(A) Isosurface renderings of the CT-scanned embryo.
(B) Maximum intensity projection of the same embryo, with overlying places of section.
(C–E) Sagittal, coronal, and axial sections of an E11.5 littermate.
(F–H) Sagittal, coronal, and axial computed tomography sections of the embryo in panels (A) and (B), corresponding to the planes of section in panels (C–E). At low-power magnification, virtual and true paraffin histology demonstrate a similar level of detail. Scale bar indicates 400 μm.
a, cardiac atrium; cv, cardinal vein; drg, dorsal root ganglia; fv, forebrain vesicle; liv, liver; nt, neural tube; v, cardiac ventricle; v4, fourth ventricle.

(A–D) Isosurfaces of E9.5, E10.5, E11.5, and E12.5 embryos scanned at 8-μm resolution.
(E–H) Corresponding sagittal sections. Vertical scale bars to the right of each embryo indicate 1.62, 2.94, 4.50, and 6.73 mm, respectively.
mv, midbrain vesicle.

(A–D) Wild-type E12.5 embryo scanned at 8-μm resolution. (A) Orientation of the planes of section. (B) Sagittal plane. (C) Coronal plane. (D) Axial plane.
(E–H) The same embryo as in (A–D), scanned by a more rapid protocol at 27-μm resolution. Most of the features present at 8-μm resolution are also appreciable at the lower 27-μm resolution.
(I–P) Comparison of segmentation analysis of cardiac chambers for the 8-μm and 27-μm scans, respectively. The right atrium is teal, the right ventricle is blue, the left atrium is pink, the left ventricle is red, and the cardiac wall is transparent grey. A region of the right atrium that could not be segmented on the 27-μm scan is shown with a white asterisk (*).
Scale bars in panels (B) and (F) represent 1.2 mm. Movies of sagittal, coronal, and axial planes corresponding to panels (B–D) are presented as , , and S3.
a, cardiac atrium; cc, central canal of the neural tube; fl, forelimb; sc, semicircular canal; v, cardiac ventricle.

Wild-type E11.5 embryo (A–E) compared to a mutant littermate (F–J) that expresses the Pax3:Fkhr oncogene in neural crest and myogenic tissue. (A and F) Isosurface renderings.
(B–E) and (G–J) Segmentation renderings of cranial neural crest (grey), brain vesicles (red), liver (brown), cardiac muscle (blue), and the conotruncal cavity (red within the blue cardiac muscle). From the segmented renderings, the mutant embryo is noted to have partial neural tube closure failure resulting in absence of the hindbrain vesicle, overgrown midbrain mesenchyme (mm), as well as severely hypomorphic telencephalic vesicles (fv, shown in red). Movies of rotating renderings for mutant and wild-type embryos are presented as and .
(K and L) MicroCT axial sections of the neural tube at the level of the forelimbs (dorsal surface is up) from wild-type and control embryos, respectively. Magnification of the neural tube is shown in the upper right insets of each panel. The sulcus limitans, which separates the dorsal and ventral neural tube, is shown as a red line. Severe blunting of the dorsal neural tube is evident in the mutant embryo.
(M and N) Axial confocal microscopy sections from embryos of the same genotype and developmental stage as the corresponding axial cross-section as in panels (K and L), respectively. Sections were stained with the Pax7 immunohistochemical marker of the dorsal neural tube. Pax7-stained cells of the dorsal neural tube and flanking dermomyotome are white. The sulcus limitans is shown as a red line, confirming the dorsal neural tube blunting seen in the microCT sections.
Scale bars in panels (B) and (F) are each 1.2 mm.