Reconstruction of image sequences from ungated and scanning-aberrated laser scanning microscopy images of the beating heart

Mariani, O.; Ernst, Alexander; Mercader, Nadia; Liebling, Michael (2019). Reconstruction of image sequences from ungated and scanning-aberrated laser scanning microscopy images of the beating heart. IEEE transactions on computational imaging, 6, pp. 385-395. IEEE 10.1109/TCI.2019.2948772

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Fluorescence laser-scanning microscopy is a wellestablished imaging technique in biology, available in many imaging facilities to investigate structures within live animal embryos such as zebrafish. Laser scanning microscopes (LSM) are limited when used to study dynamic heart morphology or function. Despite their ability to resolve static cardiac structures, the fast motion of the beating heart introduces severe artifacts in the scanned images and gating the acquisitions to the heartbeat is difficult to implement on traditional microscopes. Furthermore, although alternative high-speed imaging instruments exist, they are not widely available (due to cost or hardware complications), putting dynamic cardio-vascular imaging off-limits for many researchers. Here, we propose a method that allows imaging the beating heart on conventional LSMs. Our approach takes a set of images containing scanning aberrations, each triggered at an arbitrary time in the cardiac cycle, and assembles an image sequence that covers a single cardiac heartbeat. The steps are: (i) frame sorting by solving a traveling salesman problem; (ii) heartbeat duration estimation; and (iii) scan-delay compensation via space-time resampling. We characterize the performance of our method on synthetic data under several light intensities and scanning speeds. We further illustrate our method's applicability on experimental images acquired in live zebrafish larvae, and show that the reconstruction quality approaches that of fast, state-of-the-art microscopes. Our technique opens the possibility of using LSMs to carry out studies of cardiac dynamics, without the need for prospective gating or fast microscopes.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Anatomy

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Ernst, Alexander Uwe Johann and Mercader Huber, Nadia Isabel


600 Technology > 610 Medicine & health
500 Science
500 Science > 570 Life sciences; biology






[4] Swiss National Science Foundation
[UNSPECIFIED] Agence Nationale De La Recherche




Alexander Uwe Johann Ernst

Date Deposited:

28 Jan 2020 09:40

Last Modified:

14 Apr 2020 10:31

Publisher DOI:


Uncontrolled Keywords:

Microscopy;Image reconstruction;Heart beat;Optical microscopy;Sorting;Computational microscopy;laser scanning microscopy;confocal microscopy;fast microscopy;scanning aberration compensation;combinatorial optimization;traveling salesman problem;image and video sampling;cardiac imaging;zebrafish imaging




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