Systems and methods for using multimodal imaging to determine structure and atomic composition of specimens

An imaging system for analyzing specimens, the imaging system comprising:

• a chamber having a controlled gas atmosphere and configured to receive a specimen;
• a detector;
• an energy applying component configured to apply energy to the specimen disposed in the chamber having the controlled gas atmosphere such that the detector provides a first image of the specimen acquired in a first, non-destructive imaging mode of the imaging system, and a second image of the specimen acquired in a second, destructive imaging mode of the imaging system, wherein:
• the first and second images are alternately acquired while the controlled gas atmosphere is maintained in the chamber, and
• the energy applying component is configured to, after the first image is acquired and before the second image is acquired, apply energy to the specimen to cause gas atoms adsorbed on the specimen to desorb without being ionized;
• and
• a data processing and feature recognition system configured to combine information from the first and second images to determine a position and identity of at least one atom of the specimen.