Optical tomography principles and results. (A) Scheme of the acquisition system. During the measurement the specimen is translated and rotated through the focal plane of the detection objective lens (x,y). The specimen is sampled along a spiral. (B) Scheme of the system from the top. The spiral is formed on the transverse section of the specimen. The detection objective′s depth of field, δ_z, is highlighted in red. (C-E) Transverse (C), coronal (D) and sagittal (E) slices of a wild-type 2dpf zebrafish head obtained in vivo with optical tomography (reconstructed virtual sections). Segmented head organs: retina (pink), eye lens (orange), brain ventricles (green), brain (cyan). Annotated brain domains: optic tectum (OT), hypothalamus (H), cerebellum (Ce) and olfactory bulb (OB). (F,G) Coronal (F) and sagittal (G) slices of a 5dpf zebrafish. SB, swim bladder; OC, otic capsule; Li, liver; So, somites; No, notochord. (H) Lateral view of the 3D reconstructed sample. Scale bars: 100µm.

Multimodal imaging. (A-D) Sagittal (A,B) or transverse (C,D) slice of a transgenic Tg(neurog1:GFP)×Tg(kdrl:rasCherry) zebrafish (3.5dpf) visualized with (A,C) SPIM or (B,D) SPIM (red/green) combined with optical tomography (gray). The dotted lines in the sagittal sections indicate the position of the transverse section and vice versa. (E-F′) Lateral (E) and dorsal (F) views of the sample created with weighted intensity projection. The boxed regions in E,F are enlarged in E′,F′ to illustrate the fine details in the data. Scale bars: 100µm.

Long-term time-lapse. Time-lapse development of a Tg(kdrl:GFP) zebrafish from 16-38hpf acquired every 10min. SPIM signal (yellow) is superimposed on tomographic reconstruction (gray). The optical tomography data are inverted in all panels. Scale bar: 100µm.