A system for holographic imaging, the system comprising: an ion filter coupled to select a sample ion from an ionized sample supply, the ion filter including a quadrupole filter to select the sample ion from the sample supply; an energy reduction cell coupled to receive the selected sample ion and reduce a kinetic energy of the sample ion; a substrate coupled to receive the sample, wherein the substrate is electron transparent; an ion transport module coupled to receive the sample ion from the energy reduction cell and transport the sample ion downstream to the substrate; and an imaging system arranged to image, with a low energy coherent electron beam, the sample located on the substrate, wherein the substrate is arranged in an analysis location, the imaging system (204, 304) including: an emitter coupled to direct the low energy coherent electron beam toward the sample; and a detector arranged to detect interference patterns formed from interaction of electrons of the low energy coherent electron beam and the sample characterized in that the ion transport module includes a plurality of differential pumping stages, wherein the ion transport module receives the sample ion at a first vacuum level and provides the sample ion at a second vacuum level, the second vacuum level higher than the first vacuum level, wherein each differential pumping stage of the plurality of differential pumping stages respectively increases the vacuum level from the first to second vacuum level. an ion filter coupled to select a sample ion from an ionized sample supply, the ion filter including a quadrupole filter to select the sample ion from the sample supply; an energy reduction cell coupled to receive the selected sample ion and reduce a kinetic energy of the sample ion; a substrate coupled to receive the sample, wherein the substrate is electron transparent; an ion transport module coupled to receive the sample ion from the energy reduction cell and transport the sample ion downstream to the substrate; and an imaging system arranged to image, with a low energy coherent electron beam, the sample located on the substrate, wherein the substrate is arranged in an analysis location, the imaging system (204, 304) including: an emitter coupled to direct the low energy coherent electron beam toward the sample; and a detector arranged to detect interference patterns formed from interaction of electrons of the low energy coherent electron beam and the sample characterized in that the ion transport module includes a plurality of differential pumping stages, wherein the ion transport module receives the sample ion at a first vacuum level and provides the sample ion at a second vacuum level, the second vacuum level higher than the first vacuum level, wherein each differential pumping stage of the plurality of differential pumping stages respectively increases the vacuum level from the first to second vacuum level. an emitter coupled to direct the low energy coherent electron beam toward the sample; and a detector arranged to detect interference patterns formed from interaction of electrons of the low energy coherent electron beam and the sample characterized in that the ion transport module includes a plurality of differential pumping stages, wherein the ion transport module receives the sample ion at a first vacuum level and provides the sample ion at a second vacuum level, the second vacuum level higher than the first vacuum level, wherein each differential pumping stage of the plurality of differential pumping stages respectively increases the vacuum level from the first to second vacuum level.