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The Ciona notochord displays planar cell polarity (PCP), with anterior localization of Prickle (Pk) and Strabismus (Stbm). We report that a myosin is polarized anteriorly in these cells and strongly colocalizes with Stbm. Disruption of the actin/myosin machinery with cytochalasin or blebbistatin disrupts polarization of Pk and Stbm, but not of myosin(More)
We present a model for the automated segmentation of cells from confocal microscopy volumes of biological samples. The segmentation task for these images is exceptionally challenging due to weak boundaries and varying intensity during the imaging process. To tackle this, a two step pruning process based on the Fast Marching Method is first applied to obtain(More)
Ascidian larvae have a hollow, dorsal central nervous system that shares many morphological features with vertebrate nervous systems yet is composed of very few cells. We show here that a null mutation in the gene dmrt1 in the ascidian Ciona savignyi results in profound abnormalities in the development of the sensory vesicle (brain), as well as other(More)
We address the problem of cell segmentation in confocal microscopy membrane volumes of the ascidian Ciona used in the study of morphogenesis. The primary challenges are non-uniform and patchy membrane staining and faint spurious boundaries from other organelles (e.g. nuclei). Traditional segmentation methods incorrectly attach to faint boundaries producing(More)
We have developed a method to automatically segment notochord cell boundaries from differential interference contrast (DIC) timelapse images of the elongating ascidian tail. The method is based on a specialized parametric active contour, the network snake, which can be initialized as a network of arbitrary but fixed topology and provides an effective(More)
Developmental biology relies heavily on microscopy to image the finely controlled cell behaviors that drive embryonic development. Most embryos are large enough that a field of view with the resolution and magnification needed to resolve single cells will not span more than a small region of the embryo. Ascidian embryos, however, are sufficiently small that(More)
Fate mapping with single cell resolution has typically been confined to embryos with completely stereotyped development. The lineages giving rise to the 40 cells of the Ciona notochord are invariant, but the intercalation of those cells into a single-file column is not. Here we use genetic labeling methods to fate map the Ciona notochord with both high(More)
Ascidians such as Ciona are close chordate relatives of the vertebrates with small, simple embryonic body plans and small, simple genomes. The tractable size of the embryo offers considerable advantages for in toto imaging and quantitative analysis of morphogenesis. For functional studies, Ciona eggs are considerably more challenging to microinject than the(More)
State of the art biological imaging methods, such as confocal microscopy, create 3D volumes by sampling on a cartesian grid. This cartesian coordinate system is often not convenient for visualization and analysis of multi layered organs or tissues. The ascidian embryonic tail, for example, is organized along anterioposterior (AP), dorsoventral (DV) and(More)
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