A poisson-gaussian denoising dataset with real fluorescence microscopy images

Yide Zhang, Yinhao Zhu, Evan Nichols, Qingfei Wang, Siyuan Zhang, Cody Smith, Scott Howard

Research output: Chapter in Book/Report/Conference proceedingConference contribution

55 Scopus citations

Abstract

Fluorescence microscopy has enabled a dramatic development in modern biology. Due to its inherently weak signal, fluorescence microscopy is not only much noisier than photography, but also presented with Poisson-Gaussian noise where Poisson noise, or shot noise, is the dominating noise source. To get clean fluorescence microscopy images, it is highly desirable to have effective denoising algorithms and datasets that are specifically designed to denoise fluorescence microscopy images. While such algorithms exist, no such datasets are available. In this paper, we fill this gap by constructing a dataset-the Fluorescence Microscopy Denoising (FMD) dataset-that is dedicated to Poisson-Gaussian denoising. The dataset consists of 12,000 real fluorescence microscopy images obtained with commercial confocal, two-photon, and wide-field microscopes and representative biological samples such as cells, zebrafish, and mouse brain tissues. We use image averaging to effectively obtain ground truth images and 60,000 noisy images with different noise levels. We use this dataset to benchmark 10 representative denoising algorithms and find that deep learning methods have the best performance. To our knowledge, this is the first real microscopy image dataset for Poisson-Gaussian denoising purposes and it could be an important tool for high-quality, real-time denoising applications in biomedical research.

Original languageEnglish (US)
Title of host publicationProceedings - 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2019
PublisherIEEE Computer Society
Pages11702-11710
Number of pages9
ISBN (Electronic)9781728132938
DOIs
StatePublished - Jun 2019
Externally publishedYes
Event32nd IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2019 - Long Beach, United States
Duration: Jun 16 2019Jun 20 2019

Publication series

NameProceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition
Volume2019-June
ISSN (Print)1063-6919

Conference

Conference32nd IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2019
Country/TerritoryUnited States
CityLong Beach
Period6/16/196/20/19

Keywords

  • Biological and Cell Microscopy
  • Datasets and Evaluation
  • Medical

ASJC Scopus subject areas

  • Software
  • Computer Vision and Pattern Recognition

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