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FIGURE 10 in Automated segmentation of insect anatomy from micro-CT images using deep learning

FIGURE 10 Application of pipeline for other insect species. The brain textures of various insect species can be very similar to those of ants, facilitating the prediction by the network even without pretraining on specific insect brain scans. (a) Raw image of wasp head (original 1000 × 1000 px) and (b) its prediction without postprocessing (original 520 × 520 px), indicating satisfactory identification of the borders of the brain area. (c) 2D image of praying mantis head (520 × 520 px) and (d) the prediction of its brain area without postprocessing. Even though the network overpredicts some small pixel islands, it excludes from its prediction areas of the muscles, fibers, and cuticle.

FIGURE 1 in Automated segmentation of insect anatomy from micro-CT images using deep learning

FIGURE 1 Segmentation pipeline overview. (a) Specimens are placed in iodine for staining for 2 weeks and then placed in small vials containing 99% ethanol to prevent them from moving during scanning. (b) The computed tomography (CT) scanner acquires successive X-ray images of the stepwise rotating specimen, and, using a user-defined reference image, automatically reconstructs them to produce orthogonal cross-section stacks that are used for the volume reconstruction of the specimen. (c) Volume rendering for future morphological studies is performed using Amira software. (d) Semiautomated segmentation of the brain volume of each scan (in orange) using the watershed method in Amira. (e) Schematic representation of the U-Net architecture used as the core of the pipeline for the development of a fully automated brain segmentation method. (f) The acquired brain images are used for training after preprocessing augmentation and manual creation of masks. (g) The network's prediction (in yellow) is postprocessed for smoothing out overpredicted areas (in red).

FIGURE 2 in Automated segmentation of insect anatomy from micro-CT images using deep learning

FIGURE 2 Exemplar images of full-body scans from different ant species. Three-dimensional (3D) reconstructed microcomputed tomography (micro-CT) image of (a) Acromyrmex versicolor and (b) Atta texana worker specimens, using volume rendering in Amira. (c) 2D micro-CT full body image of the Atta texana specimen (original 1000 × 1000 px). The brain area is the area with the most uniform pixel density within the whole body in its stained state, which makes it easy to recognize in most high-quality scans.

FIGURE 3 in Automated segmentation of insect anatomy from micro-CT images using deep learning

FIGURE 3 Example of semiautomated brain image segmentation. The brain area (in orange) of an Atta texana ant specimen was segmented using the watershed method in Amira; the 1000 × 1000 × 1000 px 3D image was manually postprocessed by smoothing and cropping oversegmented areas.

FIGURE 9 in Automated segmentation of insect anatomy from micro-CT images using deep learning

FIGURE 9 Prediction of ganglia in the thorax. As the tissue texture in the image is similar to that of the brain, the network accurately predicts other areas of nervous tissue in the organism. The pixel island detection step isolates the brain, but without this step neural tissue can be isolated.

FIGURE 8 3D in Automated segmentation of insect anatomy from micro-CT images using deep learning

FIGURE 8 3D volume of ant brain reconstructed from 2D images (original 520 × 520 px) predicted by the algorithm. 3D reconstructed brain prediction of an Atta texana worker.

FIGURE 7 in Automated segmentation of insect anatomy from micro-CT images using deep learning

FIGURE 7 Pipeline performance demonstrated both for validation (top row) and testing (bottom row) sets. (a, d) Raw images of head of Acromyrmex versicolor and Carebara atoma ant specimens, cropped along the x-y axes. The manually segmented brain areas are indicated in blue. (b, e) Network predictions before postprocessing (in yellow). Areas in yellow dotted circles are pixel islands not connected to the brain area that were overpredicted. (c, f) Predictions after postprocessing (in red). The borders of the predicted areas show good agreement with the manual segmentation in both sets. Note that in overlapping manually and automatically segmented areas in b, c, e, and f, colors appear green or purple.

