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  4. W2S: Microscopy Data with Joint Denoising and Super-Resolution for Widefield to SIM Mapping
 
conference paper

W2S: Microscopy Data with Joint Denoising and Super-Resolution for Widefield to SIM Mapping

Zhou, Ruofan  
•
El Helou, Majed  
•
Sage, Daniel  
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2020
Computer Vision – ECCV 2020 Workshops
ECCV 2020 Workshop on BioImage Computing

In fluorescence microscopy live-cell imaging, there is a critical trade-off between the signal-to-noise ratio and spatial resolution on one side, and the integrity of the biological sample on the other side. To obtain clean high-resolution (HR) images, one can either use microscopy techniques, such as structured-illumination microscopy (SIM), or apply denoising and super-resolution (SR) algorithms. However, the former option requires multiple shots that can damage the samples, and although efficient deep learning based algorithms exist for the latter option, no benchmark exists to evaluate these algorithms on the joint denoising and SR (JDSR) tasks. To study JDSR on microscopy data, we propose such a novel JDSR dataset, Widefield2SIM (W2S), acquired using a conventional fluorescence widefield and SIM imaging. W2S includes 144,000 real fluorescence microscopy images, resulting in a total of 360 sets of images. A set is comprised of noisy low-resolution (LR) widefield images with different noise levels, a noise-free LR image, and a corresponding high-quality HR SIM image. W2S allows us to benchmark the combinations of 6 denoising methods and 6 SR methods. We show that state-of-the-art SR networks perform very poorly on noisy inputs. Our evaluation also reveals that applying the best denoiser in terms of reconstruction error followed by the best SR method does not necessarily yield the best final result. Both quantitative and qualitative results show that SR networks are sensitive to noise and the sequential application of denoising and SR algorithms is sub-optimal. Lastly, we demonstrate that SR networks retrained end-to-end for JDSR outperform any combination of state-of-the-art deep denoising and SR networks

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Type
conference paper
DOI
10.1007/978-3-030-67070-2_30
Author(s)
Zhou, Ruofan  
El Helou, Majed  
Sage, Daniel  
Laroche, Thierry  
Seitz, Arne  
Süsstrunk, Sabine  
Date Issued

2020

Published in
Computer Vision – ECCV 2020 Workshops
Start page

499

End page

518

Subjects

Image Restoration Dataset

•

Denoising

•

Super-resolution

•

Microscopy Imaging

•

Joint Optimization

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
IVRL  
Event nameEvent placeEvent date
ECCV 2020 Workshop on BioImage Computing

Glasgow, United Kingdom

August 23-28, 2020

Available on Infoscience
August 24, 2020
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/171081
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