Video Bioinformatics


Video Bioinformatics



Video bioinformatics includes the development and application of software tools for extracting and mining information from video data. Tremendous amounts of time can be saved with proper use of video bioinformatics since such tools can extract more accurate, reproducible data than a human manually performing the same task. In our lab we use CL-Quant software, a commercially available video bioinformatics software package, to extract and quantitative data on: growth and proliferation, cell and colony migration, reactive oxygen species production, and neural differentiation. We have also developed our own video bioinformatics software, StemCellQC™, which evaluates stem cell colony health.


Selected Publications

Evaluating Cell Processes, Quality, and Biomarkers in Pluripotent Stem Cells Using Video Bioinformatics

Zahedi A, On V, Lin SC, Bays BC, Omaiye E, Bhanu B, Talbot P. PLoS One. 2016.


There is a foundational need for quality control tools in stem cell laboratories engaged in basic research, regenerative therapies, and toxicological studies. These tools require automated methods for evaluating cell processes and quality during in vitro passaging, expansion, maintenance, and differentiation. In this paper, an unbiased, automated high-content profiling toolkit, StemCellQC, is presented that non-invasively extracts information on cell quality and cellular processes from time-lapse phase-contrast videos. Video analysis algorithms allowed assessment of biological phenomena using automatic detection analysis, which can aid facilities where maintaining stem cell quality and/or monitoring changes in cellular processes are essential. In the future StemCellQC can be expanded to include other features, cell types, treatments, and differentiating cells.


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