Cross-modality synthesis of EM time series and live fluorescence imaging
- Molecular Cytology Core, Memorial Sloan Kettering Cancer Center, United States
- Electron Microscopy Facility, University of Lausanne, Switzerland
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, United States
Figures
Figure 1 with 2 supplements
EM and FM time series of C. elegans embryogenesis with complementary spatial and temporal resolution.
All scale bars indicate 5 μm. (a) Overview of EM data and their placement in the time course of C. elegans embryogenesis. Cartoons show body shape and the approximate physical sectioning plane …
Figure 1—figure supplement 1
Overview of FM datasets.
Max projection of representative time point for the FM data used. Each strain carries a ubiquitous histone marker (red) and a cell membrane marker (green) driven by a specific promoter (shown in …
Figure 1—video 1
FM embryo.
Max projection movie of 8 hours of development of a C. elegans embryo with a ubiquitous histone marker (red) and a cnd-1 promoter -driven membrane marker labeling a subset of neurons (green). …
Figure 2 with 1 supplement
The co-optimization algorithm for cross-modality alignment of developmental data.
(a) Components of the ensemble model. Circles represent landmarks. Numbers in each circle mark the corresponding landmarks across individual labeled data (L1 to Ln). 1a and 1b denote a split of 1 …
Figure 2—figure supplement 1
Method details.
(a) Pre-alignment Example. Effect of nonlinear pre-alignment. Equivalent nucleus locations in two temporally aligned FM data sets are connected with a tapered cone to show displacement. The top …
Figure 3 with 3 supplements
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 …
Figure 3—figure supplement 1
Cross-modality alignments.
(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 …
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Figure 3—figure supplement 1—source data 1
EM annotation bean stage.
Excel spreadsheet containing position and annotation information for bean stage EM.
- https://cdn.elifesciences.org/articles/77918/elife-77918-fig3-figsupp1-data1-v2.zip
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Figure 3—figure supplement 1—source data 2
EM annotation comma stage.
Excel spreadsheet containing position and annotation information for comma stage EM.
- https://cdn.elifesciences.org/articles/77918/elife-77918-fig3-figsupp1-data2-v2.xlsx
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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.
- https://cdn.elifesciences.org/articles/77918/elife-77918-fig3-figsupp1-data3-v2.xlsx
Figure 3—figure supplement 2
Consistency and change of adjacency over time.
(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 …
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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.
- https://cdn.elifesciences.org/articles/77918/elife-77918-fig3-figsupp2-data1-v2.xlsx
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Figure 3—figure supplement 2—source data 2
All adjacency information comma stage.
Adjacency information for bean stage, see above for additional details.
- https://cdn.elifesciences.org/articles/77918/elife-77918-fig3-figsupp2-data2-v2.zip
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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.
- https://cdn.elifesciences.org/articles/77918/elife-77918-fig3-figsupp2-data3-v2.zip
Figure 3—video 1
3D rendering of embryo landmarks.
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.
Figure 4 with 2 supplements
Spatial and temporal organization of neuropil formation.
All scale bars 1 μm. (a) FM cross section of a comma stage embryo with a ubiquitous histone marker (red) and a broadly expressed cell membrane label (green) (Barnes et al., 2020). Anterior view. …
Figure 4—figure supplement 1
Earliest neurite outgrowths.
All scale bars 1 μm. (a) Illustration of cell groups at bean stage and approximate extent as in Figure 4c. (b–c) EM image of each outgrowth location with cell areas shaded to match cartoon, also …
Figure 4—figure supplement 2
Early neurites at the comma stage.
All scale bars 1 μm. (a) Illustration of cell groups at comma stage and approximate extent as in Figure 4c. (b–g) EM image of each location with cell areas shaded to match cartoon. Also pictured …
Figure 5 with 2 supplements
Cell-cell interactions and ultrastructure during amphid organogenesis.
All scale bars 1 μm. (a) FM view of amphid dendrite development with a cnd-1 promoter driven membrane label. Dashed line shows embryo contour. Dot indicates the location of dendrite tips, and arrow …
Figure 5—figure supplement 1
Amphid organogenesis.
All scale bars 1 μm. (a) Cross section of dendrite tips at bean stage. Amphids and support cells are labeled and tinted in varying tones to allow individual cells to be distinguished. Confirmed cell …
Figure 5—video 1
Socket, sheath cell migration.
Selective max projection movie of socket and sheath cell migration in C. elegans embryo with cnd-1 -driven membrane label. Same embryo as shown in Figure 5d. A slightly looser cropping is chosen for …
Additional files
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Supplementary file 1
Additional summary tables detailing EM imaging conditions, EM and FM landmark properties, alignment accuracy, strains used in FM imaging, annotation extent and landmarks used to initialize alignment.
- https://cdn.elifesciences.org/articles/77918/elife-77918-supp1-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/77918/elife-77918-transrepform1-v2.docx
