MicroCT-based phenomics in the axial skeleton of adult zebrafish.

(A) MicroCT scans are acquired in adult fish (image shows 3D volume rendering). (B) For segmentation, individual vertebrae are isolated using FishCuT (image shows 16 vertebrae from the same fish, colors indicate local thickness), and (C) each vertebral body is segmented into three skeletal elements: the Neural Arch (green), Centrum (white), and Haemal Arch/Pleural Ribs (red). A representative segmentation can be seen in (D), which depicts the same fish in (A) with an alternating color scheme used to highlight individual skeletal elements segmented by FishCuT (top: lateral view; bottom: anteroposterior view). (E) For each skeletal element, FishCuT computes the following: Tissue Mineral Density, Volume, Thickness, Surface Area, Length (centrum only), Tissue Mineral Density Variation, and Thickness Variation. (F) For analysis, each combination of element/outcome is computed as a function of vertebra number, and subjected to the global test. Shown is a plot of one combination of element/outcomes, Cent.TMD, as a function of vertebra number in WT vs. bmp1a^-/- fish. (G) Standard scores are computed and arranged into ‘skeletal barcodes’ that facilitate visualization of phenotypic trends both within individuals and across groups. Shown are the skeletal barcodes for a single WT (left) and bmp1a^-/- fish (right).

ZFIN is incorporating published figure images and captions as part of an ongoing project. Figures from some publications have not yet been curated, or are not available for display because of copyright restrictions.

Analysis of bmp1a^-/- fish.

(A) Skeletal barcodes for WT and bmp1a^-/- fish (n = 3/group). Each barcode represents a single fish. Standard scores are computed as the difference between the value of the feature in the individual and the mean value of the feature across all vertebrae in the control population, divided by the standard deviation of the feature across all vertebrae in the control population (see text for details). (B–K) Phenotypic features plotted as a function of vertebra (mean ± SE, n = 3/group). Plots associated with a significant difference are colored in a lighter coloring scheme (see text for p-values). The same plots with y axis set to zero are shown in Figure 5—figure supplement 2. (L) Maximum intensity projection of microCT scans.

Analysis of plod2^-/- fish.

(A) Skeletal barcodes for WT and plod2^-/- fish (n = 3/group). WT fish in this figure are different from those in Figure 5. (B–K) Phenotypic features plotted as a function of vertebra (mean ±SE, n = 3/group). Plots associated with a significant difference are colored in a lighter coloring scheme (see text for p-values). The same plots with y axis set to zero are shown in Figure 6—figure supplement 1. (L) Maximum intensity projection of microCT scans.

ZFIN is incorporating published figure images and captions as part of an ongoing project. Figures from some publications have not yet been curated, or are not available for display because of copyright restrictions.

Analysis of plod2^-/- fish following removal of allometric effects of body size.

(A) Skeletal barcodes for WT and plod2^-/- fish following removal of allometric effects of body size (n = 3/group). (B–K) Phenotypic features as a function of vertebra (mean ± SE, n = 3/group). Phenotypic data in WT sibling controls were subjected to allometric normalization; data in plod2^-/- fish are identical to those in Figure 6. Plots associated with a significant difference are colored in a lighter coloring scheme (see text for p-values). Values for TMD were derived by a two-step process in which TMC and volume were subjected to allometric normalization independently, and normalized values for TMC and volume were used to calculate normalized values for TMD. The same plots with y axis set to zero are shown in Figure 8—figure supplement 1. (L) Transverse sections of microCT scans. Centra are highlighted by a red box in each animal. plod2^-/- mutants (left) exhibit increased centrum diameter compared to standard length matched, non-clutchmate WT controls (right), and to a lesser extent, WT siblings (middle) of greater standard length. Images show posterior endplate of the sixth precaudal vertebra in all fish.

Identification of opallus as a novel axial skeletal mutant.

(A) Skeletal barcodes for WT, opallus, and pissarro (n = 2 fish/group). Barcodes for opallus, but not pissarro, appear different from WT fish (B–K) Phenotypic features in opallus plotted as a function of vertebra (mean ±SE, n = 5/group). Plots associated with a significant difference are colored in a lighter coloring scheme (see text for p-values). The same plots with y axis set to zero are shown in Figure 9—figure supplement 2. (L) Maximum intensity projections of microCT scans.