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Automated Analysis of Human Protein Atlas Immunofluorescence Images
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
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2009 (English)In: 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Vols 1 and 2 / [ed] IEEE, Boston: IEEE conference proceedings, 2009, Vol. 5193229, 1023-1026 p.Conference paper (Refereed)
Abstract [en]

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.

Place, publisher, year, edition, pages
Boston: IEEE conference proceedings, 2009. Vol. 5193229, 1023-1026 p.
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Medical and Health Sciences
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URN: urn:nbn:se:uu:diva-153098DOI: 10.1109/ISBI.2009.5193229PubMedID: 20628548ISBN: 978-1-4244-3931-7OAI: oai:DiVA.org:uu-153098DiVA: diva2:415172
IEEE Internaional Symposium on Biomedical Imaging - From Nano to Macro, Boston, USA, Jun 28-Jul 01, 2009
Available from: 2011-05-05 Created: 2011-05-05 Last updated: 2012-05-29Bibliographically approved

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Pontén, Fredrik
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