Combining mathematical morphology and the Hilbert transform for fully automatic nuclei detection in fluorescence microscopy

Nelson, C. J. , Jackson, P. T.G. and Obara, B. (2019) Combining mathematical morphology and the Hilbert transform for fully automatic nuclei detection in fluorescence microscopy. In: Burgeth, B., Kleefeld, A., Naegel, B., Passat, N. and Perret, B. (eds.) Mathematical Morphology and Its Applications to Signal and Image Processing: 14th International Symposium, ISMM 2019, Saarbrücken, Germany, July 8-10, 2019, Proceedings. Series: Lecture notes in computer science (11564). Springer: Cham, pp. 532-543. ISBN 9783030208660 (doi: 10.1007/978-3-030-20867-7_41)

Abstract

Accurate and reliable nuclei identification is an essential part of quantification in microscopy. A range of mathematical and machine learning approaches are used but all methods have limitations. Such limitations include sensitivity to user parameters or a need for pre-processing in classical approaches or the requirement for relatively large amounts of training data in deep learning approaches. Here we demonstrate a new approach for nuclei detection that combines mathematical morphology with the Hilbert transform to detect the centres, sizes and orientations of elliptical objects. We evaluate this approach on datasets from the Broad Bioimage Benchmark Collection and compare it to established algorithms and previously published results. We show this new approach to outperform established classical approaches and be comparable in performance to deep-learning approaches. We believe this approach to be a competitive algorithm for nuclei detection in microscopy.

• Item Type: Book Sections
• Additional Information: During this work, CJN was supported by an EPSRC (UK) Doctoral Scholarship (EP/K502832/1). PTGJ is supported by an EPSRC (UK) Doctoral Scholarship (EP/M507854/1). The work in this paper was supported by an academic grant from The Royal Society (UK; RF080232).
• Status: Published
• Glasgow Author(s) Enlighten ID: Nelson, Dr Chas
• Authors: Nelson, C. J., Jackson, P. T.G., and Obara, B.
• College/School: College of Science and Engineering > School of Physics and Astronomy
• Publisher: Springer
• ISBN: 9783030208660
• Published Online: 31 May 2019
• Copyright Holders: Copyright © 2019 Springer Nature Switzerland AG
• First Published: First published in Mathematical Morphology and Its Applications to Signal and Image Processing: 14th International Symposium, ISMM 2019, Saarbrücken, Germany, July 8-10, 2019, Proceedings: 532-543
• Publisher Policy: Reproduced in accordance with the publisher copyright policy