An endomicroscope assembly comprising: a fiber ferrule and a single-mode optical fiber extending into the fiber ferrule, the fiber ferrule having a distal end positioned to emit an illumination beam when provided to the single-mode optical fiber; a compact scanning assembly mounted to a flexible tubing, the compact scanning assembly having a folded beam configuration to receive the illumination beam, to convert the illumination beam to a higher numerical aperture illumination beam, and to scan the higher numerical aperture illumination beam across a lateral sample region, the compact scanning assembly comprising: an outer housing; a dual mirror lateral scanning assembly (M1, M2) fixedly positioned within the outer housing and adjacent the distal end of the flexible tubing, the dual mirror lateral scanning assembly having a first scanning mirror with an aperture aligned with the single mode fiber to receive the illumination beam into a folded beam path for converting to the higher numerical aperture illumination beam, the folded beam path being defined by the first scanning mirror and a second mirror; and a lens assembly (L1, L2, L3) fixedly positioned within the rigid outer housing, the lens assembly (L1, L2, L3) positioned distally to and spaced from the lateral scanning assembly (M1, M2) to scan the higher numerical aperture illumination beam across the lateral sample region and to collect fluorescence from the lateral sample region. a fiber ferrule and a single-mode optical fiber extending into the fiber ferrule, the fiber ferrule having a distal end positioned to emit an illumination beam when provided to the single-mode optical fiber; a compact scanning assembly mounted to a flexible tubing, the compact scanning assembly having a folded beam configuration to receive the illumination beam, to convert the illumination beam to a higher numerical aperture illumination beam, and to scan the higher numerical aperture illumination beam across a lateral sample region, the compact scanning assembly comprising: an outer housing; a dual mirror lateral scanning assembly (M1, M2) fixedly positioned within the outer housing and adjacent the distal end of the flexible tubing, the dual mirror lateral scanning assembly having a first scanning mirror with an aperture aligned with the single mode fiber to receive the illumination beam into a folded beam path for converting to the higher numerical aperture illumination beam, the folded beam path being defined by the first scanning mirror and a second mirror; and a lens assembly (L1, L2, L3) fixedly positioned within the rigid outer housing, the lens assembly (L1, L2, L3) positioned distally to and spaced from the lateral scanning assembly (M1, M2) to scan the higher numerical aperture illumination beam across the lateral sample region and to collect fluorescence from the lateral sample region. an outer housing; a dual mirror lateral scanning assembly (M1, M2) fixedly positioned within the outer housing and adjacent the distal end of the flexible tubing, the dual mirror lateral scanning assembly having a first scanning mirror with an aperture aligned with the single mode fiber to receive the illumination beam into a folded beam path for converting to the higher numerical aperture illumination beam, the folded beam path being defined by the first scanning mirror and a second mirror; and a lens assembly (L1, L2, L3) fixedly positioned within the rigid outer housing, the lens assembly (L1, L2, L3) positioned distally to and spaced from the lateral scanning assembly (M1, M2) to scan the higher numerical aperture illumination beam across the lateral sample region and to collect fluorescence from the lateral sample region.