An automated loading apparatus for an electron microscope, preferably for a transmission electron microscope, a scanning electron microscope, a dual beam focused ion beam microscope (DB-FIB), or a scanning transmission electron microscope (STEM), the automated loading apparatus comprising: a frame and a transport module connected to the frame, the transport module includes a multistage shuttle, wherein the frame is configured to removably couple to a port of the electron microscope; the multistage shuttle has a first shuttle stage (104S1) having multiple degrees of freedom of motion, a second shuttle stage (104S2) having multiple degrees of freedom of motion independent of the first stage, and an end effector connected to at least one of the first and second shuttle stages, the end effector being configured to hold the workpiece and transport the workpiece into and out of the electron microscope through the port, the end effector having a range of motion, defined by a combination of the first and second stage multiple degrees of freedom of motions, extending from a workpiece holding station outside the electron microscope to a processing location of an imaging process inside the electron microscope for positioning the workpiece at the processing location of the imaging process so that the end effector defines a processing stage of the imaging process of the electron microscope; and an automated loading and transport section connected to the frame and being communicably connected to the transport module, the automated loading and transport section including a load port module through which workpieces are loaded into the automated loading and transport section. a frame and a transport module connected to the frame, the transport module includes a multistage shuttle, wherein the frame is configured to removably couple to a port of the electron microscope; the multistage shuttle has a first shuttle stage (104S1) having multiple degrees of freedom of motion, a second shuttle stage (104S2) having multiple degrees of freedom of motion independent of the first stage, and an end effector connected to at least one of the first and second shuttle stages, the end effector being configured to hold the workpiece and transport the workpiece into and out of the electron microscope through the port, the end effector having a range of motion, defined by a combination of the first and second stage multiple degrees of freedom of motions, extending from a workpiece holding station outside the electron microscope to a processing location of an imaging process inside the electron microscope for positioning the workpiece at the processing location of the imaging process so that the end effector defines a processing stage of the imaging process of the electron microscope; and a first shuttle stage (104S1) having multiple degrees of freedom of motion, a second shuttle stage (104S2) having multiple degrees of freedom of motion independent of the first stage, and an end effector connected to at least one of the first and second shuttle stages, the end effector being configured to hold the workpiece and transport the workpiece into and out of the electron microscope through the port, the end effector having a range of motion, defined by a combination of the first and second stage multiple degrees of freedom of motions, extending from a workpiece holding station outside the electron microscope to a processing location of an imaging process inside the electron microscope for positioning the workpiece at the processing location of the imaging process so that the end effector defines a processing stage of the imaging process of the electron microscope; and an automated loading and transport section connected to the frame and being communicably connected to the transport module, the automated loading and transport section including a load port module through which workpieces are loaded into the automated loading and transport section.