Figure 1: Construction of spatiotemporal transcriptome and prediction of cell position.
Figure 2: Tomographic imaging of gene expression patterns and image feature extraction by Principal Component Analysis.
Figure 3: Method of tomographic imaging identifies collective cellular behaviors during gastrulation and early organogenesis.
Figure 4: Correlative image analysis of tissue boundary pattern formation along A-P axis during gastrulation.
Figure 5: Correlative image analysis and the mining of KEGG database identified the molecular signaling pathways in the morphogenetic domains (central position of sectioning).
Figure 6: The morphogenetic domain signaling network model suggested that the Notch and the Ephrin signaling pathways cross-talk and play important roles in regulating tissue morphogenesis.
Figure 7: Homozygote mutants of the genes glp-1 and skn-1 at 345 embryonic stage showed the abnormally formed tissue boundaries and the loss of tissue continuity required for normal early organogenesis.
Supplementary Figure 1: The three sectioning planes along the A-P, the L-R and the V-D body axis.
Supplementary Figure 2: Within-embryo Z-score normalization of gene expression profile across cell types.
Supplementary Figure 3: Single cell level analysis can be achieved through the integration of gene expression profiles with cell spatiotemporal information in 3-dimensional Voronoi diagram.
Supplementary Figure 4: Tomographic imaging of gene expression pattern with individual embryo samples.
Supplementary Figure 5: Spatiotemporal alignment of C. elegans embryo samples.
Supplementary Figure 6: Embryo image reconstruction with varied number of Principal Components.
Supplementary Figure 7: Correlative image analysis and the mining of KEGG database identified the molecular signaling pathways in the morphogenetic domains (the central position of sectioning).
Supplementary Figure 8: Correlative image analysis and the mining of KEGG database identified the molecular signaling pathways in the morphogenetic domains (the most anterior position of sectioning).
Supplementary Figure 9: Correlative image analysis and the mining of KEGG database identified the molecular signaling pathways in the morphogenetic domains (the most posterior position of sectioning).
Supplementary Figure 10: The morphogenetic domain signaling network model suggested that the Notch and the Ephrin signaling pathways cross-talk and play important roles in regulating tissue morphogenesis.
Supplementary Figure 11: The development process of muscle, neuron and excretory cell and intestine system involve the coordinated cellular behaviors.
Supplementary Figure 12: Point cloud model generation and tomographic imaging along the V-D and the L-R body axis in histology sectioning order and in time course.
Supplementary Figure 13: Gene expression – anatomy pattern correlative image analysis for gene pha-4 along the V-D and the L-R body axis, in histology sectioning order.
Supplementary Figure 14: Gene expression – anatomy pattern correlative image analysis for gene hlh-1 along the three body axes in histology sectioning order.
Supplementary Figure 15: Gene expression – anatomy pattern correlative image analysis for gene Pha-4 along the V-D and the L-R body axis, in temporal order.
Supplementary Figure 16: Gene expression – anatomy pattern correlative image analysis for gene hlh-1 along the three body axes, in temporal order.
Supplementary Figure 17: Anatomical graphics pattern analysis of mutants with wild type (A-P and L-R axis).
Supplementary Figure 18: PCA analysis of embryo section images in the central section position.
Supplementary Figure 19. PCA analysis of embryo section images in the most anterior section position.
Supplementary Figure 20. PCA analysis of embryo section images in the most posterior section position.
Supplementary Table 4. The 14 molecular signaling pathways that were detected in the morphogenetic domains.