ImagePlane: An Automated Image Analysis Pipeline for High-Throughput Screens Using the Planarian Schmidtea mediterranea
| Autor: | Michael S. Campbell, Mark Yandell, Barry Moore, Steven Flygare, Robert Mars Ross |
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| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Image processing
Computational biology Bioinformatics computer.software_genre Automation Schmidtea mediterranea Genetics Image Processing Computer-Assisted Animals RNA Small Interfering Molecular Biology Throughput (business) Research Articles Cell Proliferation biology business.industry Stem Cells Computational Biology Genomics Helminth Proteins Planarians biology.organism_classification Thresholding Pipeline (software) High-Throughput Screening Assays Computational Mathematics Information extraction Computational Theory and Mathematics Planarian Modeling and Simulation business computer Algorithms |
| Popis: | ImagePlane is a modular pipeline for automated, high-throughput image analysis and information extraction. Designed to support planarian research, ImagePlane offers a self-parameterizing adaptive thresholding algorithm; an algorithm that can automatically segment animals into anterior–posterior/left–right quadrants for automated identification of region-specific differences in gene and protein expression; and a novel algorithm for quantification of morphology of animals, independent of their orientations and sizes. ImagePlane also provides methods for automatic report generation, and its outputs can be easily imported into third-party tools such as R and Excel. Here we demonstrate the pipeline's utility for identification of genes involved in stem cell proliferation in the planarian Schmidtea mediterranea. Although designed to support planarian studies, ImagePlane will prove useful for cell-based studies as well. |
| Databáze: | OpenAIRE |
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