WDDD: Worm Developmental Dynamics Database

Abstract

During animal development, cells undergo dynamic changes in position and gene expression. A collection of quantitative information about morphological dynamics under a wide variety of gene perturbations would provide a rich resource for understanding the molecular mechanisms of development. Here, we created a database, the Worm Developmental Dynamics Database (http://so.qbic.riken.jp/wddd/), which stores a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos with single genes silenced by RNA-mediated interference. The information contains the three-dimensional coordinate values of the outlines of nuclear regions and the dynamics of the outlines over time. The database provides free access to 50 sets of quantitative data for wild-type embryos and 136 sets of quantitative data for RNA-mediated interference embryos corresponding to 72 of the 97 essential embryonic genes on chromosome III. The database also provides sets of four-dimensional differential interference contrast microscopy images on which the quantitative data were based. The database will provide a novel opportunity for the development of computational methods to obtain fresh insights into the mechanisms of development. The quantitative information and microscopy images can be synchronously viewed through a web browser, which is designed for easy access by experimental biologists.

Nuclear detection in 4D microscope images using enhanced probability map of top-ranked intensity-ordered descriptors

“…al. [8]. We firstly compare the transformed probability map images of two DIC images from different embryos using our proposed TRIOD and directly the texton (local patch) for pixel representation, respectively, and the local image entropy [6] in Fig.…”

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena

“…2.Visualization of quantitative data extracted from experimental measurements or predicted from computer simulations. Nuclear division dynamics data extracted from microscopy images of Danio rerio (Keller et al , 2008) ( A ), Drosophila melanogaster (Keller et al , 2010) ( B ) and Caenorhabditis elegans (Bao et al , 2006; Kyoda et al , 2013) ( C, D ) embryos. Data predicted from computer simulations of microtubule-dependent pronuclear migration in C.elegans embryos (Kimura and Onami, 2005) ( E ) and single molecule dynamics in an Escherichia coli cell (Arjunan and Tomita, 2010) ( F ) …”

“…(2010) Drosophila melanogaster Nucleus20 Bao et al . (2006) Caenorhabditis elegans Nucleus20 Kyoda et al . (2013) Caenorhabditis elegans Nucleus186186 Cronin et al .…”

“…For example, Bao et al (2006) extracted quantitative data of nuclear division dynamics in green fluorescent protein-labeled embryos using confocal microscopy with the aim of deciphering the cell lineage in Caenorhabditis elegans . Kyoda et al (2013) extracted quantitative data of nuclear division dynamics in C. elegans embryos under a wide variety of gene perturbations from differential interference contrast microscopy images to understand molecular mechanisms in early embryogenesis. Similarly, quantitative data of nuclear division dynamics in embryos were obtained for Drosophila melanogaster (Keller et al , 2010) and Danio rerio (Keller et al , 2008) using digital scanned laser light-sheet microscopy.…”

An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis

“…Based on 3D time-lapse imaging, the entire cell lineage can be automatically traced to this stage, with every cell tracked through its movements and cell division. Quantitative measurements can be made on every cell to characterize its developmental behavior [3–6]. Most recently, this has led to over 4,000 measurements per embryo in terms of tissue type, proliferation (cell cycle length) and migration [7].…”