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Wavelet-based background and noise subtraction for fluorescence microscopy images

Hüpfel, Manuel 1; Kobitski, Andrei Y. U. 1; Zhang, Weichun 1; Nienhaus, G. Ulrich 1,2,3
1 Institut für Angewandte Physik (APH), Karlsruher Institut für Technologie (KIT)
2 Institut für Nanotechnologie (INT), Karlsruher Institut für Technologie (KIT)
3 Institut für Biologische und Chemische Systeme (IBCS), Karlsruher Institut für Technologie (KIT)

Fluorescence microscopy images are inevitably contaminated by background intensity contributions. Fluorescence from out-of-focus planes and scattered light are important sources of slowly varying, low spatial frequency background, whereas background varying from pixel to pixel (high frequency noise) is introduced by the detection system. Here we present a powerful, easy-to-use software, wavelet-based background and noise subtraction (WBNS), which effectively removes both of these components. To assess its performance, we apply WBNS to synthetic images and compare the results quantitatively with the ground truth and with images processed by other background removal algorithms. We further evaluate WBNS on real images taken with a light-sheet microscope and a super-resolution stimulated emission depletion microscope. For both cases, we compare the WBNS algorithm with hardware-based background removal techniques and present a quantitative assessment of the results. WBNS shows an excellent performance in all these applications and significantly enhances the visual appearance of fluorescence images. Moreover, it may serve as a pre-processing step for further quantitative analysis.

Verlagsausgabe §
DOI: 10.5445/IR/1000130516
Veröffentlicht am 19.03.2021
DOI: 10.1364/BOE.413181
Zitationen: 6
Web of Science
Zitationen: 4
Zitationen: 6
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Angewandte Physik (APH)
Institut für Biologische und Chemische Systeme (IBCS)
Institut für Nanotechnologie (INT)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2021
Sprache Englisch
Identifikator ISSN: 2156-7085
KITopen-ID: 1000130516
HGF-Programm 43.32.03 (POF IV, LK 01) Designed Optical Devices & Systems
Erschienen in Biomedical Optics Express
Verlag Optica Publishing Group (OSA)
Band 12
Heft 2
Seiten 969-980
Nachgewiesen in Web of Science
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