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FIG. 21 in The anatomy and phylogenetic affinities of Cynthiacetus peruvianus, a large Dorudon-like basilosaurid (Cetacea, Mammalia) from the late Eocene of Peru

FIG. 21. — Ventral view of the right periotic of MNHN.F.PRU10, holotype of Cynthiacetus peruvianus. Abbreviations: aes, ventral edge of the anteroexternal sulcus; apd, anterior pedicle for the tympanic; app, anterior process of the periotic; fc, cochlear window; fo, foramen pseudovale; fpb, falcate process of the basioccipital; fps, falciform process of the squamosal; fs, facial sulcus; fv, vestibular window; gtt, groove for the tensor tempani; inc, incudal fossa; jn, jugular notch; Ma, malleus; mce, medial crest of the exoccipital; men, groove for the meningeal arteries; mf, mallear fossa; nc, nuchal crest; plc, posterolateral crest; ppd, posterior inner pedicle of the tympanic; ppe, paroccipital process of the exoccipital; ppp, posterior process of the periotic; ppt, posterior process of the tympanic bulla; pr, promontorium; V3, path of the mandibular nerve; VII, foramen for the facia nerve; vlt, ventrolateral tuberosity. Dark grey-shaded regions and hatched regions represent the sediment and broken portions of bone, respectively. Not to scale.

Figure 12 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 12. Odobenocetops leptodon, referred specimen (MNHN SAO 202). Left forelimb in lateral (A) and medial (B) views.

Figure 5 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 5. Reconstruction of the dorsal view of the rostrum of Odobenocetops leptodon. Abbreviations: Fps, fossa for the premaxillary sac; Fr, frontal; Mx, maxilla; NaF, narial fossa; Pmx, premaxilla; Sb, supplementary bone.

Figure 16 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 16. Estimation of the relative positions of various planes of the skull, atlas, and vertebral column of Odobenocetops in order to evaluate the position of the long right tusk relative to the axis of the body.

Figure 15 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 15. Auditory region of Odobenocetops peruvianus, holotype (SMNK PAL 2491). Lateral view (A) and posterolateral view showing the tympanic aperture (B). On B, the outline of the tympanic aperture has been enhanced with a white line. Abbreviations: Ap, anterior process of the periotic; Bo, basioccipital; Eam, external auditory meatus; Fo, foramen ovale; Gf, glenoid fossa; Oc, occipital condyle; Po, paroccipital process of the exoccipital; Ptp, post-tympanic process of the squamosal; Sp, sigmoid process of the tympanic; Tym, tympanic.

Figure 8 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 8. Odobenocetops cf. leptodon, referred specimen (MNHN PPI 249). Periotic in dorsal (A), lateral (B), ventral (C), and medial (D) views.

Figure 4 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 4. Odobenocetops leptodon, referred specimen (MNHN SAO 202). Skull in lateral left (A) and lateral right (B) views.

Figure 19 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 19. Approximate curvature radius of a vertical section of the occipital condyle in Odobenocetops peruvianus, Tursiops truncatus and Delphinapterus leucas.

Figure 7 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 7. Odobenocetops leptodon, referred specimen (MNHN SAO 202). Periotic in dorsal (A), lateral (B), ventral (C), and medial (D) views. Abbreviations: ac, aqueductus cochleae; ap, anterior process; av, aqueductus vestibuli; dfc, dorsal opening of the facial canal; ef, fovea epitubaria; fc, fenestra cochleae; fi, fossa incudis; fm, fossa mallei (= epitympanic recess); iam, internal auditory meatus; pbf, posterior bullar facet; pc, pars cochlearis (= promontorium); pp, posterior process; slf, sulcus facialis; so, supernumerary ossicles; st, stapes; stf, fossa for stapedial muscle; ts, tractus spiralis; vfc, ventral opening of the facial canal; vr, ventral rim of the anterior process.

Figure 18 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 18. Reconstruction of Odobenocetops leptodon in its inferred environment (painting by Mary Parrish, Smithsonian Institution, Washington DC, USA).

Figure 11 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 11. Odobenocetops leptodon, holotype (SMNK PAL 2492). Atlas in anterior (A), posterior (B), dorsal (C), ventral (D), lateral right (E), and lateral left (F) views.

Figure 3 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 3. Odobenocetops leptodon, referred specimen (MNHN SAO 202). Skull in dorsal (A), ventral (B), and anteroventral (C) views.

Figure 17 in The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

Figure 17. Positions of the head in Odobenocetops leptodon. Maximum flexion (occasional) (A); median position (swimming) (B); maximum extension (feeding) (C).