Extended Data Fig. 1: Optical design of the miniature microscope maximizing scattered fluorescence collection.

(a) The optical design of the fluorescence collection arm. (b) The optical design of the illumination arm. (c-h) Trajectory analysis of ballistic and scattered photons. A point source was implanted at the depth of 1 mm in the inhomogeneous scattering brain tissue, and a large-area detector (18 ×18 mm²) was placed at the position of the supple fiber bundle to receive all the scattered photons. Without considering scattering, the optical path structure changed from ballistic photons passing through SIMO alone (c), to passing through SIMO plus the front lenses of the Abbe condenser (e), and then to passing through SIMO plus the front lenses and rear lens of the Abbe condenser (g). SIMO, simplified infinity miniature objective; WM, white matter. Corresponding irradiation distribution and cross-section profile of scattered photons on the detector were shown in (d), (f) and (h) respectively. The position of the cross section was indicated by a black dashed line in the irradiation distribution diagram. The full widths at half-maximum of the cross-section profile in (d), (f) and (h) were 5.2, 3 and 1.1 mm respectively.