3D Imaging of Japanese Rice Fish

Japanese rice fish (Oryzias latipes) stained with 0.33% phosphotungstic acid (PTA) and 0.3% Lugol’s iodine (I₃K) and embedded in 4% agarose (volume size: 900 × 1303 × 4327 voxels). Animal husbandry and experimental procedures were performed at the Institute of Biological and Chemical Systems (IBCS) of Karlsruhe Institute of Technology (KIT) in accordance with German animal protection regulations (Regierungspräsidium Karlsruhe, Germany; Tierschutzgesetz 111, Abs. 1, Nr. 1, AZ35-9185.64/BH). The IBCS is under the supervision of the Regierungspräsidium Karlsruhe, who approved the experimental procedures. The specimen was scanned with the laboratory X-ray setup of KIT’s Institute for Photon Science and Synchrotron Radiation (see Supplementary Table 2 for scan parameters). Eleven individual body parts were pre-segmented in 231 slices. The different body parts were not always pre-segmented in the same slices. Therefore, each label was computed separately resulting in computation times between 4.80 and 57.50 min on 1 NVIDIA Tesla V100 and between 4.53 and 24.23 min on 4 NVIDIA Tesla V100.