DeepSTORM3D: dense three dimensional localization microscopy and point spread function design by deep learning

PLUTO / PLUTO-2 Spatial Light Modulators
Deep Learning / Neuronal Network Microscopy
Published on:
Authors: Nehme, Elias; Freedman, Daniel; Gordon, Racheli; Ferdman, Boris; Weiss, Lucien E.; Alalouf, Onit; Orange, Reut; Michaeli, Tomer & Shechtman, Yoav
Abstract:

“Localization microscopy is an imaging technique in which the positions of individual nanoscale point emitters (e.g. fluorescent molecules) are determined at high precision from their images. This is the key ingredient in single/multiple-particle-tracking and several super-resolution microscopy approaches. Localization in three-dimensions (3D) can be performed by modifying the image that a point-source creates on the camera, namely, the point-spread function (PSF). The PSF is engineered using additional optical elements to vary distinctively with the depth of the point-source. However, localizing multiple adjacent emitters in 3D poses a significant algorithmic challenge, due to the lateral overlap of their PSFs. Here, we train a neural network to receive an image containing densely overlapping PSFs of multiple emitters over a large axial range and output a list of their 3D positions. Furthermore, we then use the network to design the optimal PSF for the multi-emitter case. We demonstrate our approach numerically as well as experimentally by 3D STORM imaging of mitochondria, and volumetric imaging of dozens of fluorescently-labeled telomeres occupying a mammalian nucleus in a single snapshot.”

Open Access

Publication: Nature Methods 17
Issue/Year: Nature Methods 17 (2020) 734-740, Volume 17; Number 7; Pages 734–740; 2019
DOI: 10.1038/s41592-020-0853-5
Link: https://doi.org/10.1038/s41592-020-0853-5

Related Papers

PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Siyu Gao, Xiaoyun Liu, Yonghao Chen, Jinyang Jiang, Ying Liu, Tengfei Chai and Yueqiu Jiang

Oceanic turbulence parameters recognition based on convolutional neural network

Applications: Adaptive Optics / Wavefront Control,Deep Learning / Neuronal Network,Optical Communication
LETO / LETO-3 Spatial Light Modulators
Authors:Manuel Hüpfel and Gerd Ulrich Nienhaus

Beam shaping in light-sheet microscopy: an experimental analysis

Applications: Beam Shaping / Beam Steering,Microscopy
GAEA / GAEA-2 Spatial Light Modulators
Authors:Xiaofei Li, Xin Liu, Quanying Wu, Jun Zeng, Yangjian Cai, Sergey A. Ponomarenko, Chunhao Liang

Prime number factorization with light beams carrying orbital angular momentum

Applications: Deep Learning / Neuronal Network,Digital-/ Computer Holography/ CGH,Higher Order Modes / Optical Vortex / OAM
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Rui Xiong, Xiangchao Zhang, Xinyang Ma, Leheng Li, Zhanghao Ni, and Xiangqian Jiang

Adaptive coded phase mask design and high-quality image reconstruction for interference-less coded aperture correlation holography

Applications: Deep Learning / Neuronal Network,Digital-/ Computer Holography/ CGH,Imaging/ Image Processing
HES / HEO 6001 PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Omri Wengrowicz, Alex Bronstein, and Oren Cohen

Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography

Applications: Deep Learning / Neuronal Network
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Pan, Tuqiang / Ye, Jianwei / Liu, Haotian / Zhang, Fan / Xu, Pengbai / Xu, Ou / Xu, Yi / Qin, Yuwen

Non-orthogonal optical multiplexing empowered by deep learning

Applications: Complex Modulation,Deep Learning / Neuronal Network,Optical Communication
GAEA / GAEA-2 PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Fang, Xinyuan / Hu, Xiaonan / Li, Baoli / Su, Hang / Cheng, Ke / Luan, Haitao / Gu, Min

Orbital angular momentum-mediated machine learning for high-accuracy mode-feature encoding

Applications: Deep Learning / Neuronal Network,Higher Order Modes / Optical Vortex / OAM
PLUTO / PLUTO-2 Spatial Light Modulators
Authors: Yongqiang Chen, Chenggui Luo, Shiqi Wang, Yanping Li, Binglin Shen, Rui Hu, Junle Qu, Liwei Liu

Rapid, high-contrast, and steady volumetric imaging with Bessel-beam-based two-photon fluorescence microscopy

Applications: Microscopy
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Zejian Ren, Xu Yan, Kai Wen, Huijin Chen, Elnur Hajiyev, Chengdong He, Gyu-Boong Jo

