ASCIDIAN

ASCIDIAN assigns cell identities in three-dimensional time-lapse reconstructions of ascidian embryos by transferring names from a reference set of manually curated embryos, enabling reproducible cell lineage analysis and phenotypic comparisons.

Key Features:

• Automated cell naming: Assigns consistent cell names up to stages containing about 700 cells by comparing the pattern of contacts each cell forms with its neighbors.
• Reference-based transfer: Transfers cell identities from a reference set of manually curated embryos to new embryos using the Conklin nomenclature.
• Two-step process: Employs an initiation phase for global alignment of early embryos to establish initial correspondences, followed by a propagation phase that propagates names through time and cell divisions.
• Cross-species application: Demonstrated on eight wild-type Phallusia mammillata and one Ascidiella aspersa embryos.
• Conklin nomenclature extension: Extends Conklin's rules to internal tissues beyond gastrulation.
• Phenotypic comparison: Enables quantitative phenotyping of experimentally perturbed embryos, such as those with inhibited ERK signaling.
• Variability quantification: Quantifies natural variability in division timing and orientation across embryos.

Scientific Applications:

• Ascidian embryogenesis studies: Facilitates systematic, quantitative, and evolutionary analyses of animal development in ascidian model organisms.
• Cell lineage analysis: Supports reproducible tracking of cell fates through early embryonic development up to approximately 700-cell stages.
• Morphogenesis comparison: Enables quantitative comparisons of morphogenesis between individuals and species with highly reproducible cell lineages.
• Experimental perturbation analysis: Allows quantitative phenotyping of embryos with manipulated signaling pathways, such as ERK inhibition.
• Developmental variability assessment: Measures natural variability in division timing and orientation to confirm global robustness and reveal local variability of ascidian morphogenesis.

Methodology:

The framework operates in two steps: an initiation phase that globally aligns early embryos to establish initial correspondences, and a propagation phase that propagates names through time and cell divisions by comparing the pattern of contacts each cell forms with its neighbors. The pipeline builds on the ASTEC suite for 3D+t image processing.