Live-Cell Imaging and Automation of Image Analysis

Segmentation of Neural Stem Cells/Neurospheres in High Content Brightfield Microscopy Images Using Localized Level Sets

Published date : 30 Sep 2012

Neural stem cells and neural progenitors are early nervous system cells that form neurospheres when propagated in vitro. We study changes in growth using brightfield images to understand the effects of drugs. The image quality is generally poor, imposing challenges for automatic analysis. Level-set segmentation methods are able to handle topology changes but require close initializations for accurate and efficient results. Global level-set methods using single image-wide optimization objective functions are difficult to cope with large illumination and shading changes.

type
Conference Paper/Poster
journal
2012 IEEE International Conference on Image Processing, 30 Sep - 3 Oct 2012, Florida, USA

Cyclin-depended kinase 1 (Cdk1) is essential for cell division and suppression of DNA re-replication but not for liver regeneration

Published date : 21 Feb 2012

Cyclin-dependent kinase 1 (Cdk1) is an archetypical kinase and a central regulator that drives cells through G2 phase and mitosis. Knockouts of Cdk2, Cdk3, Cdk4, or Cdk6 have resulted in viable mice, but the in vivo functions of Cdk1 have not been fully explored in mammals. Here we have generated a conditional-knockout mouse model to study the functions of Cdk1 in vivo. Ablation of Cdk1 leads to arrest of embryonic development around the blastocyst stage.

type
Journal Paper
journal
PNAS, March 6, 2012, Vol. 109, No. 10, Pg 3826-3831, doi: 10.1073/pnas.1115201109
Impact Factor
9.771

Cell Cycle phase classification in 3D in vivo microscopy of Drosophila embryogenesis

Published date : 30 Nov 2011

Background

Cell divisions play critical roles in disease and development. The analysis of cell division phenotypes in high content image-based screening and time-lapse microscopy relies on automated nuclear segmentation and classification of cell cycle phases. Automated identification of the cell cycle phase helps biologists quantify the effect of genetic perturbations and drug treatments. Most existing studies have dealt with 2D images of cultured cells. Few, if any, studies have addressed the problem of cell cycle classification in 3D image stacks of intact tissues.
Results

type
Conference Paper/Poster
journal
BMC Bioinformatics 2011, 12(Supp 13):S18, doi: 10.1186/1471-2105-12-S13-S18
Impact Factor
3.03

Three-Dimensional Segmentation of Nuclei and Mitotic Chromosomes for the Study of Cell Divisions in Live Drosphila Embryos

Published date : 10 Nov 2011

Drosophila embryogenesis is an established model to investigate mechanisms and genes related to cell divisions in an intact multicellular organism. Progression through the cell cycle phases can be monitored in vivo using fluorescently labeled fusion proteins andtime-lapse microscopy. To measure cellular properties in microscopic images, accurate and fast image segmentation methods are a critical prerequisite. To quantify static and dynamic features of interphase nuclei and mitotic chromosomes, we developed a three-dimensional (3D) segmentation method based on multiple level sets.

type
Journal Paper
journal
Cytometry Part A

Ectodermal Influx and Cell Hypertrophy Provide Early Growth for All Murine Mammary Rudiments, and Are Differentially Regulated among Them by Gli3

Published date : 27 Oct 2011

Mammary gland development starts in utero with one or several pairs of mammary rudiments (MRs) budding from the surface ectodermal component of the mammalian embryonic skin. Mice develop five pairs, numbered MR1 to MR5 from pectoral to inguinal position. We have previously shown that Gli3(Xt-J/Xt-J) mutant embryos, which lack the transcription factor Gli3, do not form MR3 and MR5. We show here that two days after the MRs emerge, Gli3(Xt-J/Xt-J) MR1 is 20% smaller, and Gli3(Xt-J/Xt-J) MR2 and MR4 are 50% smaller than their wild type (wt) counterparts.

type
Journal Paper
journal
PLoS ONE Oct 2011, Vol. 6, Issue 10, doi:10.1371/journal.pone.0026242
Impact Factor
4.092

Orthodenticle is necessary for survival of a cluster of clonally related dopaminergic neurons in the Drosophila larval and adult brain

Published date : 14 Oct 2011

The dopaminergic (DA) neurons present in the central brain of the Drosophila larva are spatially arranged in stereotyped groups that define clusters of bilaterally symmetrical neurons. These clusters have been classified according to anatomical criteria (position of the cell bodies within the cortex and/or projection pattern of the axonal tracts).

type
Journal Paper
journal
Neural Development 2011, 6:34, doi:101186/1749-8104-6-34
Impact Factor
3.40

TLM-Converter: reorganization of long time-lapse microscopy datasets for downstream image analysis

Published date : 01 Jul 2011

Automated microscopy enables in vivo studies in developmental biology over long periods of time. Time-lapse recordings in three or more dimensions to study the dynamics of developmental processes can produce huge data sets that extend into the terabyte range. However, depending on the available computational resources and software design, downstream processing of very large image data sets can become highly inefficient, if not impossible.

type
Journal Paper
journal
BioTechniques, Vol. 51, No. 1, July 2011, Pg 49-54, doi: 10.2144/000113704
Impact Factor
2.55