Creation of a tweezer array for cold atoms utilizing a generative neural network

Applications: Deep Learning / Neuronal Network,Optical Trapping /-Tweezers
LETO / LETO-3 Spatial Light Modulators
Authors: Siqing Dai, Andrei Kobitski, Amirhossein Barati Sedeh, Süheyla Eroğlu-Kayıkçı, Lennart Hilbert, and G. Ulrich Nienhaus

Photon-Efficient Aberration Correction for 3D-STED Imaging of Thick Biological Specimens Using Sensorless Adaptive Optics

Applications: Adaptive Optics / Wavefront Control,Beam Shaping / Beam Steering,Microscopy
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Jawahar Prabhakar Desai, Joseph Rosen

Resolution-enhanced imaging by interferenceless coded aperture correlation holography with two competing methods of phase mask synthesis

Applications: Microscopy
HES / HEO 6001 PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Zicheng Huang, Ziyu Gu, Mengyang Shi, Yesheng Gao, and Xingzhao Liu

OP-FCNN: an optronic fully convolutional neural network for imaging through scattering media

Applications: Deep Learning / Neuronal Network,Turbid-/ Opaque Media /Multi Scattering
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Krishnendu Samanta, Anupriya Tiwari, Samsheerali P.T., Joby Joseph

Improving resolution in two orthogonal orientations from a single-shot digital holographic microscopy

Applications: Microscopy
PLUTO / PLUTO-2 Spatial Light Modulators
Authors: Grace Kuo , Florian Schiffers , Douglas Lanman , Oliver Cossairt , Nathan Matsuda

Multisource Holography

Applications: AR/VR/MR / Holographic Display,Deep Learning / Neuronal Network,Digital-/ Computer Holography/ CGH
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Zheyu Wu, Ran Gao, Sitong Zhou, Fei Wang, Zhipei Li, Huan Chang, Dong Guo, Xiangjun Xin, Qi Zhang, Feng Tian, Qiang Wu

Robust Super-Resolution Image Transmission Based on a Ring Core Fiber with Orbital Angular Momentum

Applications: Deep Learning / Neuronal Network,Higher Order Modes / Optical Vortex / OAM,Imaging/ Image Processing
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Sitong Huang, Jian Wang, Daixuan Wu, Yin Huang, and Yuecheng Shen

Projecting colorful images through scattering media via deep learning

Applications: Deep Learning / Neuronal Network
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Qingwei Liu, Jing Chen, Bingsen Qiu, Yongtian Wang, and Juan Liu

DCPNet: a dual-channel parallel deep neural network for high quality computer-generated holography

Applications: AR/VR/MR / Holographic Display,Complex Modulation,Deep Learning / Neuronal Network,Digital-/ Computer Holography/ CGH
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Marshall B. Lindsay, Scott D. Kovaleski, Andy G. Varner, Charlie T. Veal, Derek T. Anderson, Stanton R. Price, and Steven R. Price

End-to-end physics-informed deep neural network optimization of sub-Nyquist lenses

Applications: Deep Learning / Neuronal Network
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Jianan Feng, Hang Chen, Dahai Yang, Junbo Hao, Jie Lin, and Peng Jin

Multi-wavelength diffractive neural network with the weighting method

Applications: Deep Learning / Neuronal Network
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Zhang, Yantong, Huiling Huang, Feibin Wu, Jun Han, Yi Yang, and Ruyi Li

Imaging through a Scattering Medium under Different Intensities of Ambient Light Interference

Applications: Deep Learning / Neuronal Network,Imaging/ Image Processing,Turbid-/ Opaque Media /Multi Scattering
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Jiangcheng Zhao, Chuanbiao Bai, Zhiguo Zhang and Qingchuan Zhang

Deep learning-based method for analyzing the optically trapped sperm rotation

Applications: Deep Learning / Neuronal Network,Optical Trapping /-Tweezers
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Ruibo Shang, Mikaela A. O’Brien, Fei Wang, Guohai Situ & Geoffrey P. Luke

Approximating the uncertainty of deep learning reconstruction predictions in single-pixel imaging

Applications: Deep Learning / Neuronal Network
GAEA / GAEA-2 Spatial Light Modulators
Authors:Ninghe Liu, Zhengzhong Huang, Zehao He, and Liangcai Cao

DGE-CNN: 2D-to-3D holographic display based on a depth gradient extracting module and ZCNN network

Applications: AR/VR/MR / Holographic Display,Deep Learning / Neuronal Network
PLUTO / PLUTO-2 Spatial Light Modulators
Authors:Zhu, Jialong / Zou, Fucheng / Wang, Le / Lu, Xiaodong / Zhao, Shengmei

Multiplexing Perfect Optical Vortex for Holographic Data Storage

Applications: Deep Learning / Neuronal Network,Digital-/ Computer Holography/ CGH,Higher Order Modes / Optical Vortex / OAM