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. 2022 Jun 6;11:e77918. doi: 10.7554/eLife.77918

Figure 3. Cross-modality alignment conveys a single-cell view of EM data.

(a) Illustration of the ensemble model for the comma stage. Landmarks (dots) and adjacencies (edges) in a single instance of labeled data. All adjacencies are shown with the consistent adjacencies highlighted in black. Inconsistent landmarks are larger and red. (b) A visualization of the comma stage EM data after alignment. Nucleus centroids are dots colored by major predicted tissue type with color key provided. Adjacencies are shown as gray lines. (c) Accuracy of predicted identities for each EM data at the single-cell and tissue levels. (d) Illustration of EM data annotated by identities. Tissue regions are shaded following the color scheme in b to highlight overall anatomical structure. The excretory canal cell is marked with a star with the nucleus of the excretory duct and part of the pore cell body visible below it. Individual neurons are numbered. Identities as follows are from alignment (-a) or manually confirmed (-c) 1 FLPR/AIZR parent-c, 2 ASER-c, 3 AVBR-c, 4 ASHR-c, 5 AWCR-c, 6 SIBDR-c, 7 AVKR-a, 8 AIYR-a, 9 SMBDR-c, 10 SMBVL-a, 11 AIML-a, 12 AVKL-a, 13 SMDDL-c, 14 FLPL/AIZL parent-a, 15 RMGL-a, 16 ALML/BDUL parent-c. Scale bar indicates 5 μm. (e) 3D reconstruction in comma stage EM data colored to maximize local contrast and showing cell body contours for seam cells (blue and orange), gut cells (alternating shades of red), germ line (cyan), and the excretory canal, duct and pore cells (red, green, and blue respectively) as well as nuclear contours for pharynx (green). (f) 3D reconstruction of the excretory system in the 1.5-fold stage EM data. Red, green, blue and cyan are the excretory canal, duct, pore and gland cell, respectively, as in e. Black arrows point to auto fusion in the duct and pore cell. (g) EM view of lumen (white arrow) and site of auto fusion (black arrow) in the excretory pore cell at 1.5-fold stage. Scale bar indicates 1 μm.

Figure 3.

Figure 3—figure supplement 1. Cross-modality alignments.

Figure 3—figure supplement 1.

(a) Illustration of the ensemble model for each EM dataset aligned. See Figure 3a for a detailed explanation. (b) A visualization of all EM data. Nucleus centroids are dots colored by predicted tissue type, matching the color key in panel b. Computed adjacencies are shown as gray edges. (c) Summary of annotations of each EM dataset. A histogram stratified by tissue type for the type of identity available for each cell. Manually verified single cell or tissue type IDs are in blue and red respectively. The identities predicted by our alignment method are gray.
Figure 3—figure supplement 1—source data 1. EM annotation bean stage.
Excel spreadsheet containing position and annotation information for bean stage EM.
Figure 3—figure supplement 1—source data 2. EM annotation comma stage.
Excel spreadsheet containing position and annotation information for comma stage EM.
Figure 3—figure supplement 1—source data 3. EM annotation 1.5-fold stage.
Excel spreadsheet containing position and annotation information for 1.5-fold stage EM.
Figure 3—figure supplement 2. Consistency and change of adjacency over time.

Figure 3—figure supplement 2.

(a) Adjacency counts from FM data at each stage for cells that are present at all three stages. Ordered by lineage position. Only fully consistent adjacencies (white areas) are used to constrain alignment but quantitative adjacency counts provide a way of characterizing positional variability. Adjacency matrices are available in supplemental data. (b) Change in adjacencies observed between the bean and 1.5-fold stages. Color indicates whether adjacencies have been gained (blue) or lost (red) with darker colors being more consistent. (c) The same matrix as in b, displayed as a graph. Cell node positions are set by a force based layout and edge thickness is proportional to signed adjacency change. Color highlights subgraphs with high internal connectivity, i.e. similar patterns of relative motion, suggesting this representation’s potential wider use in characterizing developmental.
Figure 3—figure supplement 2—source data 1. All adjacency information bean stage.
CSV spreadsheets containing the quantitative count of adjacencies found in FM data at bean stage. Spreadsheet contains only entries for consistent landmarks (present at all three stages) to aid comparison between stages. Values vary between 0 for cells that are never adjacent to 39 for cells that are always adjacent (these are used as alignment constraints in our method) significant variation occurs between these values. Complete adjacency information data structures used in alignment are available within.mat data files in source code.
Figure 3—figure supplement 2—source data 2. All adjacency information comma stage.
Adjacency information for bean stage, see above for additional details.
Figure 3—figure supplement 2—source data 3. All adjacency information 1.5-fold stage.
Adjacency information for 1.5-fold stage, see above for additional details.
Figure 3—video 1. 3D rendering of embryo landmarks.
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Visualization of one example set of embryonic landmarks over time. Lineages with a majority fate for a given tissue type are colored to match tissue color code in Figure 3.