A modular system for organic sample analysis is disclosed which includes a sample stage including a support platform and a motorized positioning mechanism mounted on the support platform, and a sample holder mounted on the motorized positioning mechanism upon which a sample is placed. A probe support rack is mounted on the support platform and two or more bio-imaging probes mounted on the probe support and arranged in a pre-defined geometry with respect to each other, and at least one bio-imaging probe has a field of view independent of all other bio-imaging probes. The system includes a computer controller connected to the motorized positioning mechanism and the two or more bio-imaging probes. The computer is programmed for controlling motorized positioning mechanism to move the sample holder having the sample located thereon to positions in the field of view of each bio-imaging probe where the sample can be analyzed individually by each of the bio-imaging probes. The computer includes a storage medium for storing an imaging data from each bio-imaging probe. The computer is programmed for spatially correlating imaging data of the selected volume of interest with the imaging data obtained from at least one other bio-imaging probe and storing the spatially correlated imaging data in the computer storage medium.