The invention discloses a Trace Microanalysis Microscope System for high throughput screening. A multimodal imaging sensor arrangement acquires color, multispectral, hyperspectral and multi-directional polarized imaging, independently and in combinations thereof. In one aspect of this disclosure, the multimodal acquisition is combined with a plurality of sample illumination modes, further expanding the dimensionality of the generated data. In another aspect of this invention, machine learning-based methods combining and comparing a-priori data with the acquired multimodal data space, provide unique identifiers for the composition of the analyzed target objects. In yet another aspect of this invention, projection mapping of the identified compositional features navigates secondary sampling for subsequent analyses.