title: Video bioinformatics analysis of human embryonic stem cell colony growth.
abstract: Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer software. Video bioinformatics is a powerful quantitative approach for extracting spatio-temporal data from video images using computer software to perform dating mining and analysis. In this article, we introduce a video bioinformatics method for quantifying the growth of human embryonic stem cells (hESC) by analyzing time-lapse videos collected in a Nikon BioStation CT incubator equipped with a camera for video imaging. In our experiments, hESC colonies that were attached to Matrigel were filmed for 48 hours in the BioStation CT. To determine the rate of growth of these colonies, recipes were developed using CL-Quant software which enables users to extract various types of data from video images. To accurately evaluate colony growth, three recipes were created. The first segmented the image into the colony and background, the second enhanced the image to define colonies throughout the video sequence accurately, and the third measured the number of pixels in the colony over time. The three recipes were run in sequence on video data collected in a BioStation CT to analyze the rate of growth of individual hESC colonies over 48 hours. To verify the truthfulness of the CL-Quant recipes, the same data were analyzed manually using Adobe Photoshop software. When the data obtained using the CL-Quant recipes and Photoshop were compared, results were virtually identical, indicating the CL-Quant recipes were truthful. The method described here could be applied to any video data to measure growth rates of hESC or other cells that grow in colonies. In addition, other video bioinformatics recipes can be developed in the future for other cell processes such as migration, apoptosis, and cell adhesion.
authors.affiliation: UCR Stem Cell Center, University of California, USA
authors.forename: Sabrina
authors.initials: S
authors.lastname: Lin
authors.forename: Shawn
authors.initials: S
authors.lastname: Fonteno
authors.forename: Shruthi
authors.initials: S
authors.lastname: Satish
authors.forename: Bir
authors.initials: B
authors.lastname: Bhanu
authors.forename: Prue
authors.initials: P
authors.lastname: Talbot
mesh_terms: D003114:Colony-Forming Units Assay / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D053595:Embryonic Stem Cells / Q000166:cytology*; D006801:Humans; D014741:Video Recording / Q000379:methods