title: Automated Analysis of Human Protein Atlas Immunofluorescence Images.
abstract: The Human Protein Atlas is a rich source of location proteomics data. In this work, we present an automated approach for processing and classifying major subcellular patterns in the Atlas images. We demonstrate that two different classification frameworks (support vector machine and random forest) are effective at determining subcellular locations; we can analyze over 3500 Atlas images with a high degree of accuracy, up to 87.5% for all of the samples and 98.5% when only considering samples in whose classification assignments we are most confident. Moreover, the features obtained in both of these frameworks are observed to be highly consistent and generalizable. Additionally, we observe that the features relating the proteins to cell markers are especially important in automated learning approaches.
authors.affiliation: Center for Bioimage Informatics and Dept. of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
authors.forename: Justin Y
authors.initials: JY
authors.lastname: Newberg
authors.forename: Jieyue
authors.initials: J
authors.lastname: Li
authors.forename: Arvind
authors.initials: A
authors.lastname: Rao
authors.forename: Fredrik
authors.initials: F
authors.lastname: Pontén
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlén
authors.forename: Emma
authors.initials: E
authors.lastname: Lundberg
authors.forename: Robert F
authors.initials: RF
authors.lastname: Murphy