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Computational Methods for Temporal Super-resolution Microscopy

Applicant Liebling Michael
Number 159227
Funding scheme Project funding (Div. I-III)
Research institution IDIAP Institut de Recherche
Institution of higher education Idiap Research Institute - IDIAP
Main discipline Electrical Engineering
Start/End 01.04.2016 - 31.03.2018
Approved amount 128'829.00
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Keywords (6)

super-resolution; microscopy; deconvolution; fluorescence; inverse problems; video imaging

Lay Summary (French)

Lead
La microscopie en fluorescence est un outil essentiel pour l'étude des structures biologiques. Cependant, la lumière émise par les échantillons est souvent faible, ce qui limite la fréquence d'image à laquelle les processus dynamiques peuvent être observés tout en maintenant un rapport signal-sur-bruit suffisant et sans flou de mouvement. Bien que plusieurs techniques de micrsocopies ont récemment été développée pour améliorer la résolution en microscopie, beaucoup ont mis l'accent sur l'amélioration de la résolution spatiale (limitée par la diffraction de la lumière) plutôt que temporelle (qui est limitée par le faible nombre de photons émis ou des caméras trop lentes).
Lay summary

Le but de ce projet est de développer des algorithmes qui permettront de dépasser la limite de résolution temporelle imposée par les caméras de fluorescence lentes et la faible quantité de photons de fluorescence dans les échantillons biologique. Ceci permettra d'observer des processus biologiques rapides sans compromettre la résolution spatiale. 

Notre premier objectif est de développer des algorithmes discrets pour reconstruire des signaux de haute résolution temporelle à partir de multiples série d'images d'un même événements dynamique, en utilisant à chaque fois un motif d'illumination différent. Notre second objectif est de déterminer les algorithmes et les motifs d'éclairage optimisés pour des tâches d'analyse d'image spécialisés, y compris le suivi et la morphométrie de cellules dans des système multi-cellulaires, deux éléments clés de la biologie quantitative.

Nous envisageons que nos méthode puissent être directement intégrée dans la plupart des microscopes existants, et pourraient ainsi bénéficier à un large éventail de biologistes et de cliniciens et stimuler l'industrie de la microscopie. En particulier, notre technique a des applications potentielles dans le domaine de la recherche cardiaque, où la recherche sur des défauts durant le dévelopement cardiaque embryonnaire sont entravés par le manque d'outils d'imagerie de fluorescence rapide. En outre, nos méthodes pourrait ainsi faciliter le diagnostic et le traitement de certaines maladies cardiaques, qui sont une cause majeure de décès et souffrant dans la population humaine.

Direct link to Lay Summary Last update: 19.05.2015

Responsible applicant and co-applicants

Employees

Name Institute

Publications

Publication
Temporal resolution doubling in fluorescence light-sheet microscopy via a hue-encoded shutter and regularization
Jaques Christian, Ernst Alexander, Mercader Nadia, Liebling Michael (2020), Temporal resolution doubling in fluorescence light-sheet microscopy via a hue-encoded shutter and regularization, in {OSA} Continuum, 3(8), 2195-2209.
Generalized temporal sampling with active illumination in optical microscopy
Jaques Christian, Liebling Michael (2019), Generalized temporal sampling with active illumination in optical microscopy, in Wavelets and Sparsity XVIII, San Diego, United StatesSPIE, San Diego.
Temporal super-resolution microscopy using a hue-encoded shutter
Jaques Christian, Pignat Emmanuel, Calinon Sylvain, Liebling Michael (2019), Temporal super-resolution microscopy using a hue-encoded shutter, in Biomedical Optics Express, 10(9), 4727-4741.
Multi-Spectral Widefield Microscopy of the Beating Heart through Post-Acquisition Synchronization and Unmixing
Jaques Christian, Bapst-Wicht Linda, Schorderet Daniel F., Liebling Michael (2019), Multi-Spectral Widefield Microscopy of the Beating Heart through Post-Acquisition Synchronization and Unmixing, in Proceedings of the 16th {IEEE} International Symposium on Biomedical Imaging: From nano to macro ({I, Venice, ItalyIEEE, NJ, USA.
A direct inversion algorithm for focal plane scanning optical projection tomography
Chan K., Liebling M. (2017), A direct inversion algorithm for focal plane scanning optical projection tomography, in Biomedical Optics Express, 8(11), 5349-5358.

Datasets

Temporal super-resolution microscopy using a hue-encoded shutter

Author Jaques, Christian; Pignat, Emmanuel; Bapst-Wicht, Linda; Calinon, Sylvain; Schorderet, Daniel; Liebling, Michael
Publication date 01.09.2019
Persistent Identifier (PID) http://doi.org/10.5281/zenodo.3606485
Repository Temporal super-resolution microscopy using a hue-encoded shutter
Abstract
This dataset contains the data to reproduce the figures in our paper called "Temporal super-resolution microscopy using a hue-encoded shutter", Biomedical Optics Express, 2019.Together with the data, the code is available on Idiap's GitHub page.

Collaboration

Group / person Country
Types of collaboration
Vemot Lab / Institut de génétique et biologie moléculaire, Strasbourg France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Dr. Willy Supatto / Ecole Polytechnique, Paris France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Dr. Daniel Schorderet Lab/ Institut de Recherche en Ophtalmologie, Sion Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Larina Lab / Baylor College of Medicine, Houston United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results

Awards

Title Year
Best Student Paper Award First Place to Christian Jaques for the paper and presentation of “Multi-Spectral Widefield Microscopy of the Beating Heart Through Post-Acquisition Synchronization of Overlapping Filter Bands“ by C. Jaques, L. Bapst-Wich, D.F. Schorderet, M. Liebling, IEEE International Symposium on Biomedical Imaging 2019, Venice, Italy. 2019

Use-inspired outputs

Associated projects

Number Title Start Funding scheme
164022 Platform for Reproducible Acquisition, Processing, and Sharing of Dynamic, Multi-Modal Data 01.07.2016 R'EQUIP
179217 Computational biomicroscopy: advanced image processing methods to quantify live biological systems 01.04.2018 Project funding (Div. I-III)

Abstract

The goal of this proposal is to develop algorithms that will, in conjunction with hardware common in modern microscopes, allow breaking the temporal resolution limit imposed by slow fluorescence cameras and the scarcity of fluorescence photons in dim samples. It will make imaging of fast biological processes possible without compromising spatial for temporal resolution. With the ability to directly visualize dynamic processes in samples that are currently imaged fixed-rather than alive-our technique has the potential to reveal the fundamental mechanisms underlying key biological processes, both in healthy and diseased samples.Our first aim is to develop discrete algorithms for reconstructing high temporal resolution signals from multiple image series of recurring dynamic events, using temporally patterned illumination. Our second aim is to determine algorithms and illumination patterns optimized for specialized image analysis tasks including multi-cellular tracking and morphometry dynamics, two key components in quantitative biology.Our method could be directly integrated into most existing microscopes, thereby benefitting a broad range of biologists and clinicians, while also transforming the microscopy industry. In particular, our technique has direct application in the field of cardiac research, where investigations of disease and defects during heart development are hampered by the lack of fast fluorescence imaging tools. In addition, it could facilitate diagnosis and cure of certain heart diseases, which are a major cause of death and suffering in human populations.
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