A BaSiC tool for background and shading correction of optical microscopy images

Peng T, Thorn K, Schroeder T, Wang L, Theis FJ, Marr C, Navab N (2017)

Publication Type: Journal article

Publication year: 2017

Journal

Nature Communications Nature Publishing Group: Nature Communications

Book Volume: 8

Article Number: 14836

DOI: 10.1038/ncomms14836

Abstract

Quantitative analysis of bioimaging data is often skewed by both shading in space and background variation in time. We introduce BaSiC, an image correction method based on low-rank and sparse decomposition which solves both issues. In comparison to existing shading correction tools, BaSiC achieves high-accuracy with significantly fewer input images, works for diverse imaging conditions and is robust against artefacts. Moreover, it can correct temporal drift in time-lapse microscopy data and thus improve continuous single-cell quantification. BaSiC requires no manual parameter setting and is available as a Fiji/ImageJ plugin.

Involved external institutions

Technische Universität München (TUM) DE Germany (DE) University of California San Francisco (UCSF) US United States (USA) (US) Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) / Helmholtz Munich DE Germany (DE) Eidgenössische Technische Hochschule Zürich (ETHZ) / Swiss Federal Institute of Technology in Zurich CH Switzerland (CH)

How to cite

APA:

Peng, T., Thorn, K., Schroeder, T., Wang, L., Theis, F.J., Marr, C., & Navab, N. (2017). A BaSiC tool for background and shading correction of optical microscopy images. Nature Communications, 8. https://doi.org/10.1038/ncomms14836

MLA:

Peng, Tingying, et al. "A BaSiC tool for background and shading correction of optical microscopy images." Nature Communications 8 (2017).

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