device and the transport device; and memory operably coupled to the processor, wherein the memory includes instructions stored thereon for acquiring an image of the sample, wherein the instructions, when executed by the processor, cause the processor to: move the sample via the transport device to the sample holder (205, 400, 401, 402) of the imaging device; identify a fiduciary mark on the sample using the imaging device; move the sample holder (205, 400, 401, 402) so that the fiduciary mark is in substantially the same position as in a reference image; and acquire an image of the sample using the imaging device. move the sample via the transport device to the sample holder (205, 400, 401, 402) of the imaging device; identify a fiduciary mark on the sample using the imaging device; move the sample holder (205, 400, 401, 402) so that the fiduciary mark is in substantially the same position as in a reference image; and acquire an image of the sample using the imaging device.